Starting phenix.real_space_refine on Mon Mar 11 15:23:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a23_11614/03_2024/7a23_11614_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a23_11614/03_2024/7a23_11614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a23_11614/03_2024/7a23_11614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a23_11614/03_2024/7a23_11614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a23_11614/03_2024/7a23_11614_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a23_11614/03_2024/7a23_11614_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 2 6.06 5 P 13 5.49 5 S 403 5.16 5 C 37423 2.51 5 N 9681 2.21 5 O 10409 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 87": "NH1" <-> "NH2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "I ARG 88": "NH1" <-> "NH2" Residue "I ARG 89": "NH1" <-> "NH2" Residue "I GLU 118": "OE1" <-> "OE2" Residue "I ARG 119": "NH1" <-> "NH2" Residue "I PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 153": "OE1" <-> "OE2" Residue "I ARG 167": "NH1" <-> "NH2" Residue "I GLU 174": "OE1" <-> "OE2" Residue "I ARG 222": "NH1" <-> "NH2" Residue "I ARG 367": "NH1" <-> "NH2" Residue "I ARG 370": "NH1" <-> "NH2" Residue "I ARG 446": "NH1" <-> "NH2" Residue "I ARG 453": "NH1" <-> "NH2" Residue "I ARG 463": "NH1" <-> "NH2" Residue "J GLU 4": "OE1" <-> "OE2" Residue "J ARG 56": "NH1" <-> "NH2" Residue "J ARG 60": "NH1" <-> "NH2" Residue "J GLU 110": "OE1" <-> "OE2" Residue "N ARG 19": "NH1" <-> "NH2" Residue "N GLU 138": "OE1" <-> "OE2" Residue "N ARG 173": "NH1" <-> "NH2" Residue "N ARG 179": "NH1" <-> "NH2" Residue "N ARG 191": "NH1" <-> "NH2" Residue "N ARG 192": "NH1" <-> "NH2" Residue "H ARG 36": "NH1" <-> "NH2" Residue "H ARG 75": "NH1" <-> "NH2" Residue "H GLU 211": "OE1" <-> "OE2" Residue "H GLU 232": "OE1" <-> "OE2" Residue "K ARG 25": "NH1" <-> "NH2" Residue "K ARG 26": "NH1" <-> "NH2" Residue "K GLU 36": "OE1" <-> "OE2" Residue "Y ARG 28": "NH1" <-> "NH2" Residue "Y GLU 32": "OE1" <-> "OE2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 58": "NH1" <-> "NH2" Residue "Y TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 97": "OE1" <-> "OE2" Residue "Z GLU 3": "OE1" <-> "OE2" Residue "Z ARG 83": "NH1" <-> "NH2" Residue "Z ARG 96": "NH1" <-> "NH2" Residue "Z GLU 106": "OE1" <-> "OE2" Residue "Z GLU 137": "OE1" <-> "OE2" Residue "Z ARG 139": "NH1" <-> "NH2" Residue "V ARG 36": "NH1" <-> "NH2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V ARG 51": "NH1" <-> "NH2" Residue "W ARG 8": "NH1" <-> "NH2" Residue "W GLU 14": "OE1" <-> "OE2" Residue "W ARG 35": "NH1" <-> "NH2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ARG 48": "NH1" <-> "NH2" Residue "S GLU 56": "OE1" <-> "OE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "S ARG 85": "NH1" <-> "NH2" Residue "S ARG 86": "NH1" <-> "NH2" Residue "i TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 30": "NH1" <-> "NH2" Residue "j ARG 29": "NH1" <-> "NH2" Residue "j ARG 38": "NH1" <-> "NH2" Residue "j GLU 39": "OE1" <-> "OE2" Residue "j GLU 50": "OE1" <-> "OE2" Residue "j ARG 54": "NH1" <-> "NH2" Residue "j ARG 56": "NH1" <-> "NH2" Residue "j GLU 61": "OE1" <-> "OE2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "j ARG 66": "NH1" <-> "NH2" Residue "G GLU 38": "OE1" <-> "OE2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G GLU 79": "OE1" <-> "OE2" Residue "G ARG 97": "NH1" <-> "NH2" Residue "G GLU 137": "OE1" <-> "OE2" Residue "G ARG 138": "NH1" <-> "NH2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G ARG 173": "NH1" <-> "NH2" Residue "G ARG 185": "NH1" <-> "NH2" Residue "G ARG 235": "NH1" <-> "NH2" Residue "G ARG 254": "NH1" <-> "NH2" Residue "G GLU 266": "OE1" <-> "OE2" Residue "G ARG 292": "NH1" <-> "NH2" Residue "G ARG 301": "NH1" <-> "NH2" Residue "G ARG 356": "NH1" <-> "NH2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C GLU 311": "OE1" <-> "OE2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C ARG 318": "NH1" <-> "NH2" Residue "C ARG 333": "NH1" <-> "NH2" Residue "C ARG 350": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "C ARG 402": "NH1" <-> "NH2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "C PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C ARG 463": "NH1" <-> "NH2" Residue "C GLU 494": "OE1" <-> "OE2" Residue "C ARG 544": "NH1" <-> "NH2" Residue "C ARG 613": "NH1" <-> "NH2" Residue "C GLU 634": "OE1" <-> "OE2" Residue "C GLU 692": "OE1" <-> "OE2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "C GLU 708": "OE1" <-> "OE2" Residue "C GLU 720": "OE1" <-> "OE2" Residue "C ARG 730": "NH1" <-> "NH2" Residue "T ARG 57": "NH1" <-> "NH2" Residue "T ARG 100": "NH1" <-> "NH2" Residue "T ARG 107": "NH1" <-> "NH2" Residue "T ARG 126": "NH1" <-> "NH2" Residue "T ARG 152": "NH1" <-> "NH2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T GLU 205": "OE1" <-> "OE2" Residue "T ARG 302": "NH1" <-> "NH2" Residue "T GLU 303": "OE1" <-> "OE2" Residue "T ARG 306": "NH1" <-> "NH2" Residue "T ARG 322": "NH1" <-> "NH2" Residue "T ARG 382": "NH1" <-> "NH2" Residue "F TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 52": "NH1" <-> "NH2" Residue "F ARG 69": "NH1" <-> "NH2" Residue "F ARG 97": "NH1" <-> "NH2" Residue "F GLU 114": "OE1" <-> "OE2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 228": "NH1" <-> "NH2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "O GLU 48": "OE1" <-> "OE2" Residue "O ARG 52": "NH1" <-> "NH2" Residue "O ARG 120": "NH1" <-> "NH2" Residue "P GLU 93": "OE1" <-> "OE2" Residue "P ARG 103": "NH1" <-> "NH2" Residue "R GLU 43": "OE1" <-> "OE2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R ARG 62": "NH1" <-> "NH2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "R GLU 91": "OE1" <-> "OE2" Residue "R ARG 94": "NH1" <-> "NH2" Residue "R ARG 134": "NH1" <-> "NH2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "U ARG 32": "NH1" <-> "NH2" Residue "U ARG 83": "NH1" <-> "NH2" Residue "U ARG 115": "NH1" <-> "NH2" Residue "U ARG 149": "NH1" <-> "NH2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E ARG 209": "NH1" <-> "NH2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D GLU 50": "OE1" <-> "OE2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "X GLU 21": "OE1" <-> "OE2" Residue "X ARG 23": "NH1" <-> "NH2" Residue "X ARG 64": "NH1" <-> "NH2" Residue "X GLU 85": "OE1" <-> "OE2" Residue "X PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 9": "OE1" <-> "OE2" Residue "c ARG 84": "NH1" <-> "NH2" Residue "Q GLU 69": "OE1" <-> "OE2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "k GLU 91": "OE1" <-> "OE2" Residue "k GLU 92": "OE1" <-> "OE2" Residue "k GLU 96": "OE1" <-> "OE2" Residue "o ARG 47": "NH1" <-> "NH2" Residue "o ARG 56": "NH1" <-> "NH2" Residue "o GLU 115": "OE1" <-> "OE2" Residue "o ARG 116": "NH1" <-> "NH2" Residue "o ARG 137": "NH1" <-> "NH2" Residue "o ARG 148": "NH1" <-> "NH2" Residue "o ARG 173": "NH1" <-> "NH2" Residue "o GLU 177": "OE1" <-> "OE2" Residue "o ARG 186": "NH1" <-> "NH2" Residue "o ARG 187": "NH1" <-> "NH2" Residue "o ARG 200": "NH1" <-> "NH2" Residue "o GLU 209": "OE1" <-> "OE2" Residue "q ARG 6": "NH1" <-> "NH2" Residue "q ARG 24": "NH1" <-> "NH2" Residue "q ARG 36": "NH1" <-> "NH2" Residue "q GLU 37": "OE1" <-> "OE2" Residue "q ARG 43": "NH1" <-> "NH2" Residue "q ARG 75": "NH1" <-> "NH2" Residue "q ARG 86": "NH1" <-> "NH2" Residue "q ARG 170": "NH1" <-> "NH2" Residue "q ARG 174": "NH1" <-> "NH2" Residue "q GLU 179": "OE1" <-> "OE2" Residue "q ARG 187": "NH1" <-> "NH2" Residue "q GLU 226": "OE1" <-> "OE2" Residue "p ARG 16": "NH1" <-> "NH2" Residue "p ARG 75": "NH1" <-> "NH2" Residue "p ARG 86": "NH1" <-> "NH2" Residue "p GLU 158": "OE1" <-> "OE2" Residue "p ARG 170": "NH1" <-> "NH2" Residue "p ARG 174": "NH1" <-> "NH2" Residue "p GLU 179": "OE1" <-> "OE2" Residue "p ARG 187": "NH1" <-> "NH2" Residue "p GLU 196": "OE1" <-> "OE2" Residue "p GLU 226": "OE1" <-> "OE2" Residue "M ARG 35": "NH1" <-> "NH2" Residue "M GLU 70": "OE1" <-> "OE2" Residue "M ARG 73": "NH1" <-> "NH2" Residue "M ARG 113": "NH1" <-> "NH2" Residue "M ARG 163": "NH1" <-> "NH2" Residue "M ARG 165": "NH1" <-> "NH2" Residue "M ARG 211": "NH1" <-> "NH2" Residue "M ARG 212": "NH1" <-> "NH2" Residue "M PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 243": "OE1" <-> "OE2" Residue "M ARG 266": "NH1" <-> "NH2" Residue "M ARG 300": "NH1" <-> "NH2" Residue "M ARG 362": "NH1" <-> "NH2" Residue "M ARG 365": "NH1" <-> "NH2" Residue "M ARG 410": "NH1" <-> "NH2" Residue "M ARG 435": "NH1" <-> "NH2" Residue "f ARG 34": "NH1" <-> "NH2" Residue "f ARG 52": "NH1" <-> "NH2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "f GLU 62": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "g GLU 99": "OE1" <-> "OE2" Residue "g ARG 100": "NH1" <-> "NH2" Residue "a ARG 21": "NH1" <-> "NH2" Residue "a GLU 26": "OE1" <-> "OE2" Residue "a PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 60": "NH1" <-> "NH2" Residue "a ARG 214": "NH1" <-> "NH2" Residue "a ARG 309": "NH1" <-> "NH2" Residue "a ARG 366": "NH1" <-> "NH2" Residue "a ARG 455": "NH1" <-> "NH2" Residue "a ARG 544": "NH1" <-> "NH2" Residue "a ARG 554": "NH1" <-> "NH2" Residue "a PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 562": "NH1" <-> "NH2" Residue "a ARG 575": "NH1" <-> "NH2" Residue "a ARG 579": "NH1" <-> "NH2" Residue "a ARG 607": "NH1" <-> "NH2" Residue "a ARG 608": "NH1" <-> "NH2" Residue "a ARG 612": "NH1" <-> "NH2" Residue "b GLU 16": "OE1" <-> "OE2" Residue "b ARG 41": "NH1" <-> "NH2" Residue "b ARG 55": "NH1" <-> "NH2" Residue "b ARG 69": "NH1" <-> "NH2" Residue "h ARG 42": "NH1" <-> "NH2" Residue "m GLU 20": "OE1" <-> "OE2" Residue "m GLU 21": "OE1" <-> "OE2" Residue "m ARG 22": "NH1" <-> "NH2" Residue "m ARG 24": "NH1" <-> "NH2" Residue "m ARG 27": "NH1" <-> "NH2" Residue "m ARG 36": "NH1" <-> "NH2" Residue "m ARG 49": "NH1" <-> "NH2" Residue "m GLU 57": "OE1" <-> "OE2" Residue "m ARG 58": "NH1" <-> "NH2" Residue "m ARG 64": "NH1" <-> "NH2" Residue "t ARG 29": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 57959 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3328 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain: "I" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3754 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 16, 'TRANS': 464} Chain: "J" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 800 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain breaks: 1 Chain: "N" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1201 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 2, 'TRANS': 146} Chain breaks: 1 Chain: "H" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2493 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 16, 'TRANS': 301} Chain: "K" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 667 Classifications: {'peptide': 85} Link IDs: {'TRANS': 84} Chain: "Y" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 774 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "Z" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1103 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 12, 'TRANS': 127} Chain: "V" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 461 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "W" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "S" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 821 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "i" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 514 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "j" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 582 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "G" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3049 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 18, 'TRANS': 363} Chain: "C" Number of atoms: 5288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5288 Classifications: {'peptide': 693} Link IDs: {'PTRANS': 37, 'TRANS': 655} Chain: "T" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2535 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 21, 'TRANS': 306} Chain: "F" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1518 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 9, 'TRANS': 168} Chain: "B" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1702 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 17, 'TRANS': 201} Chain: "O" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 874 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "P" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 554 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 6, 'TRANS': 64} Chain: "R" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1039 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 10, 'TRANS': 118} Chain: "U" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1011 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "E" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1215 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 10, 'TRANS': 142} Chain: "D" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1438 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain: "X" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 843 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain breaks: 1 Chain: "c" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 744 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "Q" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 722 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 6, 'TRANS': 85} Chain: "k" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 614 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "r" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "n" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 205 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "o" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1568 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain: "q" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1736 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "p" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1705 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "M" Number of atoms: 3825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3825 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain: "f" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 640 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "g" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 386 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "d" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 329 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'TRANS': 65} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 168 Chain: "a" Number of atoms: 4677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4677 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 20, 'TRANS': 579} Chain breaks: 3 Chain: "b" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 519 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "h" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 232 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "e" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 417 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 4, 'TRANS': 79} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 10, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 132 Chain: "l" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 112 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 21} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "s" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "m" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 605 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 64} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "t" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 232 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 252 Unusual residues: {'CDL': 2, 'T7X': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "J" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 87 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "H" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'PEV': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' ZN': 1, 'BCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'T7X': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2707 SG CYS A 405 45.079 97.093 240.749 1.00 18.90 S ATOM 2727 SG CYS A 408 42.608 101.026 243.200 1.00 17.31 S ATOM 2688 SG CYS A 402 48.320 98.123 247.044 1.00 21.30 S ATOM 3052 SG CYS A 448 42.364 95.010 246.590 1.00 20.05 S ATOM 20796 SG CYS C 179 57.081 103.179 225.404 1.00 15.05 S ATOM 20735 SG CYS C 170 54.532 109.490 223.855 1.00 22.03 S ATOM 20756 SG CYS C 173 60.676 107.948 226.496 1.00 22.61 S ATOM 21124 SG CYS C 221 56.904 98.536 235.001 1.00 19.30 S ATOM 21101 SG CYS C 218 57.727 104.690 237.124 1.00 13.72 S ATOM 21148 SG CYS C 224 62.406 100.396 238.076 1.00 14.17 S ATOM 21469 SG CYS C 268 61.798 101.834 232.693 1.00 19.62 S ATOM 20251 SG CYS C 106 53.322 93.992 235.260 1.00 16.72 S ATOM 20335 SG CYS C 117 50.387 95.350 233.794 1.00 18.39 S ATOM 20462 SG CYS C 134 51.121 89.114 235.186 1.00 21.47 S ATOM 29959 SG CYS B 130 37.106 110.377 259.265 1.00 36.50 S ATOM 29990 SG CYS B 135 34.466 111.783 261.022 1.00 40.45 S ATOM 30263 SG CYS B 171 36.572 104.382 258.800 1.00 39.22 S ATOM 30287 SG CYS B 175 33.510 105.250 260.474 1.00 41.46 S ATOM 32009 SG CYS P 72 56.166 125.098 229.527 1.00 28.54 S ATOM 32195 SG CYS P 97 58.359 122.238 229.043 1.00 25.54 S ATOM 35074 SG CYS E 158 62.501 114.846 191.300 1.00 22.55 S ATOM 34574 SG CYS E 94 59.303 121.008 189.343 1.00 17.23 S ATOM 34568 SG CYS E 93 57.003 116.664 187.958 1.00 18.81 S ATOM 35304 SG CYS E 188 58.741 118.270 194.603 1.00 26.47 S ATOM 36539 SG CYS D 165 56.736 115.922 202.178 1.00 19.17 S ATOM 36513 SG CYS D 162 62.502 119.464 201.359 1.00 11.81 S ATOM 36560 SG CYS D 168 59.292 119.439 206.811 1.00 21.11 S ATOM 36281 SG CYS D 133 62.639 114.173 204.136 1.00 27.13 S ATOM 36589 SG CYS D 172 57.719 120.105 215.427 1.00 21.71 S ATOM 36254 SG CYS D 129 62.245 116.588 211.673 1.00 38.74 S ATOM 36212 SG CYS D 123 64.681 120.078 216.118 1.00 25.74 S ATOM 36231 SG CYS D 126 60.390 114.809 217.361 1.00 18.74 S Time building chain proxies: 23.33, per 1000 atoms: 0.40 Number of scatterers: 57959 At special positions: 0 Unit cell: (129.87, 197.58, 297.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Fe 28 26.01 S 403 16.00 P 13 15.00 O 10409 8.00 N 9681 7.00 C 37423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS I 336 " - pdb=" SG CYS I 420 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 29 " - pdb=" SG CYS Y 59 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 39 " - pdb=" SG CYS Y 49 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 81 " - pdb=" SG CYS Y 92 " distance=2.03 Simple disulfide: pdb=" SG CYS j 14 " - pdb=" SG CYS j 44 " distance=2.03 Simple disulfide: pdb=" SG CYS j 24 " - pdb=" SG CYS j 34 " distance=2.03 Simple disulfide: pdb=" SG CYS j 28 " - pdb=" SG CYS j 34 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 53 " distance=2.05 Simple disulfide: pdb=" SG CYS f 58 " - pdb=" SG CYS f 70 " distance=2.04 Simple disulfide: pdb=" SG CYS b 40 " - pdb=" SG CYS b 51 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.05 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES B 301 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 135 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 175 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 130 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 171 " pdb=" FES C 803 " pdb="FE2 FES C 803 " - pdb=" SG CYS C 134 " pdb="FE1 FES C 803 " - pdb=" SG CYS C 117 " pdb="FE1 FES C 803 " - pdb=" SG CYS C 106 " pdb="FE2 FES C 803 " - pdb=" SG CYS C 120 " pdb=" SF4 A 501 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 405 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 402 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 448 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 408 " pdb=" SF4 C 801 " pdb="FE3 SF4 C 801 " - pdb=" NE2 HIS C 166 " pdb="FE1 SF4 C 801 " - pdb=" SG CYS C 179 " pdb="FE2 SF4 C 801 " - pdb=" SG CYS C 170 " pdb="FE4 SF4 C 801 " - pdb=" SG CYS C 173 " pdb=" SF4 C 802 " pdb="FE3 SF4 C 802 " - pdb=" SG CYS C 224 " pdb="FE4 SF4 C 802 " - pdb=" SG CYS C 268 " pdb="FE1 SF4 C 802 " - pdb=" SG CYS C 221 " pdb="FE2 SF4 C 802 " - pdb=" SG CYS C 218 " pdb=" SF4 D 301 " pdb="FE4 SF4 D 301 " - pdb=" SG CYS D 133 " pdb="FE3 SF4 D 301 " - pdb=" SG CYS D 168 " pdb="FE2 SF4 D 301 " - pdb=" SG CYS D 162 " pdb="FE1 SF4 D 301 " - pdb=" SG CYS D 165 " pdb=" SF4 D 302 " pdb="FE4 SF4 D 302 " - pdb=" SG CYS D 126 " pdb="FE2 SF4 D 302 " - pdb=" SG CYS D 129 " pdb="FE3 SF4 D 302 " - pdb=" SG CYS D 123 " pdb="FE1 SF4 D 302 " - pdb=" SG CYS D 172 " pdb=" SF4 E 301 " pdb="FE1 SF4 E 301 " - pdb=" SG CYS E 158 " pdb="FE4 SF4 E 301 " - pdb=" SG CYS E 188 " pdb="FE3 SF4 E 301 " - pdb=" SG CYS E 93 " pdb="FE2 SF4 E 301 " - pdb=" SG CYS E 94 " pdb="FE3 SF4 E 301 " - pdb=" NE2 HIS G 154 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN P 201 " pdb="ZN ZN P 201 " - pdb=" NE2 HIS P 82 " pdb="ZN ZN P 201 " - pdb=" SG CYS P 72 " pdb="ZN ZN P 201 " - pdb=" SG CYS P 97 " pdb=" ZN q 801 " pdb="ZN ZN q 801 " - pdb=" NE2 HIS q 107 " pdb="ZN ZN q 801 " - pdb=" NE2 HIS p 130 " 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13646 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 280 helices and 28 sheets defined 46.6% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.87 Creating SS restraints... Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 88 through 94 Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 151 through 154 No H-bonds generated for 'chain 'A' and resid 151 through 154' Processing helix chain 'A' and resid 159 through 171 Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 232 through 240 removed outlier: 3.838A pdb=" N LEU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 268 through 279 Proline residue: A 275 - end of helix Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 406 through 422 removed outlier: 4.269A pdb=" N GLY A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 removed outlier: 4.473A pdb=" N GLY A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N HIS A 445 " --> pdb=" O GLN A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 479 Proline residue: A 457 - end of helix Proline residue: A 467 - end of helix Processing helix chain 'I' and resid 20 through 40 Processing helix chain 'I' and resid 54 through 57 No H-bonds generated for 'chain 'I' and resid 54 through 57' Processing helix chain 'I' and resid 60 through 71 Processing helix chain 'I' and resid 75 through 77 No H-bonds generated for 'chain 'I' and resid 75 through 77' Processing helix chain 'I' and resid 91 through 116 removed outlier: 3.518A pdb=" N CYS I 111 " --> pdb=" O THR I 107 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ASP I 113 " --> pdb=" O SER I 109 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE I 114 " --> pdb=" O MET I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 140 removed outlier: 3.907A pdb=" N ILE I 140 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 163 Processing helix chain 'I' and resid 170 through 201 Processing helix chain 'I' and resid 206 through 212 removed outlier: 3.969A pdb=" N LYS I 211 " --> pdb=" O ASP I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 224 through 240 Processing helix chain 'I' and resid 244 through 246 No H-bonds generated for 'chain 'I' and resid 244 through 246' Processing helix chain 'I' and resid 250 through 256 Processing helix chain 'I' and resid 259 through 282 removed outlier: 3.722A pdb=" N ILE I 267 " --> pdb=" O ALA I 263 " (cutoff:3.500A) Proline residue: I 269 - end of helix Processing helix chain 'I' and resid 291 through 311 Processing helix chain 'I' and resid 315 through 334 removed outlier: 4.568A pdb=" N GLY I 333 " --> pdb=" O TYR I 329 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE I 334 " --> pdb=" O ILE I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 365 removed outlier: 3.642A pdb=" N MET I 355 " --> pdb=" O ILE I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 377 No H-bonds generated for 'chain 'I' and resid 374 through 377' Processing helix chain 'I' and resid 385 through 399 Processing helix chain 'I' and resid 405 through 419 Processing helix chain 'I' and resid 423 through 448 Processing helix chain 'I' and resid 463 through 477 Processing helix chain 'I' and resid 480 through 482 No H-bonds generated for 'chain 'I' and resid 480 through 482' Processing helix chain 'I' and resid 484 through 496 Processing helix chain 'J' and resid 3 through 28 removed outlier: 3.783A pdb=" N ALA J 6 " --> pdb=" O LEU J 3 " (cutoff:3.500A) Proline residue: J 7 - end of helix removed outlier: 3.504A pdb=" N ILE J 10 " --> pdb=" O PRO J 7 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU J 12 " --> pdb=" O PHE J 9 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER J 15 " --> pdb=" O LEU J 12 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL J 25 " --> pdb=" O LEU J 22 " (cutoff:3.500A) Proline residue: J 26 - end of helix Processing helix chain 'J' and resid 59 through 83 removed outlier: 4.521A pdb=" N VAL J 64 " --> pdb=" O PHE J 61 " (cutoff:3.500A) Proline residue: J 80 - end of helix Processing helix chain 'J' and resid 92 through 113 Processing helix chain 'N' and resid 5 through 17 removed outlier: 3.717A pdb=" N VAL N 17 " --> pdb=" O GLY N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 43 Processing helix chain 'N' and resid 47 through 58 Processing helix chain 'N' and resid 61 through 70 Processing helix chain 'N' and resid 136 through 144 removed outlier: 4.828A pdb=" N LEU N 143 " --> pdb=" O THR N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 170 removed outlier: 4.793A pdb=" N VAL N 154 " --> pdb=" O TRP N 151 " (cutoff:3.500A) Proline residue: N 155 - end of helix removed outlier: 4.084A pdb=" N LEU N 169 " --> pdb=" O ALA N 166 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR N 170 " --> pdb=" O ILE N 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 35 Proline residue: H 15 - end of helix removed outlier: 3.840A pdb=" N LEU H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN H 35 " --> pdb=" O MET H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 59 Processing helix chain 'H' and resid 77 through 89 removed outlier: 4.549A pdb=" N TRP H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 126 removed outlier: 4.079A pdb=" N TYR H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 161 removed outlier: 3.765A pdb=" N GLU H 148 " --> pdb=" O MET H 144 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL H 149 " --> pdb=" O VAL H 145 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER H 150 " --> pdb=" O SER H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 172 Processing helix chain 'H' and resid 179 through 182 No H-bonds generated for 'chain 'H' and resid 179 through 182' Processing helix chain 'H' and resid 184 through 197 removed outlier: 3.654A pdb=" N ALA H 196 " --> pdb=" O ILE H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 215 removed outlier: 4.236A pdb=" N VAL H 213 " --> pdb=" O GLU H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 242 Processing helix chain 'H' and resid 265 through 285 Processing helix chain 'H' and resid 296 through 299 No H-bonds generated for 'chain 'H' and resid 296 through 299' Processing helix chain 'H' and resid 305 through 320 removed outlier: 3.833A pdb=" N TRP H 310 " --> pdb=" O LEU H 306 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU H 318 " --> pdb=" O VAL H 314 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 23 removed outlier: 4.097A pdb=" N SER K 10 " --> pdb=" O TYR K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 41 Processing helix chain 'K' and resid 43 through 52 Processing helix chain 'K' and resid 57 through 83 removed outlier: 4.347A pdb=" N ALA K 71 " --> pdb=" O THR K 67 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 20 Processing helix chain 'Y' and resid 22 through 27 Processing helix chain 'Y' and resid 30 through 42 Processing helix chain 'Y' and resid 47 through 67 removed outlier: 5.618A pdb=" N ASP Y 51 " --> pdb=" O LYS Y 48 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL Y 60 " --> pdb=" O THR Y 57 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU Y 61 " --> pdb=" O ARG Y 58 " (cutoff:3.500A) Processing helix chain 'Y' and resid 74 through 84 removed outlier: 3.935A pdb=" N VAL Y 79 " --> pdb=" O MET Y 75 " (cutoff:3.500A) Processing helix chain 'Y' and resid 90 through 102 removed outlier: 3.916A pdb=" N ARG Y 93 " --> pdb=" O ASP Y 90 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS Y 94 " --> pdb=" O LEU Y 91 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU Y 95 " --> pdb=" O CYS Y 92 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE Y 99 " --> pdb=" O GLN Y 96 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS Y 101 " --> pdb=" O ALA Y 98 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL Y 102 " --> pdb=" O PHE Y 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 111 removed outlier: 3.660A pdb=" N TYR Z 62 " --> pdb=" O ALA Z 58 " (cutoff:3.500A) Proline residue: Z 87 - end of helix removed outlier: 3.557A pdb=" N ASP Z 110 " --> pdb=" O GLU Z 106 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 28 removed outlier: 3.582A pdb=" N LEU V 10 " --> pdb=" O GLU V 7 " (cutoff:3.500A) Proline residue: V 11 - end of helix removed outlier: 4.616A pdb=" N GLY V 17 " --> pdb=" O ILE V 14 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET V 18 " --> pdb=" O ILE V 15 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N CYS V 20 " --> pdb=" O GLY V 17 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN V 24 " --> pdb=" O ILE V 21 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER V 25 " --> pdb=" O MET V 22 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN V 26 " --> pdb=" O GLY V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 33 No H-bonds generated for 'chain 'V' and resid 30 through 33' Processing helix chain 'V' and resid 44 through 56 Processing helix chain 'W' and resid 5 through 13 Processing helix chain 'W' and resid 15 through 18 No H-bonds generated for 'chain 'W' and resid 15 through 18' Processing helix chain 'W' and resid 25 through 28 No H-bonds generated for 'chain 'W' and resid 25 through 28' Processing helix chain 'W' and resid 30 through 37 removed outlier: 4.426A pdb=" N ARG W 35 " --> pdb=" O PRO W 31 " (cutoff:3.500A) Proline residue: W 36 - end of helix Processing helix chain 'S' and resid 64 through 66 No H-bonds generated for 'chain 'S' and resid 64 through 66' Processing helix chain 'S' and resid 91 through 100 Processing helix chain 'i' and resid 8 through 24 Processing helix chain 'i' and resid 32 through 34 No H-bonds generated for 'chain 'i' and resid 32 through 34' Processing helix chain 'i' and resid 37 through 66 Processing helix chain 'i' and resid 68 through 71 removed outlier: 4.117A pdb=" N ASN i 71 " --> pdb=" O ARG i 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 68 through 71' Processing helix chain 'j' and resid 15 through 27 Processing helix chain 'j' and resid 35 through 46 Processing helix chain 'j' and resid 48 through 69 Processing helix chain 'G' and resid 51 through 57 removed outlier: 4.845A pdb=" N GLU G 56 " --> pdb=" O GLU G 52 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR G 57 " --> pdb=" O LYS G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 69 removed outlier: 3.858A pdb=" N ASP G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 87 removed outlier: 3.794A pdb=" N GLU G 79 " --> pdb=" O MET G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 125 removed outlier: 3.509A pdb=" N LEU G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR G 119 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 148 removed outlier: 3.909A pdb=" N LEU G 132 " --> pdb=" O LEU G 128 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG G 147 " --> pdb=" O GLU G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 179 Processing helix chain 'G' and resid 182 through 191 Processing helix chain 'G' and resid 197 through 203 Processing helix chain 'G' and resid 211 through 216 Processing helix chain 'G' and resid 241 through 243 No H-bonds generated for 'chain 'G' and resid 241 through 243' Processing helix chain 'G' and resid 257 through 280 removed outlier: 4.115A pdb=" N ARG G 269 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU G 272 " --> pdb=" O MET G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 304 Processing helix chain 'G' and resid 306 through 316 Processing helix chain 'G' and resid 362 through 369 removed outlier: 4.520A pdb=" N ASP G 367 " --> pdb=" O LEU G 363 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE G 368 " --> pdb=" O GLN G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 375 through 384 removed outlier: 3.919A pdb=" N VAL G 379 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE G 381 " --> pdb=" O VAL G 378 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE G 382 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 391 No H-bonds generated for 'chain 'G' and resid 389 through 391' Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 149 through 162 Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 223 through 229 removed outlier: 3.614A pdb=" N SER C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 264 through 267 No H-bonds generated for 'chain 'C' and resid 264 through 267' Processing helix chain 'C' and resid 330 through 333 No H-bonds generated for 'chain 'C' and resid 330 through 333' Processing helix chain 'C' and resid 338 through 340 No H-bonds generated for 'chain 'C' and resid 338 through 340' Processing helix chain 'C' and resid 361 through 373 Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 390 through 402 Processing helix chain 'C' and resid 422 through 425 removed outlier: 3.526A pdb=" N TYR C 425 " --> pdb=" O ARG C 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 422 through 425' Processing helix chain 'C' and resid 433 through 436 Processing helix chain 'C' and resid 452 through 463 Processing helix chain 'C' and resid 490 through 496 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 518 through 521 Processing helix chain 'C' and resid 526 through 540 Processing helix chain 'C' and resid 557 through 564 removed outlier: 4.273A pdb=" N ALA C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 613 No H-bonds generated for 'chain 'C' and resid 610 through 613' Processing helix chain 'C' and resid 653 through 663 Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 685 through 687 No H-bonds generated for 'chain 'C' and resid 685 through 687' Processing helix chain 'C' and resid 700 through 702 No H-bonds generated for 'chain 'C' and resid 700 through 702' Processing helix chain 'C' and resid 727 through 730 No H-bonds generated for 'chain 'C' and resid 727 through 730' Processing helix chain 'T' and resid 79 through 90 removed outlier: 4.166A pdb=" N TYR T 83 " --> pdb=" O PHE T 79 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 110 Processing helix chain 'T' and resid 131 through 134 No H-bonds generated for 'chain 'T' and resid 131 through 134' Processing helix chain 'T' and resid 157 through 160 No H-bonds generated for 'chain 'T' and resid 157 through 160' Processing helix chain 'T' and resid 164 through 173 Processing helix chain 'T' and resid 195 through 210 Processing helix chain 'T' and resid 246 through 249 removed outlier: 3.591A pdb=" N GLY T 249 " --> pdb=" O ILE T 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 246 through 249' Processing helix chain 'T' and resid 258 through 270 removed outlier: 3.774A pdb=" N LEU T 269 " --> pdb=" O ILE T 265 " (cutoff:3.500A) Processing helix chain 'T' and resid 290 through 300 removed outlier: 3.579A pdb=" N ASP T 299 " --> pdb=" O GLU T 295 " (cutoff:3.500A) Processing helix chain 'T' and resid 312 through 318 Processing helix chain 'T' and resid 341 through 348 Processing helix chain 'T' and resid 360 through 363 Processing helix chain 'T' and resid 373 through 381 removed outlier: 5.758A pdb=" N PHE T 377 " --> pdb=" O PRO T 374 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN T 380 " --> pdb=" O PHE T 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 13 Processing helix chain 'F' and resid 38 through 43 Processing helix chain 'F' and resid 106 through 118 removed outlier: 3.531A pdb=" N GLY F 109 " --> pdb=" O PRO F 106 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP F 110 " --> pdb=" O SER F 107 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET F 118 " --> pdb=" O VAL F 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 69 through 83 removed outlier: 4.229A pdb=" N ILE B 74 " --> pdb=" O SER B 71 " (cutoff:3.500A) Proline residue: B 75 - end of helix Processing helix chain 'B' and resid 90 through 100 Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 133 through 138 removed outlier: 4.321A pdb=" N ARG B 138 " --> pdb=" O PRO B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 151 Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'O' and resid 47 through 49 No H-bonds generated for 'chain 'O' and resid 47 through 49' Processing helix chain 'O' and resid 111 through 120 Processing helix chain 'O' and resid 140 through 142 No H-bonds generated for 'chain 'O' and resid 140 through 142' Processing helix chain 'P' and resid 41 through 44 No H-bonds generated for 'chain 'P' and resid 41 through 44' Processing helix chain 'P' and resid 53 through 58 Processing helix chain 'R' and resid 29 through 46 removed outlier: 3.996A pdb=" N GLN R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ALA R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 70 Processing helix chain 'R' and resid 74 through 80 Processing helix chain 'R' and resid 86 through 103 Processing helix chain 'U' and resid 38 through 44 Processing helix chain 'U' and resid 96 through 98 No H-bonds generated for 'chain 'U' and resid 96 through 98' Processing helix chain 'U' and resid 105 through 110 removed outlier: 5.107A pdb=" N SER U 110 " --> pdb=" O ASP U 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 82 Processing helix chain 'E' and resid 93 through 101 Processing helix chain 'E' and resid 136 through 145 removed outlier: 3.764A pdb=" N GLN E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 160 No H-bonds generated for 'chain 'E' and resid 157 through 160' Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 192 through 207 removed outlier: 3.595A pdb=" N LYS E 204 " --> pdb=" O LEU E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 215 Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 63 through 71 Processing helix chain 'D' and resid 75 through 88 Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 190 through 193 No H-bonds generated for 'chain 'D' and resid 190 through 193' Processing helix chain 'D' and resid 201 through 218 removed outlier: 3.593A pdb=" N GLY D 204 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP D 205 " --> pdb=" O GLU D 202 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR D 209 " --> pdb=" O ARG D 206 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA D 212 " --> pdb=" O THR D 209 " (cutoff:3.500A) Processing helix chain 'X' and resid 19 through 44 Proline residue: X 38 - end of helix Processing helix chain 'X' and resid 52 through 65 Processing helix chain 'X' and resid 72 through 90 Processing helix chain 'X' and resid 99 through 102 No H-bonds generated for 'chain 'X' and resid 99 through 102' Processing helix chain 'X' and resid 123 through 127 Processing helix chain 'c' and resid 33 through 53 removed outlier: 3.597A pdb=" N THR c 41 " --> pdb=" O PHE c 37 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL c 47 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY c 52 " --> pdb=" O GLY c 48 " (cutoff:3.500A) Processing helix chain 'c' and resid 59 through 85 Processing helix chain 'c' and resid 95 through 99 Processing helix chain 'Q' and resid 26 through 42 removed outlier: 5.354A pdb=" N LYS Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP Q 38 " --> pdb=" O LYS Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 93 removed outlier: 3.605A pdb=" N GLY Q 93 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 55 Processing helix chain 'k' and resid 79 through 92 Processing helix chain 'k' and resid 99 through 104 removed outlier: 4.543A pdb=" N LYS k 104 " --> pdb=" O LYS k 100 " (cutoff:3.500A) Processing helix chain 'k' and resid 108 through 115 Processing helix chain 'n' and resid 83 through 100 Processing helix chain 'o' and resid 207 through 230 Proline residue: o 214 - end of helix removed outlier: 4.038A pdb=" N GLU o 230 " --> pdb=" O ASP o 226 " (cutoff:3.500A) Processing helix chain 'o' and resid 237 through 246 Processing helix chain 'q' and resid 10 through 27 removed outlier: 3.735A pdb=" N GLY q 26 " --> pdb=" O ASP q 23 " (cutoff:3.500A) Processing helix chain 'q' and resid 194 through 213 Processing helix chain 'q' and resid 216 through 218 No H-bonds generated for 'chain 'q' and resid 216 through 218' Processing helix chain 'q' and resid 221 through 231 removed outlier: 3.961A pdb=" N LYS q 229 " --> pdb=" O ILE q 225 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL q 230 " --> pdb=" O GLU q 226 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LEU q 231 " --> pdb=" O PHE q 227 " (cutoff:3.500A) Processing helix chain 'p' and resid 7 through 26 Processing helix chain 'p' and resid 34 through 36 No H-bonds generated for 'chain 'p' and resid 34 through 36' Processing helix chain 'p' and resid 194 through 212 removed outlier: 3.594A pdb=" N ALA p 204 " --> pdb=" O ILE p 200 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR p 205 " --> pdb=" O SER p 201 " (cutoff:3.500A) Processing helix chain 'p' and resid 221 through 228 Processing helix chain 'M' and resid 18 through 26 Processing helix chain 'M' and resid 34 through 57 Processing helix chain 'M' and resid 77 through 79 No H-bonds generated for 'chain 'M' and resid 77 through 79' Processing helix chain 'M' and resid 88 through 106 removed outlier: 3.966A pdb=" N PHE M 92 " --> pdb=" O GLY M 88 " (cutoff:3.500A) Proline residue: M 102 - end of helix Processing helix chain 'M' and resid 118 through 125 Processing helix chain 'M' and resid 129 through 135 Processing helix chain 'M' and resid 139 through 159 Proline residue: M 146 - end of helix removed outlier: 3.679A pdb=" N LEU M 150 " --> pdb=" O PRO M 146 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE M 151 " --> pdb=" O GLU M 147 " (cutoff:3.500A) Proline residue: M 152 - end of helix Processing helix chain 'M' and resid 171 through 194 Processing helix chain 'M' and resid 200 through 205 Processing helix chain 'M' and resid 210 through 227 removed outlier: 3.564A pdb=" N ILE M 214 " --> pdb=" O GLU M 210 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE M 215 " --> pdb=" O ARG M 211 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER M 223 " --> pdb=" O ALA M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 242 Processing helix chain 'M' and resid 246 through 267 removed outlier: 3.617A pdb=" N VAL M 250 " --> pdb=" O THR M 246 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU M 257 " --> pdb=" O ALA M 253 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LYS M 258 " --> pdb=" O GLY M 254 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY M 260 " --> pdb=" O LEU M 256 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR M 261 " --> pdb=" O LEU M 257 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 300 Proline residue: M 281 - end of helix removed outlier: 4.456A pdb=" N THR M 298 " --> pdb=" O THR M 294 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU M 299 " --> pdb=" O SER M 295 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG M 300 " --> pdb=" O LEU M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 323 Processing helix chain 'M' and resid 328 through 359 removed outlier: 4.116A pdb=" N SER M 346 " --> pdb=" O GLY M 342 " (cutoff:3.500A) Processing helix chain 'M' and resid 370 through 373 No H-bonds generated for 'chain 'M' and resid 370 through 373' Processing helix chain 'M' and resid 375 through 388 removed outlier: 4.429A pdb=" N ALA M 387 " --> pdb=" O SER M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 395 through 405 Processing helix chain 'M' and resid 415 through 437 removed outlier: 4.381A pdb=" N LEU M 420 " --> pdb=" O THR M 416 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY M 425 " --> pdb=" O GLY M 421 " (cutoff:3.500A) Processing helix chain 'M' and resid 454 through 472 Proline residue: M 462 - end of helix Processing helix chain 'M' and resid 474 through 478 Processing helix chain 'M' and resid 482 through 491 Processing helix chain 'f' and resid 23 through 25 No H-bonds generated for 'chain 'f' and resid 23 through 25' Processing helix chain 'f' and resid 27 through 62 removed outlier: 3.772A pdb=" N ARG f 39 " --> pdb=" O GLU f 35 " (cutoff:3.500A) Processing helix chain 'f' and resid 71 through 80 removed outlier: 3.774A pdb=" N ALA f 80 " --> pdb=" O GLN f 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 78 Processing helix chain 'g' and resid 89 through 102 removed outlier: 3.775A pdb=" N GLN g 95 " --> pdb=" O THR g 91 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU g 98 " --> pdb=" O HIS g 94 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 20 No H-bonds generated for 'chain 'd' and resid 17 through 20' Processing helix chain 'd' and resid 22 through 34 removed outlier: 4.139A pdb=" N ARG d 25 " --> pdb=" O ILE d 22 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP d 30 " --> pdb=" O ALA d 27 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR d 31 " --> pdb=" O LEU d 28 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN d 33 " --> pdb=" O ASP d 30 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP d 34 " --> pdb=" O THR d 31 " (cutoff:3.500A) Processing helix chain 'd' and resid 39 through 54 Processing helix chain 'd' and resid 61 through 76 Processing helix chain 'a' and resid 8 through 22 removed outlier: 4.112A pdb=" N PHE a 18 " --> pdb=" O SER a 14 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY a 20 " --> pdb=" O ALA a 16 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ARG a 21 " --> pdb=" O GLY a 17 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE a 22 " --> pdb=" O PHE a 18 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 53 removed outlier: 3.548A pdb=" N PHE a 47 " --> pdb=" O LEU a 44 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLU a 49 " --> pdb=" O ALA a 46 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL a 50 " --> pdb=" O PHE a 47 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU a 52 " --> pdb=" O GLU a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 82 through 103 Processing helix chain 'a' and resid 110 through 128 Processing helix chain 'a' and resid 133 through 151 Processing helix chain 'a' and resid 159 through 188 removed outlier: 4.803A pdb=" N LYS a 166 " --> pdb=" O LYS a 162 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL a 170 " --> pdb=" O LYS a 166 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN a 171 " --> pdb=" O ALA a 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 194 through 203 removed outlier: 4.458A pdb=" N PHE a 198 " --> pdb=" O PHE a 194 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA a 199 " --> pdb=" O SER a 195 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL a 203 " --> pdb=" O ALA a 199 " (cutoff:3.500A) Processing helix chain 'a' and resid 217 through 231 Processing helix chain 'a' and resid 250 through 258 Processing helix chain 'a' and resid 263 through 271 removed outlier: 3.554A pdb=" N MET a 268 " --> pdb=" O ALA a 264 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE a 269 " --> pdb=" O GLY a 265 " (cutoff:3.500A) Processing helix chain 'a' and resid 273 through 277 Processing helix chain 'a' and resid 280 through 300 Processing helix chain 'a' and resid 310 through 327 removed outlier: 5.092A pdb=" N SER a 317 " --> pdb=" O TYR a 313 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET a 322 " --> pdb=" O GLN a 318 " (cutoff:3.500A) Processing helix chain 'a' and resid 331 through 361 Processing helix chain 'a' and resid 380 through 389 removed outlier: 3.503A pdb=" N LEU a 383 " --> pdb=" O ALA a 380 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER a 388 " --> pdb=" O GLY a 385 " (cutoff:3.500A) Processing helix chain 'a' and resid 402 through 415 removed outlier: 3.688A pdb=" N THR a 410 " --> pdb=" O GLU a 406 " (cutoff:3.500A) Processing helix chain 'a' and resid 427 through 438 Processing helix chain 'a' and resid 461 through 473 Proline residue: a 466 - end of helix Processing helix chain 'a' and resid 496 through 499 No H-bonds generated for 'chain 'a' and resid 496 through 499' Processing helix chain 'a' and resid 516 through 518 No H-bonds generated for 'chain 'a' and resid 516 through 518' Processing helix chain 'a' and resid 520 through 533 removed outlier: 3.799A pdb=" N PHE a 524 " --> pdb=" O ILE a 520 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA a 532 " --> pdb=" O GLY a 528 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR a 533 " --> pdb=" O ALA a 529 " (cutoff:3.500A) Processing helix chain 'a' and resid 555 through 559 removed outlier: 3.829A pdb=" N PHE a 559 " --> pdb=" O TYR a 556 " (cutoff:3.500A) Processing helix chain 'a' and resid 568 through 614 Proline residue: a 599 - end of helix Processing helix chain 'a' and resid 620 through 636 removed outlier: 5.247A pdb=" N ALA a 625 " --> pdb=" O VAL a 621 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE a 626 " --> pdb=" O TYR a 622 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA a 627 " --> pdb=" O HIS a 623 " (cutoff:3.500A) Processing helix chain 'b' and resid 22 through 24 No H-bonds generated for 'chain 'b' and resid 22 through 24' Processing helix chain 'b' and resid 34 through 43 removed outlier: 3.790A pdb=" N ASN b 38 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS b 39 " --> pdb=" O ILE b 35 " (cutoff:3.500A) Processing helix chain 'b' and resid 53 through 73 Processing helix chain 'h' and resid 22 through 28 removed outlier: 3.757A pdb=" N THR h 27 " --> pdb=" O TRP h 23 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 45 removed outlier: 5.934A pdb=" N VAL h 34 " --> pdb=" O LEU h 31 " (cutoff:3.500A) Processing helix chain 'e' and resid 47 through 58 Processing helix chain 'e' and resid 83 through 96 removed outlier: 4.703A pdb=" N GLU e 95 " --> pdb=" O MET e 91 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU e 96 " --> pdb=" O ALA e 92 " (cutoff:3.500A) Processing helix chain 'e' and resid 106 through 108 No H-bonds generated for 'chain 'e' and resid 106 through 108' Processing helix chain 'e' and resid 112 through 121 Processing helix chain 'l' and resid 39 through 59 Proline residue: l 45 - end of helix Processing helix chain 's' and resid 7 through 24 Processing helix chain 'm' and resid 19 through 37 removed outlier: 3.566A pdb=" N ARG m 22 " --> pdb=" O PRO m 19 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG m 24 " --> pdb=" O GLU m 21 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG m 36 " --> pdb=" O MET m 33 " (cutoff:3.500A) Processing helix chain 'm' and resid 54 through 60 removed outlier: 4.059A pdb=" N HIS m 59 " --> pdb=" O THR m 55 " (cutoff:3.500A) Processing helix chain 't' and resid 21 through 25 Processing helix chain 't' and resid 27 through 31 Processing helix chain 't' and resid 35 through 49 Processing sheet with id= A, first strand: chain 'A' and resid 135 through 138 removed outlier: 6.535A pdb=" N ALA A 176 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL A 138 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR A 178 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU A 217 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE A 179 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR A 219 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE A 181 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS A 221 " --> pdb=" O ILE A 181 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 337 through 341 removed outlier: 6.870A pdb=" N MET A 380 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A 340 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A 378 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 325 through 332 removed outlier: 3.570A pdb=" N THR G 327 " --> pdb=" O LEU G 342 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR G 329 " --> pdb=" O VAL G 340 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 29 through 33 removed outlier: 5.886A pdb=" N ASN G 33 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N VAL G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 74 through 78 Processing sheet with id= F, first strand: chain 'C' and resid 211 through 213 Processing sheet with id= G, first strand: chain 'C' and resid 238 through 240 Processing sheet with id= H, first strand: chain 'C' and resid 288 through 290 removed outlier: 3.600A pdb=" N THR C 290 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG C 308 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 348 through 350 Processing sheet with id= J, first strand: chain 'C' and resid 439 through 443 removed outlier: 6.670A pdb=" N LYS C 468 " --> pdb=" O PHE C 440 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU C 442 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLY C 470 " --> pdb=" O LEU C 442 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'T' and resid 140 through 143 removed outlier: 6.905A pdb=" N ARG T 179 " --> pdb=" O VAL T 141 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ASN T 143 " --> pdb=" O ARG T 179 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE T 181 " --> pdb=" O ASN T 143 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'T' and resid 242 through 246 removed outlier: 6.682A pdb=" N ARG T 306 " --> pdb=" O LEU T 243 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU T 245 " --> pdb=" O ARG T 306 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL T 308 " --> pdb=" O LEU T 245 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'F' and resid 29 through 32 removed outlier: 4.341A pdb=" N ASN F 29 " --> pdb=" O ARG F 85 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP F 58 " --> pdb=" O ASN F 76 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 127 through 130 Processing sheet with id= O, first strand: chain 'B' and resid 180 through 182 Processing sheet with id= P, first strand: chain 'O' and resid 54 through 58 Processing sheet with id= Q, first strand: chain 'O' and resid 83 through 85 removed outlier: 3.524A pdb=" N TRP O 84 " --> pdb=" O SER O 93 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'U' and resid 60 through 63 Processing sheet with id= S, first strand: chain 'E' and resid 126 through 128 removed outlier: 6.076A pdb=" N ILE E 153 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE E 183 " --> pdb=" O SER E 154 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'D' and resid 110 through 113 Processing sheet with id= U, first strand: chain 'D' and resid 138 through 144 removed outlier: 6.185A pdb=" N GLU D 143 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N THR D 152 " --> pdb=" O GLU D 143 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'Q' and resid 47 through 50 removed outlier: 3.663A pdb=" N GLN Q 59 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'o' and resid 84 through 86 removed outlier: 7.158A pdb=" N ILE o 105 " --> pdb=" O THR o 85 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'o' and resid 118 through 120 Processing sheet with id= Y, first strand: chain 'q' and resid 92 through 94 removed outlier: 6.791A pdb=" N THR q 120 " --> pdb=" O SER q 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'q' and resid 179 through 182 removed outlier: 5.386A pdb=" N GLY q 182 " --> pdb=" O PHE q 188 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N PHE q 188 " --> pdb=" O GLY q 182 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'p' and resid 53 through 55 removed outlier: 5.836A pdb=" N VAL p 71 " --> pdb=" O ILE p 54 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'p' and resid 179 through 181 removed outlier: 4.010A pdb=" N ARG p 190 " --> pdb=" O VAL p 180 " (cutoff:3.500A) 2208 hydrogen bonds defined for protein. 5991 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.52 Time building geometry restraints manager: 19.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.39: 23475 1.39 - 1.61: 35157 1.61 - 1.84: 601 1.84 - 2.07: 0 2.07 - 2.29: 80 Bond restraints: 59313 Sorted by residual: bond pdb=" C8 U10 H 501 " pdb=" C9 U10 H 501 " ideal model delta sigma weight residual 1.470 1.316 0.154 2.00e-02 2.50e+03 5.90e+01 bond pdb=" C13 U10 H 501 " pdb=" C14 U10 H 501 " ideal model delta sigma weight residual 1.470 1.327 0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" C23 U10 H 501 " pdb=" C24 U10 H 501 " ideal model delta sigma weight residual 1.470 1.328 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C18 U10 H 501 " pdb=" C19 U10 H 501 " ideal model delta sigma weight residual 1.470 1.329 0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" C33 U10 H 501 " pdb=" C34 U10 H 501 " ideal model delta sigma weight residual 1.470 1.331 0.139 2.00e-02 2.50e+03 4.86e+01 ... (remaining 59308 not shown) Histogram of bond angle deviations from ideal: 73.13 - 85.37: 72 85.37 - 97.61: 9 97.61 - 109.85: 8599 109.85 - 122.08: 61718 122.08 - 134.32: 9950 Bond angle restraints: 80348 Sorted by residual: angle pdb=" S1 FES C 803 " pdb="FE2 FES C 803 " pdb=" S2 FES C 803 " ideal model delta sigma weight residual 104.33 89.56 14.77 1.14e+00 7.69e-01 1.68e+02 angle pdb=" S1 FES B 301 " pdb="FE2 FES B 301 " pdb=" S2 FES B 301 " ideal model delta sigma weight residual 104.33 89.97 14.36 1.14e+00 7.69e-01 1.59e+02 angle pdb=" PA NDP T 501 " pdb=" O3 NDP T 501 " pdb=" PN NDP T 501 " ideal model delta sigma weight residual 107.74 131.98 -24.24 1.95e+00 2.62e-01 1.54e+02 angle pdb=" S1 FES C 803 " pdb="FE1 FES C 803 " pdb=" S2 FES C 803 " ideal model delta sigma weight residual 104.33 89.45 14.88 1.20e+00 6.94e-01 1.54e+02 angle pdb=" S1 FES B 301 " pdb="FE1 FES B 301 " pdb=" S2 FES B 301 " ideal model delta sigma weight residual 104.33 90.08 14.25 1.20e+00 6.94e-01 1.41e+02 ... (remaining 80343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 34520 35.49 - 70.98: 780 70.98 - 106.46: 49 106.46 - 141.95: 10 141.95 - 177.44: 6 Dihedral angle restraints: 35365 sinusoidal: 14157 harmonic: 21208 Sorted by residual: dihedral pdb=" C THR I 356 " pdb=" N THR I 356 " pdb=" CA THR I 356 " pdb=" CB THR I 356 " ideal model delta harmonic sigma weight residual -122.00 -146.04 24.04 0 2.50e+00 1.60e-01 9.25e+01 dihedral pdb=" C PHE H 229 " pdb=" N PHE H 229 " pdb=" CA PHE H 229 " pdb=" CB PHE H 229 " ideal model delta harmonic sigma weight residual -122.60 -145.38 22.78 0 2.50e+00 1.60e-01 8.31e+01 dihedral pdb=" N THR I 356 " pdb=" C THR I 356 " pdb=" CA THR I 356 " pdb=" CB THR I 356 " ideal model delta harmonic sigma weight residual 123.40 144.62 -21.22 0 2.50e+00 1.60e-01 7.20e+01 ... (remaining 35362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.238: 8949 4.238 - 8.475: 0 8.475 - 12.713: 0 12.713 - 16.951: 0 16.951 - 21.189: 20 Chirality restraints: 8969 Sorted by residual: chirality pdb="FE4 SF4 E 301 " pdb=" S1 SF4 E 301 " pdb=" S2 SF4 E 301 " pdb=" S3 SF4 E 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.63 21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE2 SF4 E 301 " pdb=" S1 SF4 E 301 " pdb=" S3 SF4 E 301 " pdb=" S4 SF4 E 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.45 21.00 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE1 SF4 E 301 " pdb=" S2 SF4 E 301 " pdb=" S3 SF4 E 301 " pdb=" S4 SF4 E 301 " both_signs ideal model delta sigma weight residual False -10.55 10.44 -20.99 2.00e-01 2.50e+01 1.10e+04 ... (remaining 8966 not shown) Planarity restraints: 10136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 H 501 " 0.004 2.00e-02 2.50e+03 1.01e-01 1.80e+02 pdb=" C1M U10 H 501 " -0.008 2.00e-02 2.50e+03 pdb=" C2 U10 H 501 " -0.119 2.00e-02 2.50e+03 pdb=" C3 U10 H 501 " 0.112 2.00e-02 2.50e+03 pdb=" C4 U10 H 501 " 0.019 2.00e-02 2.50e+03 pdb=" C5 U10 H 501 " -0.154 2.00e-02 2.50e+03 pdb=" C6 U10 H 501 " 0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP T 501 " 0.180 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" C3N NDP T 501 " 0.041 2.00e-02 2.50e+03 pdb=" C4N NDP T 501 " 0.021 2.00e-02 2.50e+03 pdb=" C7N NDP T 501 " -0.100 2.00e-02 2.50e+03 pdb=" N1N NDP T 501 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 T7X I 501 " -0.064 2.00e-02 2.50e+03 6.39e-02 4.08e+01 pdb=" C21 T7X I 501 " 0.063 2.00e-02 2.50e+03 pdb=" C22 T7X I 501 " 0.065 2.00e-02 2.50e+03 pdb=" C23 T7X I 501 " -0.064 2.00e-02 2.50e+03 ... (remaining 10133 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 63 2.26 - 2.92: 26456 2.92 - 3.58: 90464 3.58 - 4.24: 147997 4.24 - 4.90: 245513 Nonbonded interactions: 510493 Sorted by model distance: nonbonded pdb=" OE2 GLU I 340 " pdb=" CD LYS m 38 " model vdw 1.596 3.440 nonbonded pdb=" CG1 ILE S 84 " pdb=" OD1 ASN R 122 " model vdw 1.707 3.440 nonbonded pdb=" CG GLU q 17 " pdb=" O GLY p 19 " model vdw 2.026 3.440 nonbonded pdb=" NH2 ARG A 182 " pdb=" O CYS B 171 " model vdw 2.052 2.520 nonbonded pdb=" O LYS C 205 " pdb=" OG1 THR C 213 " model vdw 2.055 2.440 ... (remaining 510488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'p' and resid 6 through 229) selection = (chain 'q' and resid 6 through 229) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 12.070 Check model and map are aligned: 0.640 Set scattering table: 0.400 Process input model: 132.200 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.218 59313 Z= 0.508 Angle : 1.036 24.242 80348 Z= 0.668 Chirality : 0.992 21.189 8969 Planarity : 0.006 0.114 10136 Dihedral : 15.860 177.440 21689 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 24.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.54 % Favored : 89.27 % Rotamer: Outliers : 1.07 % Allowed : 9.16 % Favored : 89.76 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.08), residues: 7252 helix: -2.03 (0.07), residues: 3636 sheet: -3.81 (0.26), residues: 279 loop : -3.39 (0.09), residues: 3337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP m 65 HIS 0.012 0.002 HIS q 107 PHE 0.032 0.002 PHE D 185 TYR 0.036 0.002 TYR R 115 ARG 0.009 0.001 ARG S 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2527 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 2462 time to evaluate : 4.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.6685 (m-30) cc_final: 0.5406 (m-30) REVERT: I 144 ASP cc_start: 0.6096 (t0) cc_final: 0.5794 (t0) REVERT: I 264 PHE cc_start: 0.7394 (m-80) cc_final: 0.7118 (m-80) REVERT: I 299 ILE cc_start: 0.8126 (mt) cc_final: 0.6944 (mt) REVERT: I 369 THR cc_start: 0.5258 (p) cc_final: 0.5026 (t) REVERT: J 60 ARG cc_start: 0.7030 (mtm-85) cc_final: 0.6757 (ptm160) REVERT: J 100 LEU cc_start: 0.8847 (tp) cc_final: 0.8637 (tt) REVERT: J 111 TRP cc_start: 0.8069 (t60) cc_final: 0.7628 (t60) REVERT: N 29 PHE cc_start: 0.8177 (m-80) cc_final: 0.7907 (m-10) REVERT: N 56 VAL cc_start: 0.8536 (m) cc_final: 0.8117 (m) REVERT: N 148 TYR cc_start: 0.8415 (m-80) cc_final: 0.7500 (m-80) REVERT: N 174 THR cc_start: 0.6830 (p) cc_final: 0.6407 (p) REVERT: H 41 ASP cc_start: 0.8154 (t0) cc_final: 0.7782 (t0) REVERT: H 50 GLN cc_start: 0.8393 (tp40) cc_final: 0.7621 (tm-30) REVERT: H 126 TRP cc_start: 0.7807 (t60) cc_final: 0.7237 (t-100) REVERT: H 199 ASN cc_start: 0.7753 (m-40) cc_final: 0.7549 (m-40) REVERT: K 5 LYS cc_start: 0.7024 (tttt) cc_final: 0.6792 (mmtt) REVERT: K 18 ILE cc_start: 0.8199 (tt) cc_final: 0.7989 (tt) REVERT: K 29 LEU cc_start: 0.8736 (tp) cc_final: 0.8430 (tt) REVERT: V 22 MET cc_start: 0.5366 (mtp) cc_final: 0.5095 (mtm) REVERT: S 97 MET cc_start: 0.7562 (mtt) cc_final: 0.7132 (ttm) REVERT: i 29 MET cc_start: 0.2208 (ptt) cc_final: 0.1810 (ptp) REVERT: i 31 HIS cc_start: 0.7202 (OUTLIER) cc_final: 0.6902 (p-80) REVERT: j 10 ASN cc_start: 0.8540 (m-40) cc_final: 0.8043 (m-40) REVERT: j 59 LYS cc_start: 0.8322 (ttpt) cc_final: 0.8105 (tptt) REVERT: j 62 GLN cc_start: 0.6267 (tp40) cc_final: 0.5882 (tt0) REVERT: G 94 VAL cc_start: 0.9190 (m) cc_final: 0.8966 (m) REVERT: G 174 ASP cc_start: 0.7053 (m-30) cc_final: 0.6838 (m-30) REVERT: G 302 MET cc_start: 0.7855 (ppp) cc_final: 0.6649 (ppp) REVERT: G 384 THR cc_start: 0.8034 (p) cc_final: 0.7229 (p) REVERT: C 218 CYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7939 (t) REVERT: C 500 HIS cc_start: 0.7104 (t70) cc_final: 0.6443 (t70) REVERT: C 633 THR cc_start: 0.8135 (p) cc_final: 0.7858 (p) REVERT: T 222 MET cc_start: 0.7207 (mtm) cc_final: 0.6759 (mtm) REVERT: T 356 ASN cc_start: 0.5463 (p0) cc_final: 0.4208 (t0) REVERT: T 368 HIS cc_start: 0.7180 (m170) cc_final: 0.6966 (m90) REVERT: T 381 TYR cc_start: 0.7869 (m-80) cc_final: 0.7376 (m-80) REVERT: F 155 VAL cc_start: 0.7795 (m) cc_final: 0.7556 (m) REVERT: O 65 GLN cc_start: 0.7856 (pt0) cc_final: 0.7532 (pt0) REVERT: O 68 SER cc_start: 0.8141 (m) cc_final: 0.7843 (t) REVERT: O 142 ASP cc_start: 0.7342 (m-30) cc_final: 0.7129 (m-30) REVERT: P 57 ILE cc_start: 0.8948 (tp) cc_final: 0.8623 (tp) REVERT: P 88 CYS cc_start: 0.6898 (t) cc_final: 0.6615 (t) REVERT: U 35 PRO cc_start: 0.8149 (Cg_endo) cc_final: 0.7824 (Cg_exo) REVERT: U 50 THR cc_start: 0.7470 (p) cc_final: 0.7138 (m) REVERT: U 75 TRP cc_start: 0.8017 (p90) cc_final: 0.7783 (p90) REVERT: E 141 LYS cc_start: 0.7553 (ttpt) cc_final: 0.7068 (ttmt) REVERT: E 164 TYR cc_start: 0.8908 (t80) cc_final: 0.8420 (t80) REVERT: E 188 CYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7326 (t) REVERT: E 205 LYS cc_start: 0.8445 (tttp) cc_final: 0.8049 (ttmm) REVERT: D 54 LYS cc_start: 0.5027 (mmtt) cc_final: 0.3836 (mmtt) REVERT: X 73 LYS cc_start: 0.8459 (mttt) cc_final: 0.8164 (mttm) REVERT: X 125 LYS cc_start: 0.5669 (mppt) cc_final: 0.5254 (mptt) REVERT: c 20 PRO cc_start: 0.8829 (Cg_exo) cc_final: 0.8545 (Cg_endo) REVERT: c 38 SER cc_start: 0.8489 (m) cc_final: 0.8268 (t) REVERT: c 86 MET cc_start: 0.7480 (mtm) cc_final: 0.7269 (mtm) REVERT: Q 21 SER cc_start: 0.7351 (m) cc_final: 0.6622 (p) REVERT: Q 63 ARG cc_start: 0.7496 (mtp-110) cc_final: 0.6417 (mtp-110) REVERT: k 80 LEU cc_start: 0.8270 (tp) cc_final: 0.7967 (tp) REVERT: k 105 ILE cc_start: 0.4398 (mp) cc_final: 0.3788 (mt) REVERT: o 123 TRP cc_start: 0.5668 (t-100) cc_final: 0.5420 (m-90) REVERT: o 156 CYS cc_start: 0.5402 (m) cc_final: 0.5181 (m) REVERT: q 108 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7891 (m) REVERT: q 147 MET cc_start: 0.6373 (ptp) cc_final: 0.6136 (ptp) REVERT: q 157 VAL cc_start: 0.7977 (t) cc_final: 0.7667 (t) REVERT: p 29 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7749 (tt) REVERT: p 34 TYR cc_start: 0.6586 (m-80) cc_final: 0.6132 (m-80) REVERT: p 49 PHE cc_start: 0.4456 (m-80) cc_final: 0.3544 (m-80) REVERT: M 86 ILE cc_start: 0.7767 (pt) cc_final: 0.7149 (mt) REVERT: M 261 THR cc_start: 0.8935 (p) cc_final: 0.8634 (p) REVERT: M 316 MET cc_start: 0.7220 (mmm) cc_final: 0.6992 (mmm) REVERT: M 338 MET cc_start: 0.7280 (mtm) cc_final: 0.6997 (mtm) REVERT: M 362 ARG cc_start: 0.6264 (mmp-170) cc_final: 0.5920 (mtm180) REVERT: M 367 TYR cc_start: 0.6042 (m-80) cc_final: 0.5802 (m-80) REVERT: M 397 PHE cc_start: 0.7738 (t80) cc_final: 0.7139 (t80) REVERT: M 458 PHE cc_start: 0.7422 (t80) cc_final: 0.7093 (t80) REVERT: f 39 ARG cc_start: 0.6647 (tpt170) cc_final: 0.6411 (mmm160) REVERT: f 54 LYS cc_start: 0.6281 (mttt) cc_final: 0.5951 (tmtt) REVERT: g 70 SER cc_start: 0.8316 (m) cc_final: 0.8013 (p) REVERT: a 45 ILE cc_start: 0.6979 (mm) cc_final: 0.6643 (mm) REVERT: a 137 PHE cc_start: 0.8245 (t80) cc_final: 0.7789 (t80) REVERT: a 341 HIS cc_start: 0.5105 (t70) cc_final: 0.4861 (t-90) REVERT: a 349 PHE cc_start: 0.5619 (m-80) cc_final: 0.5144 (m-80) REVERT: a 615 GLN cc_start: 0.2407 (tt0) cc_final: 0.1516 (mm-40) REVERT: b 70 MET cc_start: 0.7576 (tpt) cc_final: 0.7022 (tpt) REVERT: m 15 LEU cc_start: 0.5699 (pt) cc_final: 0.4678 (tp) REVERT: t 21 HIS cc_start: 0.3708 (p-80) cc_final: 0.2753 (m170) outliers start: 65 outliers final: 21 residues processed: 2498 average time/residue: 0.6528 time to fit residues: 2702.5156 Evaluate side-chains 1485 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1459 time to evaluate : 4.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain E residue 188 CYS Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 107 HIS Chi-restraints excluded: chain q residue 108 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 391 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 602 optimal weight: 0.0570 chunk 540 optimal weight: 7.9990 chunk 299 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 chunk 364 optimal weight: 5.9990 chunk 288 optimal weight: 0.4980 chunk 558 optimal weight: 0.0020 chunk 216 optimal weight: 0.8980 chunk 339 optimal weight: 8.9990 chunk 415 optimal weight: 7.9990 chunk 647 optimal weight: 0.4980 overall best weight: 0.3906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN A 436 GLN A 441 GLN I 53 ASN ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 ASN I 97 GLN ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 GLN I 326 HIS ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 GLN Y 33 ASN Y 45 ASN Y 87 ASN Z 8 ASN Z 126 ASN ** V 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 13 GLN ** i 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 10 ASN ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 GLN ** G 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 116 ASN C 165 ASN C 284 ASN ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 ASN C 569 GLN ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 GLN T 94 GLN T 117 GLN ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 174 HIS ** T 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 209 ASN ** T 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 340 ASN F 54 GLN F 125 ASN B 53 ASN B 70 GLN B 84 ASN ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 HIS O 77 ASN ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 149 ASN ** U 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 HIS U 141 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 HIS E 121 GLN D 111 HIS ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS ** X 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 ASN ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 160 GLN o 197 ASN q 33 ASN ** q 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 218 ASN q 223 ASN ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 135 HIS p 206 ASN ** p 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 GLN ** f 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 66 HIS a 417 ASN a 495 ASN a 541 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.273 59313 Z= 0.560 Angle : 1.629 51.281 80348 Z= 1.033 Chirality : 0.302 6.479 8969 Planarity : 0.006 0.071 10136 Dihedral : 10.599 168.599 8479 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.07 % Favored : 91.88 % Rotamer: Outliers : 4.29 % Allowed : 19.17 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.09), residues: 7252 helix: -1.02 (0.08), residues: 3575 sheet: -3.11 (0.28), residues: 265 loop : -2.85 (0.10), residues: 3412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP U 93 HIS 0.020 0.002 HIS G 154 PHE 0.054 0.002 PHE H 229 TYR 0.035 0.002 TYR I 373 ARG 0.008 0.001 ARG I 463 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1949 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1689 time to evaluate : 4.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TRP cc_start: 0.7962 (m100) cc_final: 0.7387 (m100) REVERT: A 150 ASP cc_start: 0.6783 (OUTLIER) cc_final: 0.6302 (m-30) REVERT: I 76 LEU cc_start: 0.8433 (mt) cc_final: 0.8208 (mt) REVERT: I 107 THR cc_start: 0.7601 (p) cc_final: 0.7330 (p) REVERT: I 143 TYR cc_start: 0.6922 (t80) cc_final: 0.6307 (t80) REVERT: I 162 ILE cc_start: 0.8849 (pt) cc_final: 0.8525 (pt) REVERT: I 297 CYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6852 (t) REVERT: J 100 LEU cc_start: 0.8879 (tp) cc_final: 0.8679 (tt) REVERT: J 111 TRP cc_start: 0.7974 (t60) cc_final: 0.7624 (t60) REVERT: N 32 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7678 (mm) REVERT: N 42 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8383 (mm) REVERT: N 57 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.6428 (m-80) REVERT: N 148 TYR cc_start: 0.8496 (m-80) cc_final: 0.7736 (m-10) REVERT: H 95 ASP cc_start: 0.7104 (t0) cc_final: 0.6845 (t70) REVERT: H 103 LEU cc_start: 0.7371 (mp) cc_final: 0.7067 (mp) REVERT: H 126 TRP cc_start: 0.7778 (t60) cc_final: 0.7293 (t-100) REVERT: H 236 MET cc_start: 0.7828 (ttp) cc_final: 0.7573 (ttp) REVERT: H 244 THR cc_start: 0.7655 (m) cc_final: 0.7451 (m) REVERT: H 281 ILE cc_start: 0.8839 (mm) cc_final: 0.8575 (mm) REVERT: K 5 LYS cc_start: 0.7600 (tttt) cc_final: 0.7211 (mmtt) REVERT: K 54 ASP cc_start: 0.7234 (t0) cc_final: 0.6936 (t0) REVERT: K 66 LEU cc_start: 0.8301 (mt) cc_final: 0.7518 (mt) REVERT: Y 95 GLU cc_start: 0.7122 (mp0) cc_final: 0.6526 (mt-10) REVERT: Z 35 TYR cc_start: 0.8195 (p90) cc_final: 0.7959 (p90) REVERT: i 31 HIS cc_start: 0.6816 (OUTLIER) cc_final: 0.6244 (p-80) REVERT: i 68 ARG cc_start: 0.6892 (tpt90) cc_final: 0.6606 (tpp-160) REVERT: j 10 ASN cc_start: 0.8433 (m110) cc_final: 0.7922 (m-40) REVERT: j 16 ASP cc_start: 0.7517 (m-30) cc_final: 0.7315 (m-30) REVERT: j 19 MET cc_start: 0.7088 (tmm) cc_final: 0.6801 (tmm) REVERT: G 153 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7494 (mtm) REVERT: G 174 ASP cc_start: 0.7073 (m-30) cc_final: 0.6812 (m-30) REVERT: G 188 GLU cc_start: 0.6583 (mt-10) cc_final: 0.6299 (mt-10) REVERT: G 259 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7537 (t0) REVERT: G 302 MET cc_start: 0.8087 (ppp) cc_final: 0.7211 (ppp) REVERT: C 119 MET cc_start: 0.8418 (tpp) cc_final: 0.7976 (tpp) REVERT: T 356 ASN cc_start: 0.5538 (p0) cc_final: 0.4859 (t0) REVERT: F 49 THR cc_start: 0.6217 (m) cc_final: 0.5939 (m) REVERT: O 65 GLN cc_start: 0.7828 (pt0) cc_final: 0.7443 (pt0) REVERT: O 124 ASP cc_start: 0.6697 (t70) cc_final: 0.6179 (t70) REVERT: P 57 ILE cc_start: 0.8690 (tp) cc_final: 0.8442 (tp) REVERT: U 35 PRO cc_start: 0.8176 (Cg_endo) cc_final: 0.7819 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8281 (p90) cc_final: 0.7808 (p90) REVERT: U 93 TRP cc_start: 0.8025 (m100) cc_final: 0.7705 (m100) REVERT: U 129 ASP cc_start: 0.7212 (m-30) cc_final: 0.6883 (m-30) REVERT: E 164 TYR cc_start: 0.9047 (t80) cc_final: 0.8738 (t80) REVERT: D 54 LYS cc_start: 0.4929 (mmtt) cc_final: 0.3769 (mmtt) REVERT: D 95 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.7866 (p0) REVERT: D 197 LYS cc_start: 0.5118 (OUTLIER) cc_final: 0.4792 (mppt) REVERT: X 18 ASN cc_start: 0.7429 (p0) cc_final: 0.7066 (p0) REVERT: X 63 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8416 (tp) REVERT: X 73 LYS cc_start: 0.8379 (mttt) cc_final: 0.8147 (mttm) REVERT: X 125 LYS cc_start: 0.5465 (mppt) cc_final: 0.4737 (mmtt) REVERT: c 38 SER cc_start: 0.8814 (m) cc_final: 0.8224 (t) REVERT: o 123 TRP cc_start: 0.5629 (t-100) cc_final: 0.5339 (m-90) REVERT: o 223 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8133 (mt) REVERT: q 108 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7926 (m) REVERT: M 65 LYS cc_start: 0.6116 (ptmt) cc_final: 0.5447 (pttp) REVERT: M 80 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8596 (mm) REVERT: M 86 ILE cc_start: 0.7577 (pt) cc_final: 0.6972 (mt) REVERT: M 136 MET cc_start: 0.7422 (tpp) cc_final: 0.7033 (tpp) REVERT: M 153 MET cc_start: 0.8547 (tpp) cc_final: 0.8065 (tpp) REVERT: M 261 THR cc_start: 0.8893 (p) cc_final: 0.8556 (p) REVERT: M 316 MET cc_start: 0.7263 (mmm) cc_final: 0.6895 (mmm) REVERT: M 338 MET cc_start: 0.7373 (mtm) cc_final: 0.7071 (mtm) REVERT: M 367 TYR cc_start: 0.6103 (m-80) cc_final: 0.5788 (m-80) REVERT: M 389 MET cc_start: 0.8309 (ptm) cc_final: 0.7772 (ptp) REVERT: M 460 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7270 (m-80) REVERT: f 54 LYS cc_start: 0.6170 (mttt) cc_final: 0.5909 (tmtt) REVERT: g 70 SER cc_start: 0.7989 (m) cc_final: 0.7749 (p) REVERT: g 72 LEU cc_start: 0.8083 (mt) cc_final: 0.7839 (mt) REVERT: a 78 PHE cc_start: 0.1442 (m-80) cc_final: 0.1117 (t80) REVERT: a 104 MET cc_start: 0.6993 (mmp) cc_final: 0.6682 (mmp) REVERT: a 126 MET cc_start: 0.7782 (mtp) cc_final: 0.7568 (mtp) REVERT: a 137 PHE cc_start: 0.8152 (t80) cc_final: 0.7315 (t80) REVERT: a 168 MET cc_start: 0.7143 (tpt) cc_final: 0.6797 (tpt) REVERT: a 341 HIS cc_start: 0.4962 (t70) cc_final: 0.4658 (t-90) REVERT: m 15 LEU cc_start: 0.5955 (pt) cc_final: 0.4948 (tp) REVERT: t 21 HIS cc_start: 0.3967 (OUTLIER) cc_final: 0.2843 (m170) outliers start: 260 outliers final: 135 residues processed: 1827 average time/residue: 0.5767 time to fit residues: 1789.1439 Evaluate side-chains 1544 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1393 time to evaluate : 4.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 297 CYS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain I residue 495 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 317 LEU Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain Y residue 19 THR Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain Z residue 89 LEU Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 45 PHE Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain j residue 34 CYS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 213 GLU Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 307 TYR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 143 ASN Chi-restraints excluded: chain O residue 147 LYS Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 101 THR Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 141 ASN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 126 ASN Chi-restraints excluded: chain c residue 3 THR Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 62 MET Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 168 SER Chi-restraints excluded: chain o residue 223 LEU Chi-restraints excluded: chain o residue 238 TYR Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 107 HIS Chi-restraints excluded: chain q residue 108 VAL Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 138 THR Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 141 ASP Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 312 SER Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain M residue 460 PHE Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 51 LEU Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 493 TRP Chi-restraints excluded: chain a residue 566 ASP Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain t residue 21 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 359 optimal weight: 0.5980 chunk 200 optimal weight: 1.9990 chunk 538 optimal weight: 10.0000 chunk 440 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 648 optimal weight: 2.9990 chunk 700 optimal weight: 5.9990 chunk 577 optimal weight: 0.9990 chunk 643 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 520 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN I 80 HIS I 84 ASN ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 HIS H 104 ASN ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 ASN Z 90 GLN ** V 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 27 HIS G 91 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 284 ASN ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 368 HIS B 53 ASN ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 GLN U 46 ASN U 141 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 18 ASN ** X 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 102 GLN ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 HIS ** q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 206 ASN ** p 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 615 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.264 59313 Z= 0.573 Angle : 1.614 51.079 80348 Z= 1.029 Chirality : 0.302 6.412 8969 Planarity : 0.005 0.069 10136 Dihedral : 9.870 166.785 8462 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 25.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.26 % Favored : 91.69 % Rotamer: Outliers : 5.27 % Allowed : 21.30 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.09), residues: 7252 helix: -0.57 (0.08), residues: 3578 sheet: -2.67 (0.28), residues: 305 loop : -2.57 (0.10), residues: 3369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP g 92 HIS 0.013 0.002 HIS T 368 PHE 0.034 0.002 PHE a 133 TYR 0.028 0.002 TYR I 373 ARG 0.014 0.001 ARG M 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1794 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 1474 time to evaluate : 5.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TRP cc_start: 0.7997 (m100) cc_final: 0.7373 (m100) REVERT: A 439 THR cc_start: 0.8636 (p) cc_final: 0.8389 (p) REVERT: I 152 ILE cc_start: 0.8805 (mt) cc_final: 0.8399 (mt) REVERT: I 162 ILE cc_start: 0.9005 (pt) cc_final: 0.8689 (pt) REVERT: I 174 GLU cc_start: 0.6643 (tm-30) cc_final: 0.5954 (tp30) REVERT: I 283 TYR cc_start: 0.7072 (t80) cc_final: 0.6805 (t80) REVERT: I 297 CYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7030 (t) REVERT: J 111 TRP cc_start: 0.7981 (t60) cc_final: 0.7560 (t60) REVERT: N 29 PHE cc_start: 0.7908 (m-80) cc_final: 0.7626 (m-10) REVERT: N 42 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8366 (mm) REVERT: N 123 ARG cc_start: 0.7532 (ptm160) cc_final: 0.7255 (ptm160) REVERT: N 148 TYR cc_start: 0.8575 (m-80) cc_final: 0.7759 (m-10) REVERT: H 41 ASP cc_start: 0.7645 (t0) cc_final: 0.7436 (t0) REVERT: H 82 PHE cc_start: 0.7306 (t80) cc_final: 0.7017 (t80) REVERT: H 126 TRP cc_start: 0.7915 (t60) cc_final: 0.7477 (t-100) REVERT: H 204 ASP cc_start: 0.6873 (t0) cc_final: 0.6666 (t0) REVERT: H 236 MET cc_start: 0.7854 (ttp) cc_final: 0.7616 (ttp) REVERT: H 244 THR cc_start: 0.7915 (m) cc_final: 0.7709 (m) REVERT: H 272 LYS cc_start: 0.8058 (mttp) cc_final: 0.7827 (mtmm) REVERT: K 5 LYS cc_start: 0.7601 (tttt) cc_final: 0.7336 (mmtt) REVERT: K 31 MET cc_start: 0.7661 (mmm) cc_final: 0.7049 (tpp) REVERT: K 54 ASP cc_start: 0.7204 (t0) cc_final: 0.6893 (t0) REVERT: S 65 GLU cc_start: 0.7227 (pm20) cc_final: 0.6552 (pm20) REVERT: j 16 ASP cc_start: 0.7691 (m-30) cc_final: 0.7466 (m-30) REVERT: j 19 MET cc_start: 0.7195 (tmm) cc_final: 0.6844 (tmm) REVERT: j 42 LEU cc_start: 0.8807 (mt) cc_final: 0.8492 (mm) REVERT: G 153 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7828 (mtm) REVERT: G 174 ASP cc_start: 0.7038 (m-30) cc_final: 0.6771 (m-30) REVERT: G 259 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7803 (t0) REVERT: C 119 MET cc_start: 0.8523 (tpp) cc_final: 0.8298 (tpp) REVERT: T 86 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8341 (tm-30) REVERT: T 87 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7927 (mm-40) REVERT: T 325 MET cc_start: 0.6801 (pmm) cc_final: 0.6526 (pmm) REVERT: T 356 ASN cc_start: 0.6248 (p0) cc_final: 0.4773 (t0) REVERT: F 49 THR cc_start: 0.6542 (m) cc_final: 0.5982 (m) REVERT: O 65 GLN cc_start: 0.8148 (pt0) cc_final: 0.7672 (pt0) REVERT: U 35 PRO cc_start: 0.8185 (Cg_endo) cc_final: 0.7826 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8269 (p90) cc_final: 0.7758 (p90) REVERT: E 164 TYR cc_start: 0.9063 (t80) cc_final: 0.8575 (t80) REVERT: E 169 TYR cc_start: 0.8689 (p90) cc_final: 0.8455 (p90) REVERT: D 54 LYS cc_start: 0.5074 (mmtt) cc_final: 0.4082 (mmtt) REVERT: D 76 MET cc_start: 0.6269 (OUTLIER) cc_final: 0.6041 (mtm) REVERT: D 95 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7749 (p0) REVERT: D 197 LYS cc_start: 0.5567 (OUTLIER) cc_final: 0.5155 (mppt) REVERT: X 18 ASN cc_start: 0.7236 (OUTLIER) cc_final: 0.6953 (p0) REVERT: X 63 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8386 (tp) REVERT: c 38 SER cc_start: 0.8871 (m) cc_final: 0.8309 (t) REVERT: o 61 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8478 (pp) REVERT: o 212 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6820 (mt-10) REVERT: o 223 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7978 (mt) REVERT: p 24 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.5374 (ptt180) REVERT: p 88 ASP cc_start: 0.6612 (OUTLIER) cc_final: 0.6404 (t0) REVERT: p 104 SER cc_start: 0.6699 (m) cc_final: 0.6223 (t) REVERT: p 141 ASP cc_start: 0.6112 (OUTLIER) cc_final: 0.5776 (p0) REVERT: M 51 TYR cc_start: 0.5714 (m-80) cc_final: 0.5416 (m-10) REVERT: M 80 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8769 (mm) REVERT: M 86 ILE cc_start: 0.7740 (pt) cc_final: 0.7207 (mt) REVERT: M 153 MET cc_start: 0.8518 (tpp) cc_final: 0.7915 (tpp) REVERT: M 261 THR cc_start: 0.8821 (p) cc_final: 0.8558 (p) REVERT: M 316 MET cc_start: 0.7312 (mmm) cc_final: 0.6863 (mmm) REVERT: M 367 TYR cc_start: 0.6158 (m-80) cc_final: 0.5879 (m-80) REVERT: M 389 MET cc_start: 0.8397 (ptm) cc_final: 0.7968 (ptp) REVERT: M 458 PHE cc_start: 0.7505 (t80) cc_final: 0.7195 (t80) REVERT: f 54 LYS cc_start: 0.5994 (mttt) cc_final: 0.5567 (tmtt) REVERT: f 79 ASP cc_start: 0.6263 (OUTLIER) cc_final: 0.5859 (m-30) REVERT: g 70 SER cc_start: 0.8075 (m) cc_final: 0.7756 (p) REVERT: a 104 MET cc_start: 0.7359 (mmp) cc_final: 0.7014 (mmp) REVERT: a 137 PHE cc_start: 0.8247 (t80) cc_final: 0.7516 (t80) REVERT: a 147 SER cc_start: 0.8768 (t) cc_final: 0.8542 (t) REVERT: a 182 ILE cc_start: 0.7979 (pt) cc_final: 0.7750 (pt) REVERT: a 322 MET cc_start: 0.5747 (ttm) cc_final: 0.5399 (mtp) REVERT: a 406 GLU cc_start: 0.4531 (mm-30) cc_final: 0.4197 (mm-30) REVERT: m 7 PHE cc_start: 0.5897 (p90) cc_final: 0.5528 (p90) REVERT: m 15 LEU cc_start: 0.6225 (pt) cc_final: 0.4844 (tp) REVERT: m 51 TYR cc_start: 0.6972 (OUTLIER) cc_final: 0.6749 (p90) REVERT: t 21 HIS cc_start: 0.3923 (OUTLIER) cc_final: 0.2651 (m170) outliers start: 320 outliers final: 189 residues processed: 1646 average time/residue: 0.5354 time to fit residues: 1505.4014 Evaluate side-chains 1521 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1314 time to evaluate : 4.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 297 CYS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 369 THR Chi-restraints excluded: chain I residue 373 TYR Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 495 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 317 LEU Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain Y residue 10 ASN Chi-restraints excluded: chain Y residue 19 THR Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain Z residue 89 LEU Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain V residue 15 ILE Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain S residue 105 ASP Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain j residue 7 ILE Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 268 MET Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 145 ILE Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 256 VAL Chi-restraints excluded: chain T residue 369 LYS Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 101 THR Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 139 THR Chi-restraints excluded: chain U residue 141 ASN Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain X residue 18 ASN Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain X residue 126 ASN Chi-restraints excluded: chain c residue 3 THR Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 62 MET Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 57 GLN Chi-restraints excluded: chain o residue 61 LEU Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 107 VAL Chi-restraints excluded: chain o residue 146 LEU Chi-restraints excluded: chain o residue 168 SER Chi-restraints excluded: chain o residue 223 LEU Chi-restraints excluded: chain o residue 238 TYR Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 17 GLU Chi-restraints excluded: chain q residue 23 ASP Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 88 ASP Chi-restraints excluded: chain q residue 92 VAL Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 138 THR Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 51 LYS Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 88 ASP Chi-restraints excluded: chain p residue 125 ASN Chi-restraints excluded: chain p residue 130 HIS Chi-restraints excluded: chain p residue 134 LEU Chi-restraints excluded: chain p residue 141 ASP Chi-restraints excluded: chain p residue 163 VAL Chi-restraints excluded: chain p residue 169 VAL Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 104 CYS Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 302 ILE Chi-restraints excluded: chain M residue 312 SER Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 398 ILE Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain a residue 22 PHE Chi-restraints excluded: chain a residue 97 HIS Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 493 TRP Chi-restraints excluded: chain m residue 51 TYR Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain t residue 21 HIS Chi-restraints excluded: chain t residue 24 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 640 optimal weight: 5.9990 chunk 487 optimal weight: 6.9990 chunk 336 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 309 optimal weight: 0.0050 chunk 435 optimal weight: 0.9990 chunk 650 optimal weight: 9.9990 chunk 689 optimal weight: 20.0000 chunk 340 optimal weight: 6.9990 chunk 616 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN I 53 ASN I 84 ASN ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 ASN ** Y 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 10 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN B 81 GLN B 84 ASN ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 GLN U 141 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** X 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 HIS ** q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 76 GLN ** a 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 59 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.251 59313 Z= 0.584 Angle : 1.618 50.986 80348 Z= 1.030 Chirality : 0.301 6.396 8969 Planarity : 0.005 0.068 10136 Dihedral : 9.453 169.372 8455 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 25.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.51 % Favored : 91.45 % Rotamer: Outliers : 6.21 % Allowed : 22.53 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.09), residues: 7252 helix: -0.41 (0.08), residues: 3588 sheet: -2.76 (0.28), residues: 313 loop : -2.40 (0.10), residues: 3351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP g 92 HIS 0.013 0.002 HIS R 129 PHE 0.048 0.002 PHE a 153 TYR 0.032 0.002 TYR Z 79 ARG 0.008 0.001 ARG i 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1781 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 377 poor density : 1404 time to evaluate : 4.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 THR cc_start: 0.8695 (p) cc_final: 0.8440 (p) REVERT: I 35 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7613 (t-90) REVERT: I 91 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.7205 (m-40) REVERT: I 139 MET cc_start: 0.8037 (ttm) cc_final: 0.7801 (mtm) REVERT: I 148 MET cc_start: 0.8230 (ptm) cc_final: 0.7737 (ptm) REVERT: I 162 ILE cc_start: 0.9075 (pt) cc_final: 0.8748 (pt) REVERT: I 297 CYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6902 (t) REVERT: I 492 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7696 (tm-30) REVERT: J 111 TRP cc_start: 0.8159 (t60) cc_final: 0.7549 (t60) REVERT: N 42 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8412 (mm) REVERT: N 123 ARG cc_start: 0.7455 (ptm160) cc_final: 0.7213 (ptm160) REVERT: N 148 TYR cc_start: 0.8549 (m-80) cc_final: 0.7560 (m-10) REVERT: H 41 ASP cc_start: 0.7832 (t0) cc_final: 0.7527 (t0) REVERT: H 76 MET cc_start: 0.8184 (mpp) cc_final: 0.7942 (mpp) REVERT: H 126 TRP cc_start: 0.7851 (t60) cc_final: 0.7483 (t-100) REVERT: H 204 ASP cc_start: 0.7202 (t0) cc_final: 0.6860 (t0) REVERT: H 244 THR cc_start: 0.8113 (m) cc_final: 0.7906 (m) REVERT: H 290 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.8459 (m-80) REVERT: K 5 LYS cc_start: 0.7682 (tttt) cc_final: 0.7311 (mmtt) REVERT: K 31 MET cc_start: 0.7357 (mmm) cc_final: 0.6816 (tpp) REVERT: K 54 ASP cc_start: 0.7273 (t0) cc_final: 0.6908 (t0) REVERT: Z 47 MET cc_start: 0.7210 (mmt) cc_final: 0.6904 (mtm) REVERT: i 31 HIS cc_start: 0.7045 (OUTLIER) cc_final: 0.6394 (p-80) REVERT: j 16 ASP cc_start: 0.7644 (m-30) cc_final: 0.7423 (m-30) REVERT: j 19 MET cc_start: 0.7162 (tmm) cc_final: 0.6845 (tmm) REVERT: G 107 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6890 (mm-30) REVERT: G 136 GLU cc_start: 0.7341 (tp30) cc_final: 0.7102 (tp30) REVERT: G 259 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7890 (t0) REVERT: C 119 MET cc_start: 0.8444 (tpp) cc_final: 0.8167 (tmm) REVERT: C 163 LEU cc_start: 0.8965 (mt) cc_final: 0.8757 (mm) REVERT: C 164 MET cc_start: 0.6969 (tmm) cc_final: 0.6593 (tmm) REVERT: C 284 ASN cc_start: 0.8763 (t160) cc_final: 0.8476 (t0) REVERT: T 86 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8376 (tm-30) REVERT: T 197 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8210 (tp) REVERT: U 35 PRO cc_start: 0.8289 (Cg_endo) cc_final: 0.7951 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8263 (p90) cc_final: 0.7783 (p90) REVERT: E 164 TYR cc_start: 0.9144 (t80) cc_final: 0.8749 (t80) REVERT: E 169 TYR cc_start: 0.8721 (p90) cc_final: 0.8249 (p90) REVERT: D 54 LYS cc_start: 0.5153 (mmtt) cc_final: 0.4094 (mmtt) REVERT: D 95 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7775 (p0) REVERT: D 197 LYS cc_start: 0.5734 (OUTLIER) cc_final: 0.5192 (mppt) REVERT: X 95 GLN cc_start: 0.4783 (OUTLIER) cc_final: 0.3767 (mt0) REVERT: c 38 SER cc_start: 0.8968 (m) cc_final: 0.8402 (t) REVERT: c 86 MET cc_start: 0.7518 (mtp) cc_final: 0.7147 (mtm) REVERT: o 61 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8484 (pp) REVERT: o 123 TRP cc_start: 0.6460 (m100) cc_final: 0.6036 (m100) REVERT: o 212 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6872 (mt-10) REVERT: o 223 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8024 (mt) REVERT: p 20 GLN cc_start: 0.7944 (mt0) cc_final: 0.7614 (mt0) REVERT: p 24 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.5411 (ptt180) REVERT: p 51 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6609 (pttt) REVERT: M 51 TYR cc_start: 0.5622 (m-80) cc_final: 0.5404 (m-10) REVERT: M 80 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8859 (mm) REVERT: M 86 ILE cc_start: 0.7814 (pt) cc_final: 0.7360 (mt) REVERT: M 106 LEU cc_start: 0.9090 (tp) cc_final: 0.8809 (mt) REVERT: M 153 MET cc_start: 0.8424 (tpp) cc_final: 0.7872 (tpp) REVERT: M 261 THR cc_start: 0.8844 (p) cc_final: 0.8524 (p) REVERT: M 316 MET cc_start: 0.7348 (mmm) cc_final: 0.6879 (mmm) REVERT: M 367 TYR cc_start: 0.6208 (m-80) cc_final: 0.5924 (m-80) REVERT: M 389 MET cc_start: 0.8304 (ptm) cc_final: 0.8026 (ptm) REVERT: M 458 PHE cc_start: 0.7355 (t80) cc_final: 0.7100 (t80) REVERT: f 34 ARG cc_start: 0.8380 (ttp80) cc_final: 0.8121 (mtp85) REVERT: f 40 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: f 54 LYS cc_start: 0.6188 (mttt) cc_final: 0.5678 (tmtt) REVERT: f 79 ASP cc_start: 0.6226 (OUTLIER) cc_final: 0.5794 (m-30) REVERT: g 70 SER cc_start: 0.8060 (m) cc_final: 0.7757 (p) REVERT: g 72 LEU cc_start: 0.8028 (mt) cc_final: 0.7736 (mt) REVERT: a 137 PHE cc_start: 0.8285 (t80) cc_final: 0.7585 (t80) REVERT: a 147 SER cc_start: 0.8823 (t) cc_final: 0.8571 (t) REVERT: a 155 PHE cc_start: 0.4033 (OUTLIER) cc_final: 0.3559 (t80) REVERT: a 168 MET cc_start: 0.7525 (tpt) cc_final: 0.6968 (tpt) REVERT: a 278 TYR cc_start: 0.3203 (p90) cc_final: 0.2573 (p90) REVERT: h 35 MET cc_start: 0.4138 (ptt) cc_final: 0.3767 (ttp) REVERT: m 7 PHE cc_start: 0.6215 (p90) cc_final: 0.5660 (p90) REVERT: m 15 LEU cc_start: 0.6152 (pt) cc_final: 0.4930 (tp) REVERT: t 21 HIS cc_start: 0.3764 (OUTLIER) cc_final: 0.2360 (m170) outliers start: 377 outliers final: 232 residues processed: 1624 average time/residue: 0.5352 time to fit residues: 1487.3367 Evaluate side-chains 1538 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1286 time to evaluate : 4.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 91 ASN Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 297 CYS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 369 THR Chi-restraints excluded: chain I residue 373 TYR Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 466 SER Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain I residue 495 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 315 SER Chi-restraints excluded: chain H residue 317 LEU Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain Y residue 10 ASN Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain V residue 15 ILE Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 105 ASP Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain j residue 34 CYS Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 268 MET Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 686 ASN Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 145 ILE Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 256 VAL Chi-restraints excluded: chain T residue 369 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 141 ASN Chi-restraints excluded: chain U residue 148 THR Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain c residue 3 THR Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 44 SER Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 62 MET Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 61 LEU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 94 ASN Chi-restraints excluded: chain o residue 107 VAL Chi-restraints excluded: chain o residue 146 LEU Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 168 SER Chi-restraints excluded: chain o residue 223 LEU Chi-restraints excluded: chain o residue 238 TYR Chi-restraints excluded: chain q residue 17 GLU Chi-restraints excluded: chain q residue 23 ASP Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 88 ASP Chi-restraints excluded: chain q residue 92 VAL Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 134 LEU Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 138 THR Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 45 LEU Chi-restraints excluded: chain p residue 51 LYS Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 122 ILE Chi-restraints excluded: chain p residue 125 ASN Chi-restraints excluded: chain p residue 134 LEU Chi-restraints excluded: chain p residue 141 ASP Chi-restraints excluded: chain p residue 157 VAL Chi-restraints excluded: chain p residue 163 VAL Chi-restraints excluded: chain p residue 169 VAL Chi-restraints excluded: chain p residue 192 LEU Chi-restraints excluded: chain p residue 227 PHE Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 104 CYS Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 193 PHE Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 302 ILE Chi-restraints excluded: chain M residue 312 SER Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 76 GLN Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain g residue 92 TRP Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 22 PHE Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain a residue 155 PHE Chi-restraints excluded: chain a residue 176 PHE Chi-restraints excluded: chain a residue 185 CYS Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 333 VAL Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 493 TRP Chi-restraints excluded: chain a residue 563 TRP Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain t residue 21 HIS Chi-restraints excluded: chain t residue 24 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 573 optimal weight: 1.9990 chunk 391 optimal weight: 0.0470 chunk 10 optimal weight: 9.9990 chunk 513 optimal weight: 3.9990 chunk 284 optimal weight: 9.9990 chunk 588 optimal weight: 0.8980 chunk 476 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 351 optimal weight: 4.9990 chunk 618 optimal weight: 50.0000 chunk 173 optimal weight: 9.9990 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN I 53 ASN ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN K 45 ASN ** V 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 35 HIS G 91 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 174 HIS ** T 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 146 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN X 54 GLN ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 HIS ** q 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 76 GLN ** a 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.252 59313 Z= 0.566 Angle : 1.609 50.888 80348 Z= 1.025 Chirality : 0.301 6.377 8969 Planarity : 0.005 0.066 10136 Dihedral : 9.178 165.398 8448 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 24.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.58 % Favored : 91.38 % Rotamer: Outliers : 5.97 % Allowed : 23.83 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.10), residues: 7252 helix: -0.28 (0.08), residues: 3584 sheet: -2.45 (0.29), residues: 317 loop : -2.29 (0.10), residues: 3351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP M 236 HIS 0.014 0.001 HIS R 129 PHE 0.048 0.002 PHE M 142 TYR 0.032 0.002 TYR a 379 ARG 0.007 0.001 ARG R 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1740 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 1378 time to evaluate : 4.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 59 LEU cc_start: 0.8708 (tt) cc_final: 0.8398 (tt) REVERT: I 162 ILE cc_start: 0.9107 (pt) cc_final: 0.8817 (pt) REVERT: I 174 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6028 (tp30) REVERT: I 297 CYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7008 (t) REVERT: I 471 MET cc_start: 0.6912 (mtm) cc_final: 0.6443 (mtp) REVERT: J 111 TRP cc_start: 0.8145 (t60) cc_final: 0.7588 (t60) REVERT: J 112 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8222 (mmmt) REVERT: N 42 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8458 (mm) REVERT: N 123 ARG cc_start: 0.7429 (ptm160) cc_final: 0.7214 (ptm160) REVERT: N 148 TYR cc_start: 0.8578 (m-80) cc_final: 0.8083 (m-10) REVERT: H 41 ASP cc_start: 0.7943 (t0) cc_final: 0.7572 (t70) REVERT: H 62 GLU cc_start: 0.8040 (mp0) cc_final: 0.7742 (mp0) REVERT: H 95 ASP cc_start: 0.7457 (t0) cc_final: 0.7196 (t0) REVERT: H 126 TRP cc_start: 0.7825 (t60) cc_final: 0.7450 (t60) REVERT: H 290 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8448 (m-80) REVERT: K 5 LYS cc_start: 0.7725 (tttt) cc_final: 0.7333 (mmtt) REVERT: K 54 ASP cc_start: 0.7193 (t0) cc_final: 0.6817 (t0) REVERT: Z 47 MET cc_start: 0.7110 (mmt) cc_final: 0.6905 (mtm) REVERT: Z 79 TYR cc_start: 0.6119 (m-80) cc_final: 0.5642 (m-80) REVERT: i 31 HIS cc_start: 0.7183 (OUTLIER) cc_final: 0.6509 (p-80) REVERT: i 63 MET cc_start: 0.7553 (mtt) cc_final: 0.7190 (mpp) REVERT: j 16 ASP cc_start: 0.7693 (m-30) cc_final: 0.7408 (m-30) REVERT: j 19 MET cc_start: 0.7229 (tmm) cc_final: 0.6859 (tmm) REVERT: G 107 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6756 (mm-30) REVERT: C 164 MET cc_start: 0.6923 (tmm) cc_final: 0.6616 (tmm) REVERT: C 284 ASN cc_start: 0.8678 (t160) cc_final: 0.8477 (t0) REVERT: C 393 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7560 (mtm) REVERT: C 705 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6744 (pp20) REVERT: T 86 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8431 (tm-30) REVERT: F 78 LEU cc_start: 0.8637 (tt) cc_final: 0.8183 (tp) REVERT: F 84 SER cc_start: 0.8905 (p) cc_final: 0.8621 (t) REVERT: P 47 ASP cc_start: 0.7870 (m-30) cc_final: 0.7619 (m-30) REVERT: U 35 PRO cc_start: 0.8288 (Cg_endo) cc_final: 0.7978 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8225 (p90) cc_final: 0.7758 (p90) REVERT: E 107 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6741 (m-30) REVERT: E 123 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6820 (m-30) REVERT: E 164 TYR cc_start: 0.9141 (t80) cc_final: 0.8688 (t80) REVERT: E 169 TYR cc_start: 0.8749 (p90) cc_final: 0.8384 (p90) REVERT: D 54 LYS cc_start: 0.5125 (mmtt) cc_final: 0.3843 (mmtt) REVERT: D 95 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7762 (p0) REVERT: D 195 TYR cc_start: 0.8572 (m-10) cc_final: 0.8046 (m-80) REVERT: D 197 LYS cc_start: 0.5998 (OUTLIER) cc_final: 0.5426 (mppt) REVERT: X 95 GLN cc_start: 0.5054 (OUTLIER) cc_final: 0.4429 (mt0) REVERT: c 38 SER cc_start: 0.9005 (m) cc_final: 0.8425 (t) REVERT: o 61 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8537 (pp) REVERT: o 180 SER cc_start: 0.7534 (m) cc_final: 0.7229 (p) REVERT: o 212 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6982 (mt-10) REVERT: p 24 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.5469 (ptt90) REVERT: p 50 ASP cc_start: 0.5304 (m-30) cc_final: 0.4970 (m-30) REVERT: p 153 ASP cc_start: 0.5165 (OUTLIER) cc_final: 0.4962 (m-30) REVERT: M 51 TYR cc_start: 0.5567 (m-80) cc_final: 0.5340 (m-10) REVERT: M 65 LYS cc_start: 0.5992 (ptmt) cc_final: 0.5515 (pttp) REVERT: M 86 ILE cc_start: 0.7770 (pt) cc_final: 0.7295 (mt) REVERT: M 106 LEU cc_start: 0.9012 (tp) cc_final: 0.8754 (mt) REVERT: M 142 PHE cc_start: 0.8646 (t80) cc_final: 0.8244 (t80) REVERT: M 153 MET cc_start: 0.8288 (tpp) cc_final: 0.7936 (tpp) REVERT: M 261 THR cc_start: 0.8804 (p) cc_final: 0.8481 (p) REVERT: M 316 MET cc_start: 0.7363 (mmm) cc_final: 0.6903 (mmm) REVERT: M 367 TYR cc_start: 0.6316 (m-80) cc_final: 0.6103 (m-80) REVERT: M 458 PHE cc_start: 0.7157 (t80) cc_final: 0.6916 (t80) REVERT: f 34 ARG cc_start: 0.8325 (ttp80) cc_final: 0.8123 (mtp85) REVERT: f 40 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6346 (mp0) REVERT: f 54 LYS cc_start: 0.6088 (mttt) cc_final: 0.5608 (tmtt) REVERT: g 70 SER cc_start: 0.8030 (m) cc_final: 0.7759 (p) REVERT: g 72 LEU cc_start: 0.8186 (mt) cc_final: 0.7867 (mt) REVERT: a 137 PHE cc_start: 0.8252 (t80) cc_final: 0.7546 (t80) REVERT: a 147 SER cc_start: 0.8804 (t) cc_final: 0.8515 (t) REVERT: a 155 PHE cc_start: 0.3842 (OUTLIER) cc_final: 0.3360 (t80) REVERT: a 186 PHE cc_start: 0.5805 (OUTLIER) cc_final: 0.4378 (t80) REVERT: a 406 GLU cc_start: 0.4581 (mm-30) cc_final: 0.4159 (mm-30) REVERT: h 35 MET cc_start: 0.4046 (ptt) cc_final: 0.3618 (ttp) REVERT: m 7 PHE cc_start: 0.6094 (p90) cc_final: 0.5546 (p90) REVERT: m 15 LEU cc_start: 0.6140 (pt) cc_final: 0.5061 (tp) REVERT: t 21 HIS cc_start: 0.4273 (OUTLIER) cc_final: 0.2712 (m-70) outliers start: 362 outliers final: 243 residues processed: 1595 average time/residue: 0.5357 time to fit residues: 1462.0785 Evaluate side-chains 1533 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1273 time to evaluate : 4.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 267 ILE Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 297 CYS Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 369 THR Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 466 SER Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 317 LEU Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain Y residue 10 ASN Chi-restraints excluded: chain Y residue 15 SER Chi-restraints excluded: chain Y residue 19 THR Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 91 LEU Chi-restraints excluded: chain Y residue 99 PHE Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 89 LEU Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain V residue 15 ILE Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain j residue 7 ILE Chi-restraints excluded: chain j residue 28 CYS Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 268 MET Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 686 ASN Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 145 ILE Chi-restraints excluded: chain T residue 174 HIS Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 256 VAL Chi-restraints excluded: chain T residue 369 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 101 THR Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 141 ASN Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain c residue 3 THR Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 44 SER Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 62 MET Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain k residue 53 VAL Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 61 LEU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 107 VAL Chi-restraints excluded: chain o residue 144 TYR Chi-restraints excluded: chain o residue 146 LEU Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 168 SER Chi-restraints excluded: chain o residue 238 TYR Chi-restraints excluded: chain q residue 17 GLU Chi-restraints excluded: chain q residue 23 ASP Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 88 ASP Chi-restraints excluded: chain q residue 92 VAL Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 128 ILE Chi-restraints excluded: chain q residue 134 LEU Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 138 THR Chi-restraints excluded: chain q residue 229 LYS Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 51 LYS Chi-restraints excluded: chain p residue 122 ILE Chi-restraints excluded: chain p residue 134 LEU Chi-restraints excluded: chain p residue 141 ASP Chi-restraints excluded: chain p residue 153 ASP Chi-restraints excluded: chain p residue 157 VAL Chi-restraints excluded: chain p residue 169 VAL Chi-restraints excluded: chain p residue 192 LEU Chi-restraints excluded: chain p residue 227 PHE Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 193 PHE Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 302 ILE Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 312 SER Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 22 PHE Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 97 HIS Chi-restraints excluded: chain a residue 100 SER Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain a residue 155 PHE Chi-restraints excluded: chain a residue 176 PHE Chi-restraints excluded: chain a residue 186 PHE Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 333 VAL Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 493 TRP Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain m residue 57 GLU Chi-restraints excluded: chain t residue 21 HIS Chi-restraints excluded: chain t residue 24 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 231 optimal weight: 5.9990 chunk 620 optimal weight: 30.0000 chunk 136 optimal weight: 0.8980 chunk 404 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 689 optimal weight: 20.0000 chunk 572 optimal weight: 0.5980 chunk 319 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 chunk 362 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 ASN ** V 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 174 HIS ** T 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 GLN U 141 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 18 ASN ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 57 GLN ** o 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 120 HIS ** q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 HIS ** q 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 184 ASN ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.252 59313 Z= 0.550 Angle : 1.605 50.776 80348 Z= 1.022 Chirality : 0.301 6.366 8969 Planarity : 0.005 0.065 10136 Dihedral : 8.963 162.668 8448 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 24.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.16 % Favored : 91.80 % Rotamer: Outliers : 5.13 % Allowed : 25.58 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.10), residues: 7252 helix: -0.20 (0.09), residues: 3589 sheet: -2.16 (0.30), residues: 299 loop : -2.26 (0.10), residues: 3364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP M 236 HIS 0.008 0.001 HIS T 291 PHE 0.042 0.002 PHE K 61 TYR 0.033 0.002 TYR a 379 ARG 0.010 0.001 ARG c 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1693 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1382 time to evaluate : 4.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 162 ILE cc_start: 0.9157 (pt) cc_final: 0.8831 (pt) REVERT: I 232 PHE cc_start: 0.8579 (m-10) cc_final: 0.8364 (m-10) REVERT: I 471 MET cc_start: 0.6810 (mtm) cc_final: 0.6371 (mtp) REVERT: J 111 TRP cc_start: 0.8090 (t60) cc_final: 0.7597 (t60) REVERT: N 42 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8354 (mm) REVERT: N 148 TYR cc_start: 0.8585 (m-80) cc_final: 0.8105 (m-10) REVERT: H 41 ASP cc_start: 0.7944 (t0) cc_final: 0.7550 (t70) REVERT: H 62 GLU cc_start: 0.8146 (mp0) cc_final: 0.7808 (mp0) REVERT: H 126 TRP cc_start: 0.7802 (t60) cc_final: 0.7373 (t60) REVERT: H 290 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: K 5 LYS cc_start: 0.7718 (tttt) cc_final: 0.7251 (mmtt) REVERT: K 31 MET cc_start: 0.7382 (mmm) cc_final: 0.7140 (tpt) REVERT: K 56 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6806 (ttt) REVERT: S 63 ASP cc_start: 0.8034 (p0) cc_final: 0.7489 (p0) REVERT: S 97 MET cc_start: 0.6886 (mtp) cc_final: 0.6606 (ttm) REVERT: i 31 HIS cc_start: 0.7103 (OUTLIER) cc_final: 0.6237 (p-80) REVERT: i 63 MET cc_start: 0.7626 (mtt) cc_final: 0.7404 (mtt) REVERT: j 19 MET cc_start: 0.7160 (tmm) cc_final: 0.6778 (tmm) REVERT: G 94 VAL cc_start: 0.9101 (m) cc_final: 0.8774 (m) REVERT: G 107 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6653 (mm-30) REVERT: G 136 GLU cc_start: 0.7175 (tp30) cc_final: 0.6820 (tp30) REVERT: G 302 MET cc_start: 0.8341 (ppp) cc_final: 0.8131 (ppp) REVERT: G 355 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8213 (pp) REVERT: C 164 MET cc_start: 0.6845 (tmm) cc_final: 0.6549 (tmm) REVERT: C 393 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7436 (mtm) REVERT: C 421 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6411 (mm) REVERT: C 453 MET cc_start: 0.7645 (mmm) cc_final: 0.7438 (mmm) REVERT: C 705 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6739 (pp20) REVERT: T 86 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8529 (tm-30) REVERT: T 369 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7091 (mtpp) REVERT: F 78 LEU cc_start: 0.8653 (tt) cc_final: 0.8222 (tp) REVERT: F 84 SER cc_start: 0.8876 (p) cc_final: 0.8595 (t) REVERT: O 65 GLN cc_start: 0.7949 (pt0) cc_final: 0.7553 (pt0) REVERT: O 80 SER cc_start: 0.8923 (OUTLIER) cc_final: 0.8698 (p) REVERT: U 35 PRO cc_start: 0.8158 (Cg_endo) cc_final: 0.7848 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8231 (p90) cc_final: 0.7834 (p90) REVERT: E 107 ASP cc_start: 0.6927 (OUTLIER) cc_final: 0.6586 (m-30) REVERT: E 123 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6787 (m-30) REVERT: E 164 TYR cc_start: 0.9114 (t80) cc_final: 0.8793 (t80) REVERT: E 169 TYR cc_start: 0.8685 (p90) cc_final: 0.8475 (p90) REVERT: D 54 LYS cc_start: 0.5154 (mmtt) cc_final: 0.3847 (mmtt) REVERT: D 95 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7712 (p0) REVERT: D 195 TYR cc_start: 0.8500 (m-10) cc_final: 0.7968 (m-10) REVERT: D 197 LYS cc_start: 0.5744 (OUTLIER) cc_final: 0.5285 (mppt) REVERT: X 56 ARG cc_start: 0.6281 (ptp-170) cc_final: 0.6029 (ptp-170) REVERT: X 95 GLN cc_start: 0.4934 (OUTLIER) cc_final: 0.4439 (mt0) REVERT: c 38 SER cc_start: 0.8999 (m) cc_final: 0.8390 (t) REVERT: Q 66 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6381 (tmm) REVERT: o 61 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8553 (pp) REVERT: o 160 GLN cc_start: 0.7502 (mm110) cc_final: 0.7241 (mm-40) REVERT: o 212 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6991 (mt-10) REVERT: q 38 GLN cc_start: 0.5877 (mt0) cc_final: 0.5661 (mt0) REVERT: p 20 GLN cc_start: 0.7893 (mt0) cc_final: 0.7619 (mt0) REVERT: p 23 ASP cc_start: 0.4467 (t0) cc_final: 0.4011 (t0) REVERT: p 24 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.5197 (ptt90) REVERT: p 50 ASP cc_start: 0.5323 (m-30) cc_final: 0.4976 (m-30) REVERT: M 33 ARG cc_start: 0.5337 (OUTLIER) cc_final: 0.5068 (ppt170) REVERT: M 65 LYS cc_start: 0.6140 (ptmt) cc_final: 0.5786 (pttp) REVERT: M 86 ILE cc_start: 0.7710 (pt) cc_final: 0.7369 (mm) REVERT: M 261 THR cc_start: 0.8804 (p) cc_final: 0.8452 (p) REVERT: M 316 MET cc_start: 0.7337 (mmm) cc_final: 0.6950 (mmm) REVERT: M 367 TYR cc_start: 0.6219 (m-80) cc_final: 0.5877 (m-80) REVERT: f 34 ARG cc_start: 0.8306 (ttp80) cc_final: 0.8070 (mtp85) REVERT: f 36 HIS cc_start: 0.4891 (OUTLIER) cc_final: 0.4491 (t70) REVERT: f 54 LYS cc_start: 0.5905 (mttt) cc_final: 0.5428 (tmtt) REVERT: g 70 SER cc_start: 0.7909 (m) cc_final: 0.7670 (p) REVERT: g 72 LEU cc_start: 0.8039 (mt) cc_final: 0.7759 (mt) REVERT: a 104 MET cc_start: 0.7153 (mmp) cc_final: 0.6849 (mmp) REVERT: a 126 MET cc_start: 0.8013 (ttp) cc_final: 0.6845 (tmm) REVERT: a 137 PHE cc_start: 0.8099 (t80) cc_final: 0.7554 (t80) REVERT: a 152 HIS cc_start: 0.6832 (p90) cc_final: 0.6583 (p90) REVERT: a 155 PHE cc_start: 0.3818 (OUTLIER) cc_final: 0.3591 (t80) REVERT: a 168 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7159 (tpt) REVERT: a 186 PHE cc_start: 0.5750 (OUTLIER) cc_final: 0.5500 (m-10) REVERT: a 406 GLU cc_start: 0.4605 (mm-30) cc_final: 0.4245 (mm-30) REVERT: h 35 MET cc_start: 0.4104 (ptt) cc_final: 0.3699 (ttp) REVERT: m 15 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5034 (tp) REVERT: m 54 TRP cc_start: 0.5307 (p-90) cc_final: 0.5061 (p-90) REVERT: t 21 HIS cc_start: 0.4304 (OUTLIER) cc_final: 0.2882 (m-70) outliers start: 311 outliers final: 220 residues processed: 1548 average time/residue: 0.5349 time to fit residues: 1415.2894 Evaluate side-chains 1524 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1280 time to evaluate : 4.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 267 ILE Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 369 THR Chi-restraints excluded: chain I residue 373 TYR Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 466 SER Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 236 MET Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 317 LEU Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 56 MET Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain Y residue 10 ASN Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 91 LEU Chi-restraints excluded: chain Y residue 99 PHE Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain V residue 15 ILE Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 41 LEU Chi-restraints excluded: chain j residue 34 CYS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain G residue 355 ILE Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 145 ILE Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 369 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain P residue 108 HIS Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 50 ASP Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 139 THR Chi-restraints excluded: chain U residue 141 ASN Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain X residue 18 ASN Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 44 SER Chi-restraints excluded: chain c residue 62 MET Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain Q residue 13 GLU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 57 GLN Chi-restraints excluded: chain o residue 61 LEU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 107 VAL Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 168 SER Chi-restraints excluded: chain o residue 238 TYR Chi-restraints excluded: chain q residue 17 GLU Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 88 ASP Chi-restraints excluded: chain q residue 92 VAL Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 138 THR Chi-restraints excluded: chain q residue 229 LYS Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 122 ILE Chi-restraints excluded: chain p residue 141 ASP Chi-restraints excluded: chain p residue 157 VAL Chi-restraints excluded: chain p residue 169 VAL Chi-restraints excluded: chain p residue 192 LEU Chi-restraints excluded: chain p residue 227 PHE Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain M residue 185 LEU Chi-restraints excluded: chain M residue 193 PHE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 302 ILE Chi-restraints excluded: chain M residue 312 SER Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 357 ASP Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 36 HIS Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 22 PHE Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 97 HIS Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain a residue 155 PHE Chi-restraints excluded: chain a residue 168 MET Chi-restraints excluded: chain a residue 176 PHE Chi-restraints excluded: chain a residue 186 PHE Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 333 VAL Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 493 TRP Chi-restraints excluded: chain a residue 563 TRP Chi-restraints excluded: chain a residue 566 ASP Chi-restraints excluded: chain m residue 15 LEU Chi-restraints excluded: chain m residue 32 GLU Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain m residue 57 GLU Chi-restraints excluded: chain t residue 21 HIS Chi-restraints excluded: chain t residue 24 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 665 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 393 optimal weight: 0.9980 chunk 503 optimal weight: 9.9990 chunk 390 optimal weight: 8.9990 chunk 580 optimal weight: 0.9990 chunk 385 optimal weight: 6.9990 chunk 687 optimal weight: 10.0000 chunk 430 optimal weight: 1.9990 chunk 418 optimal weight: 4.9990 chunk 317 optimal weight: 0.0670 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN A 436 GLN ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 491 HIS K 45 ASN K 59 GLN ** V 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 141 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 18 ASN ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 HIS ** q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 94 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.253 59313 Z= 0.557 Angle : 1.612 50.821 80348 Z= 1.025 Chirality : 0.301 6.360 8969 Planarity : 0.005 0.085 10136 Dihedral : 8.819 161.636 8447 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 24.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.62 % Favored : 91.34 % Rotamer: Outliers : 5.52 % Allowed : 26.29 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.10), residues: 7252 helix: -0.14 (0.09), residues: 3589 sheet: -2.05 (0.30), residues: 300 loop : -2.21 (0.10), residues: 3363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP M 236 HIS 0.009 0.001 HIS j 27 PHE 0.060 0.002 PHE K 61 TYR 0.026 0.002 TYR M 119 ARG 0.012 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1655 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 1320 time to evaluate : 4.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 35 HIS cc_start: 0.7855 (OUTLIER) cc_final: 0.7581 (t-90) REVERT: I 162 ILE cc_start: 0.9147 (pt) cc_final: 0.8822 (pt) REVERT: I 174 GLU cc_start: 0.6881 (tm-30) cc_final: 0.6029 (tp30) REVERT: I 461 MET cc_start: 0.7684 (ppp) cc_final: 0.7342 (ppp) REVERT: I 471 MET cc_start: 0.6835 (mtm) cc_final: 0.6383 (mtp) REVERT: J 111 TRP cc_start: 0.8052 (t60) cc_final: 0.7559 (t60) REVERT: N 28 LEU cc_start: 0.8281 (tp) cc_final: 0.7497 (mt) REVERT: N 42 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8328 (mm) REVERT: N 148 TYR cc_start: 0.8598 (m-80) cc_final: 0.7791 (m-10) REVERT: H 20 VAL cc_start: 0.7689 (OUTLIER) cc_final: 0.7482 (p) REVERT: H 41 ASP cc_start: 0.7975 (t0) cc_final: 0.7545 (t70) REVERT: H 62 GLU cc_start: 0.8202 (mp0) cc_final: 0.7879 (mp0) REVERT: H 95 ASP cc_start: 0.7283 (t0) cc_final: 0.6987 (t0) REVERT: H 126 TRP cc_start: 0.7824 (t60) cc_final: 0.7388 (t60) REVERT: H 228 PHE cc_start: 0.6600 (t80) cc_final: 0.6296 (t80) REVERT: H 290 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.8415 (m-80) REVERT: K 5 LYS cc_start: 0.7664 (tttt) cc_final: 0.7230 (mmtt) REVERT: K 33 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7108 (mmm) REVERT: K 34 SER cc_start: 0.7872 (OUTLIER) cc_final: 0.7636 (p) REVERT: Z 84 THR cc_start: 0.8441 (t) cc_final: 0.8100 (t) REVERT: Z 113 LYS cc_start: 0.7235 (mptt) cc_final: 0.6555 (mttt) REVERT: S 63 ASP cc_start: 0.8147 (p0) cc_final: 0.7632 (p0) REVERT: S 97 MET cc_start: 0.6759 (mtp) cc_final: 0.6427 (ttm) REVERT: i 31 HIS cc_start: 0.7157 (OUTLIER) cc_final: 0.6241 (p-80) REVERT: i 63 MET cc_start: 0.7616 (mtt) cc_final: 0.7367 (mtt) REVERT: j 19 MET cc_start: 0.7110 (tmm) cc_final: 0.6679 (tmm) REVERT: G 107 GLU cc_start: 0.6800 (mm-30) cc_final: 0.6527 (mm-30) REVERT: G 136 GLU cc_start: 0.7195 (tp30) cc_final: 0.6790 (tp30) REVERT: G 294 LEU cc_start: 0.8893 (tp) cc_final: 0.8375 (tt) REVERT: G 355 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8218 (pp) REVERT: C 164 MET cc_start: 0.7211 (tmm) cc_final: 0.6691 (tmm) REVERT: C 393 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7455 (mtm) REVERT: C 453 MET cc_start: 0.7732 (mmm) cc_final: 0.7518 (mmm) REVERT: T 86 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8446 (tm-30) REVERT: T 369 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7144 (mtpp) REVERT: F 37 TYR cc_start: 0.6715 (m-80) cc_final: 0.6074 (m-80) REVERT: F 78 LEU cc_start: 0.8660 (tt) cc_final: 0.8244 (tp) REVERT: F 84 SER cc_start: 0.8917 (p) cc_final: 0.8616 (t) REVERT: O 65 GLN cc_start: 0.7961 (pt0) cc_final: 0.7549 (pt0) REVERT: U 35 PRO cc_start: 0.8182 (Cg_endo) cc_final: 0.7878 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8214 (p90) cc_final: 0.7840 (p90) REVERT: E 107 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6637 (m-30) REVERT: E 164 TYR cc_start: 0.9131 (t80) cc_final: 0.8804 (t80) REVERT: D 54 LYS cc_start: 0.5210 (mmtt) cc_final: 0.4057 (mmtt) REVERT: D 95 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7714 (p0) REVERT: D 195 TYR cc_start: 0.8523 (m-10) cc_final: 0.7984 (m-10) REVERT: D 197 LYS cc_start: 0.5994 (OUTLIER) cc_final: 0.5492 (mtpt) REVERT: X 56 ARG cc_start: 0.6175 (ptp-170) cc_final: 0.5939 (ptp-170) REVERT: X 95 GLN cc_start: 0.5089 (OUTLIER) cc_final: 0.4616 (mt0) REVERT: Q 66 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6398 (tmm) REVERT: o 61 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8421 (pp) REVERT: o 91 SER cc_start: 0.6177 (t) cc_final: 0.5934 (t) REVERT: o 160 GLN cc_start: 0.7577 (mm110) cc_final: 0.7278 (mm-40) REVERT: q 153 ASP cc_start: 0.4874 (OUTLIER) cc_final: 0.3539 (p0) REVERT: p 20 GLN cc_start: 0.7925 (mt0) cc_final: 0.7645 (mt0) REVERT: p 23 ASP cc_start: 0.4583 (t0) cc_final: 0.4317 (t0) REVERT: p 24 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.5459 (ptm-80) REVERT: p 220 LYS cc_start: 0.6101 (mtpt) cc_final: 0.5846 (mtpt) REVERT: M 33 ARG cc_start: 0.5314 (OUTLIER) cc_final: 0.5062 (ppt170) REVERT: M 65 LYS cc_start: 0.6317 (ptmt) cc_final: 0.5936 (pttp) REVERT: M 86 ILE cc_start: 0.7665 (pt) cc_final: 0.7138 (mt) REVERT: M 236 TRP cc_start: 0.7167 (p-90) cc_final: 0.5799 (t60) REVERT: M 261 THR cc_start: 0.8786 (p) cc_final: 0.8523 (p) REVERT: M 316 MET cc_start: 0.7280 (mmm) cc_final: 0.6864 (mmm) REVERT: M 323 MET cc_start: 0.6777 (ttp) cc_final: 0.6181 (tmm) REVERT: M 354 VAL cc_start: 0.7345 (t) cc_final: 0.6981 (t) REVERT: f 34 ARG cc_start: 0.8331 (ttp80) cc_final: 0.8058 (mtp85) REVERT: f 36 HIS cc_start: 0.4984 (OUTLIER) cc_final: 0.4589 (t70) REVERT: f 54 LYS cc_start: 0.5834 (mttt) cc_final: 0.5303 (tmtt) REVERT: g 67 TYR cc_start: 0.3852 (p90) cc_final: 0.3645 (p90) REVERT: g 72 LEU cc_start: 0.8050 (mt) cc_final: 0.7807 (mt) REVERT: g 99 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7788 (mm-30) REVERT: a 137 PHE cc_start: 0.8184 (t80) cc_final: 0.7429 (t80) REVERT: a 186 PHE cc_start: 0.5847 (OUTLIER) cc_final: 0.4466 (t80) REVERT: a 406 GLU cc_start: 0.4415 (mm-30) cc_final: 0.4113 (mm-30) REVERT: a 635 PHE cc_start: 0.4743 (m-80) cc_final: 0.4431 (m-10) REVERT: m 15 LEU cc_start: 0.5966 (pt) cc_final: 0.5025 (tp) REVERT: m 54 TRP cc_start: 0.5105 (p-90) cc_final: 0.4849 (p-90) REVERT: t 21 HIS cc_start: 0.4497 (OUTLIER) cc_final: 0.3130 (m-70) outliers start: 335 outliers final: 238 residues processed: 1518 average time/residue: 0.5388 time to fit residues: 1397.9421 Evaluate side-chains 1503 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1243 time to evaluate : 5.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 310 MET Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 369 THR Chi-restraints excluded: chain I residue 373 TYR Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 466 SER Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 236 MET Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 317 LEU Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 61 PHE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain Y residue 10 ASN Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Y residue 91 LEU Chi-restraints excluded: chain Y residue 99 PHE Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain V residue 15 ILE Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 105 ASP Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain G residue 355 ILE Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 145 ILE Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 307 TYR Chi-restraints excluded: chain T residue 369 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain P residue 108 HIS Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 50 ASP Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 101 THR Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 139 THR Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 44 SER Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain k residue 53 VAL Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 61 LEU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 107 VAL Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 168 SER Chi-restraints excluded: chain o residue 238 TYR Chi-restraints excluded: chain q residue 17 GLU Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 88 ASP Chi-restraints excluded: chain q residue 92 VAL Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 105 LEU Chi-restraints excluded: chain q residue 107 HIS Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 134 LEU Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 138 THR Chi-restraints excluded: chain q residue 153 ASP Chi-restraints excluded: chain q residue 210 LEU Chi-restraints excluded: chain q residue 229 LYS Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 45 LEU Chi-restraints excluded: chain p residue 122 ILE Chi-restraints excluded: chain p residue 141 ASP Chi-restraints excluded: chain p residue 157 VAL Chi-restraints excluded: chain p residue 169 VAL Chi-restraints excluded: chain p residue 227 PHE Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 138 ASP Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 193 PHE Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 302 ILE Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 36 HIS Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain f residue 75 GLN Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 92 TRP Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 22 PHE Chi-restraints excluded: chain a residue 35 CYS Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain a residue 176 PHE Chi-restraints excluded: chain a residue 186 PHE Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 296 LEU Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 333 VAL Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 563 TRP Chi-restraints excluded: chain a residue 566 ASP Chi-restraints excluded: chain m residue 32 GLU Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain m residue 57 GLU Chi-restraints excluded: chain t residue 21 HIS Chi-restraints excluded: chain t residue 24 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 425 optimal weight: 6.9990 chunk 274 optimal weight: 9.9990 chunk 410 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 436 optimal weight: 3.9990 chunk 468 optimal weight: 8.9990 chunk 339 optimal weight: 9.9990 chunk 64 optimal weight: 0.4980 chunk 540 optimal weight: 1.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN I 53 ASN ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 ASN ** V 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 21 ASN G 91 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 18 ASN ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 57 GLN ** o 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 HIS ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 453 ASN a 257 HIS ** a 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.251 59313 Z= 0.593 Angle : 1.632 51.020 80348 Z= 1.034 Chirality : 0.301 6.390 8969 Planarity : 0.005 0.070 10136 Dihedral : 8.805 166.194 8446 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 25.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.03 % Favored : 90.93 % Rotamer: Outliers : 5.60 % Allowed : 26.83 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.10), residues: 7252 helix: -0.18 (0.08), residues: 3606 sheet: -2.03 (0.30), residues: 303 loop : -2.22 (0.10), residues: 3343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP M 236 HIS 0.044 0.002 HIS g 94 PHE 0.060 0.002 PHE M 142 TYR 0.055 0.002 TYR H 147 ARG 0.011 0.001 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1616 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 1276 time to evaluate : 4.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6934 (mpp) cc_final: 0.6630 (mpp) REVERT: I 35 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7865 (t-90) REVERT: I 50 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8472 (mm) REVERT: I 162 ILE cc_start: 0.9179 (pt) cc_final: 0.8858 (pt) REVERT: I 174 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6149 (tp30) REVERT: I 302 MET cc_start: 0.7503 (mpp) cc_final: 0.7277 (mpp) REVERT: I 471 MET cc_start: 0.6906 (mtm) cc_final: 0.6493 (mtp) REVERT: J 111 TRP cc_start: 0.8160 (t60) cc_final: 0.7623 (t60) REVERT: N 42 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8448 (mm) REVERT: N 148 TYR cc_start: 0.8657 (m-80) cc_final: 0.8151 (m-10) REVERT: H 20 VAL cc_start: 0.7978 (p) cc_final: 0.7749 (p) REVERT: H 41 ASP cc_start: 0.8001 (t0) cc_final: 0.7625 (t70) REVERT: H 95 ASP cc_start: 0.7484 (t0) cc_final: 0.7161 (t0) REVERT: H 290 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.8461 (m-80) REVERT: K 5 LYS cc_start: 0.7743 (tttt) cc_final: 0.7270 (mmtt) REVERT: K 33 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7615 (mmm) REVERT: K 56 MET cc_start: 0.7379 (tpp) cc_final: 0.6947 (ttt) REVERT: Z 84 THR cc_start: 0.8529 (t) cc_final: 0.8109 (t) REVERT: Z 112 MET cc_start: 0.6380 (mmp) cc_final: 0.6025 (mmp) REVERT: Z 113 LYS cc_start: 0.7246 (mptt) cc_final: 0.6595 (mttt) REVERT: S 97 MET cc_start: 0.6919 (mtp) cc_final: 0.6535 (ttm) REVERT: i 31 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.6638 (p-80) REVERT: i 63 MET cc_start: 0.7649 (mtt) cc_final: 0.7431 (mtt) REVERT: j 19 MET cc_start: 0.7022 (tmm) cc_final: 0.6622 (tmm) REVERT: j 41 TYR cc_start: 0.8127 (t80) cc_final: 0.7915 (t80) REVERT: G 107 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6612 (mm-30) REVERT: G 294 LEU cc_start: 0.8988 (tp) cc_final: 0.8524 (tt) REVERT: G 355 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8315 (pp) REVERT: C 164 MET cc_start: 0.7206 (tmm) cc_final: 0.6836 (tmm) REVERT: C 393 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7474 (mtm) REVERT: C 427 MET cc_start: 0.7412 (mtp) cc_final: 0.6809 (mtp) REVERT: C 453 MET cc_start: 0.7814 (mmm) cc_final: 0.7542 (mmm) REVERT: T 86 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8525 (tm-30) REVERT: T 307 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.6190 (m-80) REVERT: T 369 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7180 (mtpp) REVERT: F 84 SER cc_start: 0.8999 (p) cc_final: 0.8736 (t) REVERT: O 65 GLN cc_start: 0.8127 (pt0) cc_final: 0.7687 (pt0) REVERT: U 35 PRO cc_start: 0.8264 (Cg_endo) cc_final: 0.7931 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8261 (p90) cc_final: 0.7898 (p90) REVERT: U 82 ASP cc_start: 0.7187 (t0) cc_final: 0.6827 (t0) REVERT: U 129 ASP cc_start: 0.7386 (m-30) cc_final: 0.7043 (m-30) REVERT: E 107 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6815 (m-30) REVERT: E 123 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6805 (m-30) REVERT: E 164 TYR cc_start: 0.9220 (t80) cc_final: 0.8888 (t80) REVERT: D 54 LYS cc_start: 0.5043 (mmtt) cc_final: 0.3684 (mmtt) REVERT: D 95 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.7794 (p0) REVERT: D 195 TYR cc_start: 0.8578 (m-10) cc_final: 0.8036 (m-10) REVERT: D 197 LYS cc_start: 0.6227 (OUTLIER) cc_final: 0.5635 (mtpt) REVERT: X 95 GLN cc_start: 0.5222 (OUTLIER) cc_final: 0.4833 (tt0) REVERT: X 132 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.6791 (m-80) REVERT: o 160 GLN cc_start: 0.7788 (mm110) cc_final: 0.7475 (mm-40) REVERT: o 212 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6985 (mt-10) REVERT: q 14 TRP cc_start: 0.5753 (OUTLIER) cc_final: 0.5027 (t60) REVERT: q 153 ASP cc_start: 0.5347 (OUTLIER) cc_final: 0.3655 (p0) REVERT: p 23 ASP cc_start: 0.4510 (t0) cc_final: 0.4188 (t0) REVERT: p 24 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.5284 (ptt180) REVERT: p 50 ASP cc_start: 0.5981 (m-30) cc_final: 0.5749 (m-30) REVERT: p 144 PHE cc_start: 0.5870 (t80) cc_final: 0.5624 (t80) REVERT: M 33 ARG cc_start: 0.5212 (OUTLIER) cc_final: 0.4952 (ppt170) REVERT: M 65 LYS cc_start: 0.6312 (ptmt) cc_final: 0.5939 (pttp) REVERT: M 86 ILE cc_start: 0.7616 (pt) cc_final: 0.7196 (mt) REVERT: M 236 TRP cc_start: 0.7232 (p-90) cc_final: 0.5596 (t60) REVERT: M 237 LEU cc_start: 0.8191 (mt) cc_final: 0.7723 (mp) REVERT: M 261 THR cc_start: 0.8729 (p) cc_final: 0.8447 (p) REVERT: M 316 MET cc_start: 0.7401 (mmm) cc_final: 0.6936 (mmm) REVERT: f 34 ARG cc_start: 0.8426 (ttp80) cc_final: 0.8167 (mtp85) REVERT: f 36 HIS cc_start: 0.4823 (OUTLIER) cc_final: 0.4342 (t70) REVERT: f 54 LYS cc_start: 0.5978 (mttt) cc_final: 0.5367 (tmtt) REVERT: g 72 LEU cc_start: 0.7974 (mt) cc_final: 0.7756 (mt) REVERT: a 31 MET cc_start: 0.1797 (ttp) cc_final: 0.1585 (ttp) REVERT: a 126 MET cc_start: 0.8035 (ttp) cc_final: 0.7512 (tmm) REVERT: a 137 PHE cc_start: 0.8029 (t80) cc_final: 0.7415 (t80) REVERT: a 172 ARG cc_start: 0.7186 (mmm160) cc_final: 0.6946 (mmm160) REVERT: a 186 PHE cc_start: 0.5880 (OUTLIER) cc_final: 0.4276 (t80) REVERT: a 349 PHE cc_start: 0.6135 (OUTLIER) cc_final: 0.4664 (m-80) REVERT: a 359 MET cc_start: 0.4191 (ttp) cc_final: 0.3887 (ptm) REVERT: a 368 MET cc_start: 0.6129 (mpp) cc_final: 0.4443 (tpt) REVERT: a 406 GLU cc_start: 0.4534 (mm-30) cc_final: 0.4294 (mm-30) REVERT: a 407 LEU cc_start: 0.5482 (OUTLIER) cc_final: 0.5174 (mt) REVERT: a 635 PHE cc_start: 0.4607 (m-80) cc_final: 0.4316 (m-10) REVERT: m 5 MET cc_start: 0.5745 (ppp) cc_final: 0.5414 (ppp) REVERT: m 15 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.4987 (tp) REVERT: m 16 MET cc_start: 0.5670 (mmt) cc_final: 0.5381 (mmp) REVERT: m 54 TRP cc_start: 0.5294 (p-90) cc_final: 0.5060 (p-90) REVERT: t 21 HIS cc_start: 0.4658 (OUTLIER) cc_final: 0.3265 (m-70) outliers start: 340 outliers final: 260 residues processed: 1489 average time/residue: 0.5732 time to fit residues: 1469.4672 Evaluate side-chains 1497 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1211 time to evaluate : 4.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 310 MET Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 369 THR Chi-restraints excluded: chain I residue 373 TYR Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 466 SER Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 236 MET Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 61 PHE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain Y residue 10 ASN Chi-restraints excluded: chain Y residue 19 THR Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Y residue 91 LEU Chi-restraints excluded: chain Y residue 99 PHE Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain V residue 15 ILE Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 105 ASP Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain i residue 14 LEU Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain j residue 34 CYS Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain G residue 355 ILE Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 145 ILE Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 235 MET Chi-restraints excluded: chain T residue 256 VAL Chi-restraints excluded: chain T residue 307 TYR Chi-restraints excluded: chain T residue 369 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain P residue 108 HIS Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 50 ASP Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 139 THR Chi-restraints excluded: chain U residue 148 THR Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 89 PHE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain X residue 18 ASN Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain X residue 132 TYR Chi-restraints excluded: chain c residue 3 THR Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 38 SER Chi-restraints excluded: chain c residue 44 SER Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain k residue 53 VAL Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 57 GLN Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 107 VAL Chi-restraints excluded: chain o residue 144 TYR Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 168 SER Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 17 GLU Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 88 ASP Chi-restraints excluded: chain q residue 92 VAL Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 105 LEU Chi-restraints excluded: chain q residue 107 HIS Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 134 LEU Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 138 THR Chi-restraints excluded: chain q residue 153 ASP Chi-restraints excluded: chain q residue 210 LEU Chi-restraints excluded: chain q residue 229 LYS Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 45 LEU Chi-restraints excluded: chain p residue 117 VAL Chi-restraints excluded: chain p residue 122 ILE Chi-restraints excluded: chain p residue 141 ASP Chi-restraints excluded: chain p residue 157 VAL Chi-restraints excluded: chain p residue 169 VAL Chi-restraints excluded: chain p residue 227 PHE Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 138 ASP Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 193 PHE Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 302 ILE Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 36 HIS Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain g residue 92 TRP Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 22 PHE Chi-restraints excluded: chain a residue 35 CYS Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain a residue 176 PHE Chi-restraints excluded: chain a residue 186 PHE Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 333 VAL Chi-restraints excluded: chain a residue 349 PHE Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 470 LEU Chi-restraints excluded: chain a residue 542 PHE Chi-restraints excluded: chain a residue 563 TRP Chi-restraints excluded: chain a residue 566 ASP Chi-restraints excluded: chain b residue 73 MET Chi-restraints excluded: chain m residue 15 LEU Chi-restraints excluded: chain m residue 32 GLU Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain m residue 57 GLU Chi-restraints excluded: chain t residue 21 HIS Chi-restraints excluded: chain t residue 24 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 625 optimal weight: 20.0000 chunk 658 optimal weight: 6.9990 chunk 600 optimal weight: 20.0000 chunk 640 optimal weight: 9.9990 chunk 385 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 502 optimal weight: 8.9990 chunk 196 optimal weight: 8.9990 chunk 578 optimal weight: 0.9980 chunk 605 optimal weight: 9.9990 chunk 638 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 ASN ** V 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 18 ASN ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 HIS ** q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 202 GLN ** p 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 94 HIS ** a 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.250 59313 Z= 0.608 Angle : 1.646 51.053 80348 Z= 1.039 Chirality : 0.301 6.401 8969 Planarity : 0.005 0.067 10136 Dihedral : 8.848 168.369 8446 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 26.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.38 % Favored : 90.58 % Rotamer: Outliers : 5.42 % Allowed : 27.20 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.10), residues: 7252 helix: -0.20 (0.09), residues: 3591 sheet: -1.99 (0.30), residues: 303 loop : -2.23 (0.10), residues: 3358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP M 236 HIS 0.012 0.001 HIS U 138 PHE 0.054 0.002 PHE M 324 TYR 0.038 0.002 TYR H 147 ARG 0.010 0.001 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1584 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 1255 time to evaluate : 4.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6921 (mpp) cc_final: 0.6629 (mpp) REVERT: I 162 ILE cc_start: 0.9169 (pt) cc_final: 0.8850 (pt) REVERT: I 174 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6165 (tp30) REVERT: I 264 PHE cc_start: 0.7703 (m-80) cc_final: 0.7429 (m-10) REVERT: I 345 LEU cc_start: 0.9318 (tt) cc_final: 0.9059 (tp) REVERT: I 461 MET cc_start: 0.7822 (ppp) cc_final: 0.7588 (ppp) REVERT: I 471 MET cc_start: 0.6913 (mtm) cc_final: 0.6562 (mtp) REVERT: I 492 GLN cc_start: 0.8642 (tp40) cc_final: 0.8030 (tm-30) REVERT: J 111 TRP cc_start: 0.8224 (t60) cc_final: 0.7585 (t60) REVERT: N 42 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8534 (mm) REVERT: H 20 VAL cc_start: 0.7946 (OUTLIER) cc_final: 0.7645 (p) REVERT: H 41 ASP cc_start: 0.7955 (t0) cc_final: 0.7593 (t70) REVERT: H 95 ASP cc_start: 0.7525 (t0) cc_final: 0.7197 (t0) REVERT: H 290 TYR cc_start: 0.8939 (OUTLIER) cc_final: 0.8380 (m-80) REVERT: K 5 LYS cc_start: 0.7765 (tttt) cc_final: 0.7224 (mmtt) REVERT: K 33 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7624 (mmm) REVERT: Z 84 THR cc_start: 0.8539 (t) cc_final: 0.8092 (t) REVERT: Z 112 MET cc_start: 0.6407 (mmp) cc_final: 0.6137 (mmp) REVERT: S 97 MET cc_start: 0.6926 (mtp) cc_final: 0.6561 (ttm) REVERT: i 31 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.6652 (p-80) REVERT: i 63 MET cc_start: 0.7627 (mtt) cc_final: 0.7361 (mtt) REVERT: G 107 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6641 (mm-30) REVERT: G 294 LEU cc_start: 0.9008 (tp) cc_final: 0.8551 (tt) REVERT: C 164 MET cc_start: 0.7014 (tmm) cc_final: 0.6759 (tmm) REVERT: C 393 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7520 (mtm) REVERT: C 427 MET cc_start: 0.7464 (mtp) cc_final: 0.6845 (mtp) REVERT: C 453 MET cc_start: 0.7854 (mmm) cc_final: 0.7591 (mmm) REVERT: T 86 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8532 (tm-30) REVERT: T 119 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8733 (p) REVERT: T 307 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6458 (m-80) REVERT: T 369 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7198 (mtpp) REVERT: F 84 SER cc_start: 0.9009 (p) cc_final: 0.8734 (t) REVERT: O 65 GLN cc_start: 0.8248 (pt0) cc_final: 0.7799 (pt0) REVERT: U 35 PRO cc_start: 0.8336 (Cg_endo) cc_final: 0.8005 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8338 (p90) cc_final: 0.7960 (p90) REVERT: U 82 ASP cc_start: 0.7174 (t0) cc_final: 0.6793 (t0) REVERT: U 129 ASP cc_start: 0.7573 (m-30) cc_final: 0.7260 (m-30) REVERT: E 107 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6828 (m-30) REVERT: E 123 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6987 (m-30) REVERT: E 164 TYR cc_start: 0.9268 (t80) cc_final: 0.8941 (t80) REVERT: D 54 LYS cc_start: 0.4914 (mmtt) cc_final: 0.3493 (mmtt) REVERT: D 76 MET cc_start: 0.7469 (mmt) cc_final: 0.7248 (mmt) REVERT: D 195 TYR cc_start: 0.8557 (m-10) cc_final: 0.8109 (m-80) REVERT: D 197 LYS cc_start: 0.6294 (OUTLIER) cc_final: 0.5730 (mtpt) REVERT: X 95 GLN cc_start: 0.5447 (OUTLIER) cc_final: 0.4929 (tt0) REVERT: o 160 GLN cc_start: 0.7958 (mm110) cc_final: 0.7669 (mm-40) REVERT: o 212 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7046 (mt-10) REVERT: o 216 LEU cc_start: 0.8487 (tt) cc_final: 0.8203 (tp) REVERT: q 14 TRP cc_start: 0.5853 (OUTLIER) cc_final: 0.5234 (t60) REVERT: q 118 HIS cc_start: 0.6104 (t70) cc_final: 0.5691 (t-90) REVERT: q 138 THR cc_start: 0.6296 (OUTLIER) cc_final: 0.5988 (t) REVERT: q 153 ASP cc_start: 0.5315 (OUTLIER) cc_final: 0.3855 (p0) REVERT: p 20 GLN cc_start: 0.7901 (mt0) cc_final: 0.7576 (mt0) REVERT: p 23 ASP cc_start: 0.4613 (t0) cc_final: 0.4288 (t0) REVERT: p 24 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.5413 (ptt90) REVERT: p 102 ASP cc_start: 0.4377 (OUTLIER) cc_final: 0.3970 (t0) REVERT: p 144 PHE cc_start: 0.6099 (t80) cc_final: 0.5233 (t80) REVERT: M 33 ARG cc_start: 0.5325 (OUTLIER) cc_final: 0.5061 (ppt170) REVERT: M 65 LYS cc_start: 0.6303 (ptmt) cc_final: 0.6002 (pttp) REVERT: M 83 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.6250 (t80) REVERT: M 86 ILE cc_start: 0.7694 (pt) cc_final: 0.7314 (mt) REVERT: M 236 TRP cc_start: 0.7253 (p-90) cc_final: 0.5520 (t60) REVERT: M 237 LEU cc_start: 0.8206 (mt) cc_final: 0.7486 (mp) REVERT: M 261 THR cc_start: 0.8705 (p) cc_final: 0.8425 (p) REVERT: M 316 MET cc_start: 0.7450 (mmm) cc_final: 0.6886 (mmm) REVERT: M 321 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8055 (tp) REVERT: M 328 ILE cc_start: 0.8434 (pt) cc_final: 0.7975 (mp) REVERT: M 458 PHE cc_start: 0.7315 (t80) cc_final: 0.7046 (t80) REVERT: M 470 MET cc_start: 0.7989 (mtp) cc_final: 0.7766 (mtm) REVERT: f 34 ARG cc_start: 0.8404 (ttp80) cc_final: 0.8158 (mtp85) REVERT: f 36 HIS cc_start: 0.4878 (OUTLIER) cc_final: 0.4338 (t70) REVERT: f 54 LYS cc_start: 0.6029 (mttt) cc_final: 0.5376 (tmtt) REVERT: g 72 LEU cc_start: 0.8013 (mt) cc_final: 0.7782 (mt) REVERT: a 126 MET cc_start: 0.8099 (ttp) cc_final: 0.7361 (tmm) REVERT: a 137 PHE cc_start: 0.8131 (t80) cc_final: 0.7371 (t80) REVERT: a 145 LEU cc_start: 0.8675 (tp) cc_final: 0.8460 (tp) REVERT: a 186 PHE cc_start: 0.5855 (OUTLIER) cc_final: 0.4566 (t80) REVERT: a 349 PHE cc_start: 0.6213 (OUTLIER) cc_final: 0.4716 (m-80) REVERT: a 359 MET cc_start: 0.4097 (ttp) cc_final: 0.3816 (ptm) REVERT: a 368 MET cc_start: 0.6197 (mpp) cc_final: 0.4393 (tpt) REVERT: a 407 LEU cc_start: 0.5505 (OUTLIER) cc_final: 0.5167 (mt) REVERT: a 635 PHE cc_start: 0.4701 (m-80) cc_final: 0.4390 (m-10) REVERT: m 5 MET cc_start: 0.5612 (ppp) cc_final: 0.5313 (ppp) REVERT: m 15 LEU cc_start: 0.6030 (OUTLIER) cc_final: 0.5011 (tp) REVERT: m 16 MET cc_start: 0.5811 (mmt) cc_final: 0.5549 (mmp) REVERT: t 21 HIS cc_start: 0.4517 (OUTLIER) cc_final: 0.3123 (m-70) outliers start: 329 outliers final: 257 residues processed: 1448 average time/residue: 0.5314 time to fit residues: 1321.6469 Evaluate side-chains 1493 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 1209 time to evaluate : 4.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 310 MET Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 369 THR Chi-restraints excluded: chain I residue 373 TYR Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 466 SER Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 GLU Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 236 MET Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain Y residue 10 ASN Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Y residue 91 LEU Chi-restraints excluded: chain Y residue 99 PHE Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain V residue 15 ILE Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain W residue 7 LEU Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 105 ASP Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 41 LEU Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain j residue 34 CYS Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 145 ILE Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 235 MET Chi-restraints excluded: chain T residue 256 VAL Chi-restraints excluded: chain T residue 307 TYR Chi-restraints excluded: chain T residue 369 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain P residue 108 HIS Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 148 THR Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain c residue 3 THR Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 44 SER Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain k residue 53 VAL Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 107 VAL Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 168 SER Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 17 GLU Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 88 ASP Chi-restraints excluded: chain q residue 92 VAL Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 134 LEU Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 138 THR Chi-restraints excluded: chain q residue 153 ASP Chi-restraints excluded: chain q residue 210 LEU Chi-restraints excluded: chain q residue 229 LYS Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 102 ASP Chi-restraints excluded: chain p residue 117 VAL Chi-restraints excluded: chain p residue 122 ILE Chi-restraints excluded: chain p residue 141 ASP Chi-restraints excluded: chain p residue 157 VAL Chi-restraints excluded: chain p residue 169 VAL Chi-restraints excluded: chain p residue 227 PHE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 83 TYR Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 138 ASP Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 193 PHE Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 302 ILE Chi-restraints excluded: chain M residue 321 ILE Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 36 HIS Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain g residue 92 TRP Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 22 PHE Chi-restraints excluded: chain a residue 35 CYS Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 100 SER Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain a residue 176 PHE Chi-restraints excluded: chain a residue 186 PHE Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 333 VAL Chi-restraints excluded: chain a residue 349 PHE Chi-restraints excluded: chain a residue 387 LEU Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 510 GLU Chi-restraints excluded: chain a residue 519 LEU Chi-restraints excluded: chain a residue 542 PHE Chi-restraints excluded: chain a residue 563 TRP Chi-restraints excluded: chain b residue 73 MET Chi-restraints excluded: chain m residue 15 LEU Chi-restraints excluded: chain m residue 32 GLU Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain m residue 57 GLU Chi-restraints excluded: chain m residue 59 HIS Chi-restraints excluded: chain t residue 21 HIS Chi-restraints excluded: chain t residue 24 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 420 optimal weight: 2.9990 chunk 677 optimal weight: 7.9990 chunk 413 optimal weight: 1.9990 chunk 321 optimal weight: 10.0000 chunk 470 optimal weight: 0.9990 chunk 710 optimal weight: 20.0000 chunk 653 optimal weight: 7.9990 chunk 565 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 436 optimal weight: 1.9990 chunk 346 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 ASN Y 42 ASN ** V 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 GLN P 40 HIS ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 57 GLN ** o 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 HIS ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 453 ASN ** a 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.257 59313 Z= 0.557 Angle : 1.630 50.834 80348 Z= 1.031 Chirality : 0.301 6.370 8969 Planarity : 0.005 0.067 10136 Dihedral : 8.692 164.040 8446 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 24.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.66 % Favored : 91.30 % Rotamer: Outliers : 4.37 % Allowed : 28.55 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.10), residues: 7252 helix: -0.12 (0.09), residues: 3593 sheet: -1.86 (0.30), residues: 302 loop : -2.15 (0.10), residues: 3357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP q 181 HIS 0.013 0.001 HIS R 129 PHE 0.054 0.002 PHE M 324 TYR 0.060 0.002 TYR H 147 ARG 0.008 0.001 ARG G 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1569 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1304 time to evaluate : 4.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 50 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8278 (mm) REVERT: I 162 ILE cc_start: 0.9144 (pt) cc_final: 0.8857 (pt) REVERT: I 174 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6296 (tp30) REVERT: I 461 MET cc_start: 0.7729 (ppp) cc_final: 0.7465 (ppp) REVERT: I 471 MET cc_start: 0.6790 (mtm) cc_final: 0.6522 (mtp) REVERT: I 492 GLN cc_start: 0.8605 (tp40) cc_final: 0.7851 (tm-30) REVERT: J 111 TRP cc_start: 0.8066 (t60) cc_final: 0.7463 (t60) REVERT: N 42 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8447 (mm) REVERT: N 148 TYR cc_start: 0.8758 (m-80) cc_final: 0.8521 (m-80) REVERT: H 20 VAL cc_start: 0.7822 (p) cc_final: 0.7525 (p) REVERT: H 41 ASP cc_start: 0.7965 (t0) cc_final: 0.7573 (t70) REVERT: H 95 ASP cc_start: 0.7283 (t0) cc_final: 0.7018 (t0) REVERT: H 126 TRP cc_start: 0.7973 (t60) cc_final: 0.7316 (t60) REVERT: H 290 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: H 298 LEU cc_start: 0.8279 (mp) cc_final: 0.7693 (mp) REVERT: K 5 LYS cc_start: 0.7733 (tttt) cc_final: 0.7175 (mmtt) REVERT: K 33 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7655 (mmm) REVERT: K 34 SER cc_start: 0.7907 (OUTLIER) cc_final: 0.7628 (p) REVERT: K 45 ASN cc_start: 0.7819 (t0) cc_final: 0.7531 (t0) REVERT: K 56 MET cc_start: 0.7079 (tpp) cc_final: 0.6673 (ttt) REVERT: K 61 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.6731 (t80) REVERT: Z 84 THR cc_start: 0.8436 (t) cc_final: 0.7990 (t) REVERT: Z 112 MET cc_start: 0.6430 (mmp) cc_final: 0.6215 (mmp) REVERT: Z 113 LYS cc_start: 0.7281 (mptt) cc_final: 0.6664 (mttt) REVERT: S 97 MET cc_start: 0.6814 (mtp) cc_final: 0.6435 (ttm) REVERT: i 31 HIS cc_start: 0.7437 (OUTLIER) cc_final: 0.6301 (p-80) REVERT: i 63 MET cc_start: 0.7571 (mtt) cc_final: 0.7338 (mtt) REVERT: j 71 LYS cc_start: 0.2731 (mttt) cc_final: 0.1827 (tppt) REVERT: G 107 GLU cc_start: 0.6745 (mm-30) cc_final: 0.6497 (mm-30) REVERT: G 294 LEU cc_start: 0.9006 (tp) cc_final: 0.8593 (tt) REVERT: C 164 MET cc_start: 0.6763 (tmm) cc_final: 0.6530 (tmm) REVERT: C 393 MET cc_start: 0.7595 (mtm) cc_final: 0.7371 (mtm) REVERT: C 427 MET cc_start: 0.7357 (mtp) cc_final: 0.6774 (mtp) REVERT: C 453 MET cc_start: 0.7743 (mmm) cc_final: 0.7440 (mmm) REVERT: T 86 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8472 (tm-30) REVERT: T 307 TYR cc_start: 0.7112 (OUTLIER) cc_final: 0.6505 (m-80) REVERT: T 369 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7227 (mtpp) REVERT: F 84 SER cc_start: 0.8955 (p) cc_final: 0.8701 (t) REVERT: O 65 GLN cc_start: 0.7998 (pt0) cc_final: 0.7609 (pt0) REVERT: U 35 PRO cc_start: 0.8233 (Cg_endo) cc_final: 0.7915 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8245 (p90) cc_final: 0.7899 (p90) REVERT: U 129 ASP cc_start: 0.7390 (m-30) cc_final: 0.7080 (m-30) REVERT: E 107 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6616 (m-30) REVERT: E 164 TYR cc_start: 0.9198 (t80) cc_final: 0.8877 (t80) REVERT: D 54 LYS cc_start: 0.5093 (mmtt) cc_final: 0.3637 (mmtt) REVERT: D 197 LYS cc_start: 0.5985 (OUTLIER) cc_final: 0.5484 (mtpt) REVERT: X 95 GLN cc_start: 0.5214 (OUTLIER) cc_final: 0.4852 (tt0) REVERT: X 98 HIS cc_start: 0.6645 (m-70) cc_final: 0.6368 (m90) REVERT: X 132 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.6494 (m-80) REVERT: o 212 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7004 (mt-10) REVERT: o 216 LEU cc_start: 0.8414 (tt) cc_final: 0.8123 (tp) REVERT: q 14 TRP cc_start: 0.5877 (OUTLIER) cc_final: 0.5314 (t60) REVERT: q 153 ASP cc_start: 0.5393 (OUTLIER) cc_final: 0.4078 (p0) REVERT: p 14 TRP cc_start: 0.7371 (m-10) cc_final: 0.7108 (m-10) REVERT: p 20 GLN cc_start: 0.7866 (mt0) cc_final: 0.7556 (mt0) REVERT: p 23 ASP cc_start: 0.4342 (t0) cc_final: 0.4116 (t0) REVERT: p 24 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.5266 (ptt90) REVERT: p 147 MET cc_start: 0.5550 (tpp) cc_final: 0.5036 (tpp) REVERT: M 33 ARG cc_start: 0.5320 (OUTLIER) cc_final: 0.5073 (ppt170) REVERT: M 86 ILE cc_start: 0.7625 (pt) cc_final: 0.7124 (mt) REVERT: M 236 TRP cc_start: 0.7119 (p-90) cc_final: 0.5580 (t60) REVERT: M 237 LEU cc_start: 0.7956 (mt) cc_final: 0.7339 (mp) REVERT: M 261 THR cc_start: 0.8674 (p) cc_final: 0.8422 (p) REVERT: M 316 MET cc_start: 0.7324 (mmm) cc_final: 0.6894 (mmm) REVERT: M 321 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7827 (tp) REVERT: M 328 ILE cc_start: 0.8397 (pt) cc_final: 0.7970 (mp) REVERT: f 36 HIS cc_start: 0.4786 (OUTLIER) cc_final: 0.3674 (t70) REVERT: f 40 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: f 54 LYS cc_start: 0.5906 (mttt) cc_final: 0.5270 (tmtt) REVERT: g 67 TYR cc_start: 0.3934 (p90) cc_final: 0.3593 (p90) REVERT: g 72 LEU cc_start: 0.7964 (mt) cc_final: 0.7743 (mt) REVERT: a 126 MET cc_start: 0.8059 (ttp) cc_final: 0.7360 (tmm) REVERT: a 137 PHE cc_start: 0.7989 (t80) cc_final: 0.7315 (t80) REVERT: a 172 ARG cc_start: 0.7386 (mmm160) cc_final: 0.6877 (mmm160) REVERT: a 186 PHE cc_start: 0.6227 (OUTLIER) cc_final: 0.5777 (m-80) REVERT: a 349 PHE cc_start: 0.6197 (OUTLIER) cc_final: 0.4716 (m-80) REVERT: a 359 MET cc_start: 0.4041 (ttp) cc_final: 0.3758 (ptm) REVERT: a 368 MET cc_start: 0.6120 (mpp) cc_final: 0.4370 (tpt) REVERT: a 635 PHE cc_start: 0.4576 (m-80) cc_final: 0.4323 (m-10) REVERT: m 5 MET cc_start: 0.5461 (ppp) cc_final: 0.5199 (ppp) REVERT: m 15 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.4710 (tp) REVERT: m 16 MET cc_start: 0.5777 (mmt) cc_final: 0.5446 (mmp) REVERT: t 21 HIS cc_start: 0.4601 (OUTLIER) cc_final: 0.3185 (m-70) outliers start: 265 outliers final: 213 residues processed: 1460 average time/residue: 0.5326 time to fit residues: 1334.9341 Evaluate side-chains 1469 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 1232 time to evaluate : 4.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 310 MET Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 369 THR Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 466 SER Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 148 GLU Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 236 MET Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 61 PHE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain Y residue 10 ASN Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 91 LEU Chi-restraints excluded: chain Y residue 99 PHE Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain V residue 15 ILE Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain i residue 14 LEU Chi-restraints excluded: chain i residue 16 THR Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 41 LEU Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain j residue 34 CYS Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 145 ILE Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 235 MET Chi-restraints excluded: chain T residue 307 TYR Chi-restraints excluded: chain T residue 369 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain P residue 108 HIS Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain X residue 132 TYR Chi-restraints excluded: chain c residue 3 THR Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 44 SER Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 107 VAL Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 168 SER Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 88 ASP Chi-restraints excluded: chain q residue 92 VAL Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 134 LEU Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 153 ASP Chi-restraints excluded: chain q residue 210 LEU Chi-restraints excluded: chain q residue 229 LYS Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 45 LEU Chi-restraints excluded: chain p residue 141 ASP Chi-restraints excluded: chain p residue 157 VAL Chi-restraints excluded: chain p residue 169 VAL Chi-restraints excluded: chain p residue 227 PHE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 193 PHE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 302 ILE Chi-restraints excluded: chain M residue 321 ILE Chi-restraints excluded: chain M residue 327 ASN Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 36 HIS Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain g residue 92 TRP Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 22 PHE Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain a residue 176 PHE Chi-restraints excluded: chain a residue 186 PHE Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 333 VAL Chi-restraints excluded: chain a residue 349 PHE Chi-restraints excluded: chain a residue 387 LEU Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 493 TRP Chi-restraints excluded: chain a residue 519 LEU Chi-restraints excluded: chain a residue 542 PHE Chi-restraints excluded: chain a residue 563 TRP Chi-restraints excluded: chain b residue 73 MET Chi-restraints excluded: chain m residue 15 LEU Chi-restraints excluded: chain m residue 32 GLU Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain m residue 57 GLU Chi-restraints excluded: chain t residue 21 HIS Chi-restraints excluded: chain t residue 24 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 449 optimal weight: 10.0000 chunk 602 optimal weight: 0.0980 chunk 173 optimal weight: 0.8980 chunk 521 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 566 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 chunk 581 optimal weight: 10.0000 chunk 71 optimal weight: 0.0970 chunk 104 optimal weight: 0.6980 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 ASN ** V 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 80 ASN ** o 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 161 HIS ** q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 HIS ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 453 ASN ** a 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 337 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.137255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.113245 restraints weight = 138420.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.114458 restraints weight = 81595.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.115474 restraints weight = 51925.216| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.259 59313 Z= 0.554 Angle : 1.629 50.821 80348 Z= 1.031 Chirality : 0.301 6.371 8969 Planarity : 0.005 0.073 10136 Dihedral : 8.506 162.371 8446 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 24.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.65 % Favored : 91.31 % Rotamer: Outliers : 4.24 % Allowed : 29.19 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.10), residues: 7252 helix: -0.03 (0.09), residues: 3575 sheet: -1.82 (0.29), residues: 311 loop : -2.08 (0.10), residues: 3366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP q 181 HIS 0.017 0.001 HIS p 130 PHE 0.056 0.002 PHE M 142 TYR 0.062 0.002 TYR H 147 ARG 0.011 0.001 ARG c 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20236.80 seconds wall clock time: 352 minutes 35.29 seconds (21155.29 seconds total)