Starting phenix.real_space_refine on Mon Mar 25 15:19:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a24_11615/03_2024/7a24_11615_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a24_11615/03_2024/7a24_11615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a24_11615/03_2024/7a24_11615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a24_11615/03_2024/7a24_11615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a24_11615/03_2024/7a24_11615_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a24_11615/03_2024/7a24_11615_updated.pdb" } resolution = 3.8 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= -0.001 sd= 0.004 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 9 5.49 5 S 333 5.16 5 C 31709 2.51 5 N 8398 2.21 5 O 9018 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 GLU 153": "OE1" <-> "OE2" Residue "I ARG 167": "NH1" <-> "NH2" Residue "I GLU 174": "OE1" <-> "OE2" Residue "I ARG 222": "NH1" <-> "NH2" Residue "I GLU 340": "OE1" <-> "OE2" 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 ARG 30": "NH1" <-> "NH2" Residue "j GLU 30": "OE1" <-> "OE2" 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 GLU 121": "OE1" <-> "OE2" Residue "R ARG 134": "NH1" <-> "NH2" 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 "z ARG 124": "NH1" <-> "NH2" Residue "z ARG 148": "NH1" <-> "NH2" Residue "z ARG 165": "NH1" <-> "NH2" Residue "z GLU 179": "OE1" <-> "OE2" Residue "z ARG 186": "NH1" <-> "NH2" Residue "z ARG 194": "NH1" <-> "NH2" Residue "z ARG 216": "NH1" <-> "NH2" Residue "z ARG 234": "NH1" <-> "NH2" Residue "z GLU 240": "OE1" <-> "OE2" Residue "z ARG 259": "NH1" <-> "NH2" Residue "z ARG 270": "NH1" <-> "NH2" Residue "z ARG 289": "NH1" <-> "NH2" Residue "z GLU 291": "OE1" <-> "OE2" Residue "z GLU 294": "OE1" <-> "OE2" Residue "z GLU 303": "OE1" <-> "OE2" Residue "z ARG 360": "NH1" <-> "NH2" Residue "z ARG 371": "NH1" <-> "NH2" Residue "z ARG 396": "NH1" <-> "NH2" Residue "z GLU 425": "OE1" <-> "OE2" Residue "z ARG 428": "NH1" <-> "NH2" Residue "z ARG 492": "NH1" <-> "NH2" Residue "z ARG 524": "NH1" <-> "NH2" Residue "z ARG 526": "NH1" <-> "NH2" Residue "z GLU 532": "OE1" <-> "OE2" Residue "z ARG 537": "NH1" <-> "NH2" Residue "z GLU 552": "OE1" <-> "OE2" Residue "z ARG 572": "NH1" <-> "NH2" Residue "z ARG 576": "NH1" <-> "NH2" Residue "z ARG 586": "NH1" <-> "NH2" Residue "z ARG 587": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49497 Number of models: 1 Model: "" Number of chains: 46 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: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 492 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} 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: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 977 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} 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: "z" Number of atoms: 3992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3992 Classifications: {'peptide': 499} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 469} Chain breaks: 1 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'T7X': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'T7X:plan-2': 1, 'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 15 Chain: "i" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 90 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 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: "c" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'T7X': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'T7X:plan-2': 1, 'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 13 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2707 SG CYS A 405 55.416 63.028 195.115 1.00 18.90 S ATOM 2727 SG CYS A 408 53.525 66.702 198.356 1.00 17.31 S ATOM 2688 SG CYS A 402 59.327 62.879 201.104 1.00 21.30 S ATOM 3052 SG CYS A 448 53.121 60.273 200.857 1.00 20.05 S ATOM 20774 SG CYS C 179 66.327 70.547 179.591 1.00 15.05 S ATOM 20713 SG CYS C 170 64.164 77.175 179.247 1.00 22.03 S ATOM 20734 SG CYS C 173 70.389 74.847 180.959 1.00 22.61 S ATOM 21102 SG CYS C 221 66.705 64.532 188.387 1.00 19.30 S ATOM 21079 SG CYS C 218 68.231 70.226 191.267 1.00 13.72 S ATOM 21126 SG CYS C 224 72.613 65.536 191.082 1.00 14.17 S ATOM 21447 SG CYS C 268 71.604 67.807 186.059 1.00 19.62 S ATOM 20229 SG CYS C 106 62.805 60.249 188.379 1.00 16.72 S ATOM 20313 SG CYS C 117 59.862 62.005 187.449 1.00 18.39 S ATOM 20440 SG CYS C 134 60.216 55.596 187.846 1.00 21.47 S ATOM 29937 SG CYS B 130 50.395 73.868 216.095 1.00 36.50 S ATOM 29968 SG CYS B 135 48.062 75.165 218.311 1.00 40.45 S ATOM 30241 SG CYS B 171 49.330 68.060 214.837 1.00 39.22 S ATOM 30265 SG CYS B 175 46.526 68.868 216.940 1.00 41.46 S ATOM 31987 SG CYS P 72 67.614 91.605 186.884 1.00 28.54 S ATOM 32173 SG CYS P 97 69.508 88.711 185.761 1.00 25.54 S ATOM 34990 SG CYS E 158 69.341 86.839 147.125 1.00 22.55 S ATOM 34490 SG CYS E 94 66.483 93.425 146.428 1.00 17.23 S ATOM 34484 SG CYS E 93 63.712 89.502 144.692 1.00 18.81 S ATOM 35220 SG CYS E 188 66.213 89.968 151.271 1.00 26.47 S ATOM 36455 SG CYS D 165 64.769 86.643 158.604 1.00 19.17 S ATOM 36429 SG CYS D 162 70.698 89.876 157.681 1.00 11.81 S ATOM 36476 SG CYS D 168 68.042 89.242 163.389 1.00 21.11 S ATOM 36197 SG CYS D 133 70.671 84.229 159.641 1.00 27.13 S ATOM 36505 SG CYS D 172 67.374 88.704 172.130 1.00 21.71 S ATOM 36170 SG CYS D 129 71.211 85.500 167.444 1.00 38.74 S ATOM 36128 SG CYS D 123 74.345 88.110 172.053 1.00 25.74 S ATOM 36147 SG CYS D 126 69.779 83.011 172.986 1.00 18.74 S Time building chain proxies: 26.20, per 1000 atoms: 0.53 Number of scatterers: 49497 At special positions: 0 Unit cell: (136.53, 184.26, 250.86, 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 333 16.00 P 9 15.00 O 9018 8.00 N 8398 7.00 C 31709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.04 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 53 " distance=2.05 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.78 Conformation dependent library (CDL) restraints added in 8.9 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 " 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 224 helices and 32 sheets defined 41.1% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.95 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: 4.472A 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 71 removed outlier: 6.283A pdb=" N LEU I 59 " --> pdb=" O GLY I 55 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL I 62 " --> pdb=" O GLY I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 80 through 85 Processing helix chain 'I' and resid 91 through 117 removed outlier: 4.631A pdb=" N ASP I 113 " --> pdb=" O SER I 109 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE I 114 " --> pdb=" O MET I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 141 removed outlier: 3.501A pdb=" N VAL I 127 " --> pdb=" O PHE I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 164 Processing helix chain 'I' and resid 170 through 201 Processing helix chain 'I' and resid 206 through 213 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 Proline residue: I 269 - end of helix Processing helix chain 'I' and resid 290 through 311 removed outlier: 3.583A pdb=" N PHE I 294 " --> pdb=" O LEU I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 315 through 335 removed outlier: 4.077A pdb=" N GLY I 333 " --> pdb=" O TYR I 329 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE I 334 " --> pdb=" O ILE I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 366 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 removed outlier: 3.556A pdb=" N TYR I 398 " --> pdb=" O THR I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 420 Processing helix chain 'I' and resid 423 through 447 removed outlier: 3.814A pdb=" N TYR I 439 " --> pdb=" O ILE I 435 " (cutoff:3.500A) Processing helix chain 'I' and resid 463 through 479 removed outlier: 3.752A pdb=" N PHE I 475 " --> pdb=" O MET I 471 " (cutoff:3.500A) 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: 4.522A 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: 3.616A 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: 4.080A pdb=" N TYR H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 161 removed outlier: 3.764A 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 69 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) removed outlier: 3.727A pdb=" N HIS Y 68 " --> pdb=" O LYS Y 65 " (cutoff:3.500A) Processing helix chain 'Y' and resid 72 through 84 Processing helix chain 'Y' and resid 90 through 102 removed outlier: 3.915A pdb=" N ARG Y 93 " --> pdb=" O ASP Y 90 " (cutoff:3.500A) removed outlier: 6.333A 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: 3.639A pdb=" N PHE Y 99 " --> pdb=" O GLN Y 96 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL Y 102 " --> pdb=" O PHE Y 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 111 removed outlier: 3.698A pdb=" N ALA Z 58 " --> pdb=" O SER Z 54 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N MET Z 61 " --> pdb=" O PHE Z 57 " (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: 4.310A 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 17 Processing helix chain 'i' and resid 36 through 68 Processing helix chain 'j' and resid 15 through 25 Processing helix chain 'j' and resid 31 through 46 removed outlier: 5.081A pdb=" N LEU j 36 " --> pdb=" O LYS j 32 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU j 37 " --> pdb=" O ASP j 33 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG j 38 " --> pdb=" O CYS j 34 " (cutoff:3.500A) Processing helix chain 'j' and resid 48 through 70 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: 3.795A 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: 3.781A pdb=" N THR G 119 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 3.916A 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: 3.758A 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: 4.114A 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: 4.520A 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: 4.054A pdb=" N ILE G 381 " --> pdb=" O VAL G 378 " (cutoff:3.500A) removed outlier: 3.634A 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: 4.165A 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: 3.773A 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: 3.530A 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: 3.895A 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: 4.322A 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: 5.108A 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: 3.596A 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 68 Processing helix chain 'D' and resid 74 through 88 removed outlier: 3.502A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) 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: 3.594A 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: 4.073A 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: 3.598A pdb=" N THR c 41 " --> pdb=" O PHE c 37 " (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: 5.553A 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: 4.542A 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 82 through 101 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 22 Processing helix chain 'q' and resid 25 through 27 No H-bonds generated for 'chain 'q' and resid 25 through 27' 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: 4.968A 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 24 removed outlier: 3.697A pdb=" N LEU p 22 " --> pdb=" O THR p 18 " (cutoff:3.500A) 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: 3.595A 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 'z' and resid 132 through 145 Processing helix chain 'z' and resid 172 through 176 Processing helix chain 'z' and resid 195 through 204 Processing helix chain 'z' and resid 220 through 225 Processing helix chain 'z' and resid 238 through 241 No H-bonds generated for 'chain 'z' and resid 238 through 241' Processing helix chain 'z' and resid 263 through 271 Processing helix chain 'z' and resid 301 through 315 removed outlier: 4.614A pdb=" N LYS z 309 " --> pdb=" O LYS z 305 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS z 310 " --> pdb=" O LYS z 306 " (cutoff:3.500A) Processing helix chain 'z' and resid 390 through 401 Processing helix chain 'z' and resid 408 through 423 removed outlier: 3.641A pdb=" N LYS z 412 " --> pdb=" O VAL z 408 " (cutoff:3.500A) Processing helix chain 'z' and resid 455 through 460 Proline residue: z 459 - end of helix No H-bonds generated for 'chain 'z' and resid 455 through 460' Processing helix chain 'z' and resid 463 through 476 Processing helix chain 'z' and resid 525 through 536 Processing helix chain 'z' and resid 545 through 548 No H-bonds generated for 'chain 'z' and resid 545 through 548' Processing helix chain 'z' and resid 567 through 570 No H-bonds generated for 'chain 'z' and resid 567 through 570' Processing helix chain 'z' and resid 572 through 576 Processing helix chain 'z' and resid 580 through 589 Processing helix chain 'z' and resid 598 through 603 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: 7.330A pdb=" N VAL A 138 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 6.438A 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: 7.007A pdb=" N TYR A 219 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE A 181 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 6.494A 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: 6.332A 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: 3.571A pdb=" N THR G 327 " --> pdb=" O LEU G 342 " (cutoff:3.500A) removed outlier: 3.695A 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: 6.497A pdb=" N ARG C 308 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 5.916A 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: 6.669A 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: 6.906A 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: 5.871A 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: 4.022A 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: 6.517A 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: 3.664A 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: 7.157A 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: 6.790A 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: 5.835A 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) Processing sheet with id= AC, first strand: chain 'z' and resid 149 through 151 removed outlier: 5.511A pdb=" N GLY z 167 " --> pdb=" O ARG z 150 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'z' and resid 178 through 181 removed outlier: 6.580A pdb=" N LYS z 246 " --> pdb=" O ALA z 280 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL z 282 " --> pdb=" O SER z 244 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER z 244 " --> pdb=" O VAL z 282 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU z 247 " --> pdb=" O ILE z 255 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'z' and resid 328 through 337 removed outlier: 4.565A pdb=" N GLU z 291 " --> pdb=" O VAL z 337 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG z 428 " --> pdb=" O GLU z 294 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'z' and resid 319 through 322 removed outlier: 3.507A pdb=" N GLU z 486 " --> pdb=" O GLY z 513 " (cutoff:3.500A) 1672 hydrogen bonds defined for protein. 4557 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: 15.47 Time building geometry restraints manager: 22.26 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: 19992 1.39 - 1.61: 30086 1.61 - 1.84: 485 1.84 - 2.07: 0 2.07 - 2.29: 80 Bond restraints: 50643 Sorted by residual: bond pdb=" N PRO E 186 " pdb=" CD PRO E 186 " ideal model delta sigma weight residual 1.473 1.332 0.141 1.40e-02 5.10e+03 1.02e+02 bond pdb=" C PRO H 288 " pdb=" O PRO H 288 " ideal model delta sigma weight residual 1.233 1.159 0.074 1.18e-02 7.18e+03 3.95e+01 bond pdb=" CA SER c 44 " pdb=" CB SER c 44 " ideal model delta sigma weight residual 1.532 1.443 0.089 1.53e-02 4.27e+03 3.39e+01 bond pdb=" O2B NDP T 501 " pdb=" P2B NDP T 501 " ideal model delta sigma weight residual 1.833 1.615 0.218 3.80e-02 6.93e+02 3.30e+01 bond pdb=" CA SER H 307 " pdb=" CB SER H 307 " ideal model delta sigma weight residual 1.532 1.452 0.079 1.57e-02 4.06e+03 2.56e+01 ... (remaining 50638 not shown) Histogram of bond angle deviations from ideal: 73.14 - 85.37: 72 85.37 - 97.61: 9 97.61 - 109.84: 7932 109.84 - 122.07: 51673 122.07 - 134.30: 8933 Bond angle restraints: 68619 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 89.96 14.37 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 107.74 132.03 -24.29 1.95e+00 2.62e-01 1.55e+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 89.44 14.89 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 68614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.06: 29481 33.06 - 66.13: 799 66.13 - 99.19: 55 99.19 - 132.25: 5 132.25 - 165.32: 4 Dihedral angle restraints: 30344 sinusoidal: 12325 harmonic: 18019 Sorted by residual: 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 -145.35 22.75 0 2.50e+00 1.60e-01 8.28e+01 dihedral pdb=" CB CYS Q 19 " pdb=" SG CYS Q 19 " pdb=" SG CYS Q 53 " pdb=" CB CYS Q 53 " ideal model delta sinusoidal sigma weight residual -86.00 -158.53 72.53 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS Y 81 " pdb=" SG CYS Y 81 " pdb=" SG CYS Y 92 " pdb=" CB CYS Y 92 " ideal model delta sinusoidal sigma weight residual 93.00 162.31 -69.31 1 1.00e+01 1.00e-02 6.21e+01 ... (remaining 30341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.236: 7592 4.236 - 8.472: 0 8.472 - 12.707: 0 12.707 - 16.943: 0 16.943 - 21.179: 20 Chirality restraints: 7612 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 -10.62 21.18 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 -21.00 2.00e-01 2.50e+01 1.10e+04 ... (remaining 7609 not shown) Planarity restraints: 8730 Sorted by residual: 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=" CA VAL R 119 " 0.021 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C VAL R 119 " -0.076 2.00e-02 2.50e+03 pdb=" O VAL R 119 " 0.029 2.00e-02 2.50e+03 pdb=" N ILE R 120 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP T 501 " 0.025 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C5N NDP T 501 " -0.054 2.00e-02 2.50e+03 pdb=" C6N NDP T 501 " 0.056 2.00e-02 2.50e+03 pdb=" N1N NDP T 501 " -0.027 2.00e-02 2.50e+03 ... (remaining 8727 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.66: 5 1.66 - 2.47: 331 2.47 - 3.28: 59937 3.28 - 4.09: 132019 4.09 - 4.90: 246732 Warning: very small nonbonded interaction distances. Nonbonded interactions: 439024 Sorted by model distance: nonbonded pdb=" C GLN z 128 " pdb=" OD1 ASN z 170 " model vdw 0.850 3.270 nonbonded pdb=" O GLN z 128 " pdb=" OD1 ASN z 170 " model vdw 0.903 3.040 nonbonded pdb=" N PRO z 129 " pdb=" OD1 ASN z 170 " model vdw 1.415 3.120 nonbonded pdb=" O GLN z 128 " pdb=" CG ASN z 170 " model vdw 1.482 3.270 nonbonded pdb=" C GLN z 128 " pdb=" CG ASN z 170 " model vdw 1.509 3.500 ... (remaining 439019 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' 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: 2.370 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: 0.030 Extract box with map and model: 13.320 Check model and map are aligned: 0.870 Set scattering table: 0.520 Process input model: 145.890 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.260 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4708 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 : 0.009 0.218 50643 Z= 0.587 Angle : 1.160 24.289 68619 Z= 0.815 Chirality : 1.077 21.179 7612 Planarity : 0.006 0.114 8730 Dihedral : 15.349 165.318 18742 Min Nonbonded Distance : 0.850 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.57 % Favored : 90.09 % Rotamer: Outliers : 2.62 % Allowed : 10.02 % Favored : 87.35 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.10 (0.10), residues: 6177 helix: -1.03 (0.09), residues: 2799 sheet: -2.76 (0.27), residues: 338 loop : -3.05 (0.10), residues: 3040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 106 HIS 0.012 0.001 HIS q 107 PHE 0.032 0.002 PHE D 185 TYR 0.024 0.002 TYR G 72 ARG 0.008 0.001 ARG S 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1863 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1724 time to evaluate : 5.851 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: A 182 ARG cc_start: 0.6297 (ttt180) cc_final: 0.6092 (ttp80) REVERT: A 360 MET cc_start: 0.5068 (mmm) cc_final: 0.4208 (mtp) REVERT: I 148 MET cc_start: 0.7615 (ttp) cc_final: 0.7394 (ptm) REVERT: I 181 ILE cc_start: 0.7778 (mt) cc_final: 0.7401 (tp) REVERT: I 209 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6769 (tt) REVERT: I 214 THR cc_start: 0.5371 (OUTLIER) cc_final: 0.5061 (p) REVERT: I 272 SER cc_start: 0.8425 (t) cc_final: 0.6690 (p) REVERT: I 290 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7765 (pt) REVERT: I 292 GLN cc_start: 0.3426 (mm110) cc_final: 0.2971 (mp10) REVERT: I 438 PHE cc_start: 0.3036 (OUTLIER) cc_final: 0.1782 (t80) REVERT: J 2 MET cc_start: 0.1852 (tmm) cc_final: 0.1112 (ttt) REVERT: J 105 ILE cc_start: 0.8901 (mm) cc_final: 0.8657 (mt) REVERT: J 116 LEU cc_start: 0.7812 (mt) cc_final: 0.7157 (mt) REVERT: N 22 ASN cc_start: 0.5679 (t0) cc_final: 0.5423 (t0) REVERT: N 126 VAL cc_start: 0.5921 (p) cc_final: 0.5392 (p) REVERT: H 62 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7164 (mt-10) REVERT: H 229 PHE cc_start: 0.5449 (m-80) cc_final: 0.5051 (m-10) REVERT: V 10 LEU cc_start: 0.4333 (tp) cc_final: 0.4074 (mt) REVERT: S 70 ILE cc_start: 0.6539 (pt) cc_final: 0.5979 (pt) REVERT: S 84 ILE cc_start: 0.6421 (mp) cc_final: 0.5834 (mm) REVERT: S 100 GLU cc_start: 0.7931 (tt0) cc_final: 0.7385 (tm-30) REVERT: i 66 LYS cc_start: 0.6440 (ttpp) cc_final: 0.6234 (tttm) REVERT: G 198 ILE cc_start: 0.5575 (mt) cc_final: 0.4809 (mt) REVERT: G 257 CYS cc_start: 0.6806 (m) cc_final: 0.6560 (m) REVERT: C 74 ILE cc_start: 0.4162 (mt) cc_final: 0.3733 (mt) REVERT: C 83 VAL cc_start: 0.4399 (m) cc_final: 0.4063 (m) REVERT: C 270 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.6970 (t) REVERT: C 478 PHE cc_start: 0.7264 (m-80) cc_final: 0.7018 (m-10) REVERT: C 719 VAL cc_start: 0.7690 (t) cc_final: 0.7130 (t) REVERT: T 170 VAL cc_start: 0.5696 (m) cc_final: 0.5373 (p) REVERT: F 75 TYR cc_start: 0.6767 (m-80) cc_final: 0.6378 (m-80) REVERT: F 179 ASP cc_start: 0.7265 (t0) cc_final: 0.7050 (t70) REVERT: B 53 ASN cc_start: 0.3607 (m-40) cc_final: 0.3058 (m-40) REVERT: R 132 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.6377 (tm-30) REVERT: E 89 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.6990 (t80) REVERT: E 188 CYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7401 (t) REVERT: D 90 PRO cc_start: 0.0109 (Cg_exo) cc_final: -0.0173 (Cg_endo) REVERT: D 201 LEU cc_start: 0.6201 (mt) cc_final: 0.5848 (mt) REVERT: c 47 VAL cc_start: 0.7539 (t) cc_final: 0.7332 (t) REVERT: k 83 VAL cc_start: 0.4949 (t) cc_final: 0.4586 (t) REVERT: o 184 PRO cc_start: 0.6887 (Cg_exo) cc_final: 0.6432 (Cg_endo) REVERT: q 13 PHE cc_start: 0.5593 (m-80) cc_final: 0.5293 (m-10) REVERT: q 16 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.5342 (tpp80) REVERT: q 57 LYS cc_start: 0.4498 (mmtt) cc_final: 0.4103 (ttmm) REVERT: q 66 SER cc_start: 0.6514 (m) cc_final: 0.5298 (t) REVERT: q 94 VAL cc_start: 0.6623 (t) cc_final: 0.6392 (t) REVERT: p 13 PHE cc_start: 0.5159 (m-80) cc_final: 0.4926 (m-80) REVERT: p 14 TRP cc_start: 0.6339 (m-10) cc_final: 0.5596 (t60) REVERT: p 50 ASP cc_start: 0.3564 (m-30) cc_final: 0.3242 (m-30) REVERT: z 107 GLU cc_start: 0.5305 (OUTLIER) cc_final: 0.4961 (mm-30) REVERT: z 182 LYS cc_start: 0.1143 (OUTLIER) cc_final: 0.0568 (pttt) REVERT: z 183 GLU cc_start: 0.1968 (tt0) cc_final: 0.1630 (mt-10) REVERT: z 370 TYR cc_start: 0.3185 (t80) cc_final: 0.2300 (t80) REVERT: z 381 ASP cc_start: 0.2280 (t0) cc_final: 0.1762 (t0) REVERT: z 385 PRO cc_start: 0.0011 (Cg_endo) cc_final: -0.0859 (Cg_exo) REVERT: z 510 SER cc_start: 0.1151 (OUTLIER) cc_final: 0.0377 (p) REVERT: z 546 ASP cc_start: 0.3749 (t0) cc_final: 0.2438 (t0) outliers start: 139 outliers final: 38 residues processed: 1829 average time/residue: 0.6601 time to fit residues: 1943.8035 Evaluate side-chains 995 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 945 time to evaluate : 5.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 155 GLN Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 415 PHE Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 438 PHE Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 39 MET Chi-restraints excluded: chain i residue 50 VAL Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain j residue 46 HIS Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain R residue 132 GLN Chi-restraints excluded: chain E residue 89 PHE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 188 CYS Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain q residue 16 ARG Chi-restraints excluded: chain z residue 107 GLU Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 170 ASN Chi-restraints excluded: chain z residue 182 LYS Chi-restraints excluded: chain z residue 249 THR Chi-restraints excluded: chain z residue 317 HIS Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 387 ILE Chi-restraints excluded: chain z residue 403 ASP Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 510 SER Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 513 optimal weight: 6.9990 chunk 460 optimal weight: 0.0670 chunk 255 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 310 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 476 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 289 optimal weight: 20.0000 chunk 354 optimal weight: 0.5980 chunk 552 optimal weight: 8.9990 overall best weight: 1.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 HIS I 80 HIS ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 117 GLN I 208 GLN ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 312 GLN I 384 ASN N 25 HIS N 73 HIS ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 ASN Y 68 HIS Y 87 ASN Z 63 GLN ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 90 GLN V 39 HIS V 42 HIS ** i 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 HIS ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 HIS G 277 GLN G 364 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 GLN C 522 ASN ** C 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 GLN C 606 HIS C 716 GLN T 117 GLN ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 209 ASN T 254 GLN T 291 HIS F 54 GLN ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 HIS O 77 ASN O 149 ASN P 77 ASN P 92 ASN ** U 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 ASN U 134 HIS ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN E 166 HIS X 102 GLN Q 35 ASN o 77 ASN o 103 ASN ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 221 ASN q 33 ASN q 99 ASN ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 135 HIS ** q 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 GLN ** 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 212 GLN q 218 ASN ** p 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 72 HIS ** p 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 241 GLN z 388 GLN z 415 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5167 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.283 50643 Z= 0.586 Angle : 1.740 51.529 68619 Z= 1.109 Chirality : 0.333 6.797 7612 Planarity : 0.006 0.103 8730 Dihedral : 9.369 172.922 7110 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 25.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.61 % Favored : 92.28 % Rotamer: Outliers : 4.78 % Allowed : 17.80 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.60 (0.10), residues: 6177 helix: -0.80 (0.09), residues: 2782 sheet: -2.47 (0.25), residues: 377 loop : -2.56 (0.10), residues: 3018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 231 HIS 0.027 0.002 HIS G 154 PHE 0.032 0.002 PHE R 60 TYR 0.027 0.002 TYR c 49 ARG 0.009 0.001 ARG H 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1070 time to evaluate : 5.582 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: A 360 MET cc_start: 0.5553 (mmm) cc_final: 0.4186 (mtp) REVERT: A 447 ILE cc_start: 0.4125 (mt) cc_final: 0.3746 (mt) REVERT: I 148 MET cc_start: 0.7407 (ttp) cc_final: 0.6834 (ttp) REVERT: I 181 ILE cc_start: 0.7591 (mt) cc_final: 0.7157 (tp) REVERT: I 209 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.6977 (tt) REVERT: I 276 ASN cc_start: 0.7286 (t0) cc_final: 0.7036 (t0) REVERT: I 290 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7698 (pt) REVERT: I 292 GLN cc_start: 0.3667 (mm110) cc_final: 0.3410 (mp10) REVERT: I 401 ILE cc_start: 0.7202 (mm) cc_final: 0.6716 (tp) REVERT: I 411 PHE cc_start: 0.5665 (OUTLIER) cc_final: 0.4618 (t80) REVERT: I 438 PHE cc_start: 0.3136 (OUTLIER) cc_final: 0.2103 (t80) REVERT: I 471 MET cc_start: 0.5826 (mtm) cc_final: 0.5595 (mtm) REVERT: J 2 MET cc_start: 0.1629 (tmm) cc_final: 0.0555 (ttt) REVERT: N 53 PHE cc_start: 0.5412 (m-80) cc_final: 0.4695 (m-80) REVERT: N 126 VAL cc_start: 0.6288 (OUTLIER) cc_final: 0.6036 (p) REVERT: Y 85 TYR cc_start: 0.4470 (m-80) cc_final: 0.3316 (m-80) REVERT: S 100 GLU cc_start: 0.7964 (tt0) cc_final: 0.7437 (tm-30) REVERT: i 18 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6669 (ttm) REVERT: i 19 TYR cc_start: 0.3881 (OUTLIER) cc_final: 0.2827 (p90) REVERT: i 29 MET cc_start: 0.5304 (ppp) cc_final: 0.4972 (ppp) REVERT: j 23 GLU cc_start: 0.5954 (tm-30) cc_final: 0.5486 (tm-30) REVERT: j 25 MET cc_start: 0.7543 (tpp) cc_final: 0.6887 (tpp) REVERT: C 178 GLU cc_start: 0.6366 (pt0) cc_final: 0.6163 (pt0) REVERT: C 186 MET cc_start: 0.6269 (tmm) cc_final: 0.6006 (tmm) REVERT: C 214 VAL cc_start: 0.4483 (t) cc_final: 0.4178 (m) REVERT: C 453 MET cc_start: 0.6558 (mmp) cc_final: 0.6356 (mmp) REVERT: T 170 VAL cc_start: 0.5342 (m) cc_final: 0.5074 (p) REVERT: F 111 TRP cc_start: 0.6967 (m100) cc_final: 0.6299 (m100) REVERT: F 131 ARG cc_start: 0.4472 (OUTLIER) cc_final: 0.4007 (mmt90) REVERT: B 180 MET cc_start: 0.4978 (tmm) cc_final: 0.4513 (tmm) REVERT: O 82 LEU cc_start: 0.6833 (pp) cc_final: 0.6544 (pp) REVERT: R 76 MET cc_start: 0.6123 (mtp) cc_final: 0.5899 (ttm) REVERT: D 198 GLU cc_start: 0.5204 (tm-30) cc_final: 0.4952 (tm-30) REVERT: X 62 GLN cc_start: 0.4878 (mm110) cc_final: 0.3547 (mt0) REVERT: q 8 PHE cc_start: 0.5112 (OUTLIER) cc_final: 0.4859 (t80) REVERT: q 16 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6806 (mmp80) REVERT: q 57 LYS cc_start: 0.4420 (mmtt) cc_final: 0.3989 (ttmm) REVERT: q 112 ASN cc_start: 0.1995 (t0) cc_final: 0.1225 (m-40) REVERT: q 141 ASP cc_start: 0.4743 (t0) cc_final: 0.4413 (m-30) REVERT: q 191 LYS cc_start: 0.4907 (tptp) cc_final: 0.4417 (mmtm) REVERT: p 14 TRP cc_start: 0.5969 (m-10) cc_final: 0.5400 (t60) REVERT: p 50 ASP cc_start: 0.3636 (m-30) cc_final: 0.3293 (m-30) REVERT: p 153 ASP cc_start: 0.3825 (t0) cc_final: 0.3501 (t0) REVERT: z 107 GLU cc_start: 0.6216 (OUTLIER) cc_final: 0.4826 (mm-30) REVERT: z 182 LYS cc_start: 0.1111 (OUTLIER) cc_final: 0.0492 (pttt) REVERT: z 381 ASP cc_start: 0.1601 (t0) cc_final: 0.1381 (t0) REVERT: z 415 GLN cc_start: 0.6463 (mm110) cc_final: 0.5507 (tt0) REVERT: z 516 MET cc_start: 0.0704 (ppp) cc_final: 0.0052 (ppp) outliers start: 253 outliers final: 124 residues processed: 1236 average time/residue: 0.5922 time to fit residues: 1221.7441 Evaluate side-chains 991 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 855 time to evaluate : 5.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 409 SER Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 415 PHE Chi-restraints excluded: chain I residue 438 PHE Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 486 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 178 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain Y residue 19 THR Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain S residue 34 GLU Chi-restraints excluded: chain S residue 61 SER Chi-restraints excluded: chain S residue 108 ASP Chi-restraints excluded: chain i residue 18 MET Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 28 TYR Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 304 LEU Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain G residue 370 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 654 TRP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 256 VAL Chi-restraints excluded: chain T residue 286 ASP Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain c residue 41 THR Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain o residue 80 LEU Chi-restraints excluded: chain o residue 133 THR Chi-restraints excluded: chain o residue 146 LEU Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 8 PHE Chi-restraints excluded: chain q residue 16 ARG Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 131 SER Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain q residue 201 SER Chi-restraints excluded: chain p residue 83 CYS Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 125 ASN Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain z residue 107 GLU Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 182 LYS Chi-restraints excluded: chain z residue 284 LEU Chi-restraints excluded: chain z residue 317 HIS Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 337 VAL Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 393 THR Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 540 THR Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 306 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 459 optimal weight: 4.9990 chunk 375 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 553 optimal weight: 30.0000 chunk 597 optimal weight: 6.9990 chunk 492 optimal weight: 30.0000 chunk 548 optimal weight: 9.9990 chunk 188 optimal weight: 3.9990 chunk 443 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 ASN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 322 GLN K 27 ASN ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 ASN ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 90 GLN ** i 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 GLN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 94 GLN ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 291 HIS ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN U 41 GLN U 45 HIS ** U 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 88 GLN E 121 GLN E 207 ASN ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 45 ASN ** X 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 184 ASN ** q 202 GLN ** 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 30 GLN ** p 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 107 HIS p 212 GLN ** z 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 119 HIS z 190 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5618 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.303 50643 Z= 0.634 Angle : 1.752 51.176 68619 Z= 1.117 Chirality : 0.328 6.473 7612 Planarity : 0.006 0.069 8730 Dihedral : 8.713 175.295 7069 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 29.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.39 % Favored : 91.48 % Rotamer: Outliers : 5.80 % Allowed : 20.71 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.32 % Twisted General : 0.02 % 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: -2.44 (0.10), residues: 6177 helix: -0.71 (0.09), residues: 2736 sheet: -2.22 (0.25), residues: 396 loop : -2.42 (0.10), residues: 3045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP K 19 HIS 0.019 0.002 HIS G 154 PHE 0.033 0.003 PHE E 212 TYR 0.035 0.003 TYR T 180 ARG 0.028 0.001 ARG F 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1255 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 948 time to evaluate : 5.794 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: I 209 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.6991 (tt) REVERT: I 214 THR cc_start: 0.5336 (OUTLIER) cc_final: 0.5133 (p) REVERT: I 290 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7694 (pt) REVERT: I 401 ILE cc_start: 0.7230 (mm) cc_final: 0.6757 (tp) REVERT: J 2 MET cc_start: 0.1891 (tmm) cc_final: 0.0909 (ttt) REVERT: H 76 MET cc_start: 0.5455 (ppp) cc_final: 0.5033 (tmm) REVERT: K 31 MET cc_start: 0.6131 (tpt) cc_final: 0.5558 (tpt) REVERT: K 40 LEU cc_start: 0.3929 (tt) cc_final: 0.3639 (tt) REVERT: K 44 SER cc_start: 0.7287 (OUTLIER) cc_final: 0.6898 (t) REVERT: Y 27 MET cc_start: 0.6023 (mmt) cc_final: 0.4871 (ptp) REVERT: Z 49 MET cc_start: 0.2035 (tpp) cc_final: 0.1493 (tpp) REVERT: Z 139 ARG cc_start: 0.3809 (tpp-160) cc_final: 0.3329 (mmp80) REVERT: V 22 MET cc_start: 0.5951 (mtp) cc_final: 0.5138 (ptm) REVERT: V 24 ASN cc_start: 0.5233 (OUTLIER) cc_final: 0.4917 (t0) REVERT: S 100 GLU cc_start: 0.7906 (tt0) cc_final: 0.7588 (tm-30) REVERT: i 18 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6594 (ttm) REVERT: i 19 TYR cc_start: 0.4385 (OUTLIER) cc_final: 0.3248 (p90) REVERT: i 66 LYS cc_start: 0.7395 (pptt) cc_final: 0.7051 (ptpp) REVERT: j 25 MET cc_start: 0.7461 (tpp) cc_final: 0.6955 (tpp) REVERT: G 14 ASN cc_start: 0.7806 (m-40) cc_final: 0.7457 (t0) REVERT: G 257 CYS cc_start: 0.7718 (m) cc_final: 0.7286 (m) REVERT: C 316 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8533 (tp) REVERT: C 458 ILE cc_start: 0.7814 (mm) cc_final: 0.7610 (mm) REVERT: C 742 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6180 (mp) REVERT: T 297 MET cc_start: 0.5917 (ttp) cc_final: 0.5648 (ttt) REVERT: F 18 TRP cc_start: 0.6249 (m-10) cc_final: 0.6010 (m-10) REVERT: F 75 TYR cc_start: 0.7954 (m-80) cc_final: 0.7673 (m-80) REVERT: B 132 THR cc_start: 0.5497 (OUTLIER) cc_final: 0.5037 (m) REVERT: B 211 GLU cc_start: 0.5052 (tp30) cc_final: 0.4831 (tp30) REVERT: O 82 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6658 (pp) REVERT: R 76 MET cc_start: 0.6057 (mtp) cc_final: 0.5778 (ttm) REVERT: E 141 LYS cc_start: 0.7737 (ttpt) cc_final: 0.7150 (mptt) REVERT: X 96 ARG cc_start: 0.6557 (ttp80) cc_final: 0.6204 (ptt-90) REVERT: X 99 ILE cc_start: 0.3799 (OUTLIER) cc_final: 0.3388 (tt) REVERT: c 43 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7501 (mm) REVERT: k 116 TYR cc_start: 0.4621 (t80) cc_final: 0.4278 (t80) REVERT: o 172 THR cc_start: 0.7764 (p) cc_final: 0.7309 (p) REVERT: o 246 LYS cc_start: 0.5702 (mmpt) cc_final: 0.5094 (mmtm) REVERT: q 57 LYS cc_start: 0.4253 (mmtt) cc_final: 0.3607 (ttmm) REVERT: q 141 ASP cc_start: 0.5049 (t0) cc_final: 0.4606 (m-30) REVERT: p 30 GLN cc_start: 0.5098 (OUTLIER) cc_final: 0.4896 (mp10) REVERT: z 182 LYS cc_start: 0.1159 (OUTLIER) cc_final: 0.0682 (pttt) REVERT: z 381 ASP cc_start: 0.2681 (t0) cc_final: 0.1960 (t0) REVERT: z 387 ILE cc_start: 0.2098 (tp) cc_final: 0.1879 (tp) REVERT: z 415 GLN cc_start: 0.6608 (mm110) cc_final: 0.5664 (tt0) REVERT: z 516 MET cc_start: 0.1166 (ppp) cc_final: 0.0568 (pmm) outliers start: 307 outliers final: 188 residues processed: 1156 average time/residue: 0.5694 time to fit residues: 1113.0802 Evaluate side-chains 1010 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 807 time to evaluate : 5.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 117 GLN Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 415 PHE Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 455 TRP Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 161 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain Y residue 19 THR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 81 CYS Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 42 HIS Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain S residue 34 GLU Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 61 SER Chi-restraints excluded: chain S residue 73 HIS Chi-restraints excluded: chain i residue 18 MET Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 321 SER Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain G residue 370 SER Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 654 TRP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 95 VAL Chi-restraints excluded: chain T residue 118 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 287 VAL Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 75 ASP Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 97 CYS Chi-restraints excluded: chain R residue 38 SER Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain U residue 33 CYS Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain X residue 99 ILE Chi-restraints excluded: chain c residue 41 THR Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain c residue 57 ILE Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 94 VAL Chi-restraints excluded: chain o residue 80 LEU Chi-restraints excluded: chain o residue 97 VAL Chi-restraints excluded: chain o residue 133 THR Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 40 SER Chi-restraints excluded: chain q residue 100 ILE Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 117 VAL Chi-restraints excluded: chain q residue 145 ILE Chi-restraints excluded: chain q residue 175 ILE Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain q residue 201 SER Chi-restraints excluded: chain p residue 30 GLN Chi-restraints excluded: chain p residue 99 ASN Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 125 ASN Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain p residue 175 ILE Chi-restraints excluded: chain p residue 192 LEU Chi-restraints excluded: chain p residue 209 ASN Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 112 VAL Chi-restraints excluded: chain z residue 182 LYS Chi-restraints excluded: chain z residue 183 GLU Chi-restraints excluded: chain z residue 255 ILE Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 393 THR Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 540 THR Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 546 optimal weight: 20.0000 chunk 415 optimal weight: 7.9990 chunk 287 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 263 optimal weight: 9.9990 chunk 371 optimal weight: 1.9990 chunk 555 optimal weight: 10.0000 chunk 587 optimal weight: 10.0000 chunk 290 optimal weight: 20.0000 chunk 526 optimal weight: 30.0000 chunk 158 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 441 GLN ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 ASN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 GLN ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 HIS ** i 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 GLN G 281 GLN C 66 HIS C 93 GLN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN C 407 ASN ** C 538 GLN ** 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 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 ASN ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 GLN U 73 HIS ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN E 145 GLN E 201 GLN ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 ASN ** c 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 GLN ** 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 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 212 GLN ** z 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 357 GLN z 388 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.254 50643 Z= 0.645 Angle : 1.759 51.028 68619 Z= 1.119 Chirality : 0.327 6.411 7612 Planarity : 0.006 0.069 8730 Dihedral : 8.632 179.784 7058 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 30.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.89 % Favored : 91.03 % Rotamer: Outliers : 6.63 % Allowed : 22.79 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.32 % Twisted General : 0.00 % 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: -2.44 (0.10), residues: 6177 helix: -0.72 (0.09), residues: 2711 sheet: -2.25 (0.24), residues: 404 loop : -2.40 (0.10), residues: 3062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP G 199 HIS 0.023 0.002 HIS z 317 PHE 0.039 0.003 PHE C 334 TYR 0.030 0.003 TYR T 180 ARG 0.025 0.001 ARG q 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1242 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 351 poor density : 891 time to evaluate : 6.127 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: A 360 MET cc_start: 0.6507 (mmm) cc_final: 0.5904 (mtp) REVERT: I 148 MET cc_start: 0.7093 (ttp) cc_final: 0.6808 (ttp) REVERT: I 209 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.6848 (tt) REVERT: I 214 THR cc_start: 0.5377 (OUTLIER) cc_final: 0.5152 (p) REVERT: I 272 SER cc_start: 0.8671 (p) cc_final: 0.8417 (p) REVERT: I 290 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7630 (pt) REVERT: I 401 ILE cc_start: 0.6887 (mm) cc_final: 0.6630 (tp) REVERT: I 471 MET cc_start: 0.6145 (mtm) cc_final: 0.5842 (mtm) REVERT: J 2 MET cc_start: 0.2079 (tmm) cc_final: 0.1331 (ttt) REVERT: N 57 TYR cc_start: 0.6169 (m-10) cc_final: 0.5696 (m-10) REVERT: H 13 ILE cc_start: 0.6066 (OUTLIER) cc_final: 0.5695 (mt) REVERT: H 76 MET cc_start: 0.5157 (ppp) cc_final: 0.4783 (tmm) REVERT: K 40 LEU cc_start: 0.4074 (tt) cc_final: 0.3802 (tt) REVERT: K 44 SER cc_start: 0.7325 (OUTLIER) cc_final: 0.6967 (t) REVERT: Y 27 MET cc_start: 0.6665 (mmt) cc_final: 0.5233 (ptp) REVERT: Z 49 MET cc_start: 0.2299 (tpp) cc_final: 0.1719 (tpp) REVERT: S 100 GLU cc_start: 0.8281 (tt0) cc_final: 0.7620 (tm-30) REVERT: i 19 TYR cc_start: 0.4993 (OUTLIER) cc_final: 0.3862 (p90) REVERT: j 25 MET cc_start: 0.7623 (tpp) cc_final: 0.7085 (tpp) REVERT: G 14 ASN cc_start: 0.8219 (m-40) cc_final: 0.7679 (t0) REVERT: C 81 TYR cc_start: 0.5072 (m-80) cc_final: 0.4834 (m-10) REVERT: C 316 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8563 (tp) REVERT: T 344 ILE cc_start: 0.6179 (OUTLIER) cc_final: 0.5581 (mt) REVERT: F 18 TRP cc_start: 0.6391 (m-10) cc_final: 0.6146 (m-10) REVERT: F 23 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: U 76 VAL cc_start: 0.3647 (OUTLIER) cc_final: 0.3442 (p) REVERT: U 78 TYR cc_start: 0.2489 (m-80) cc_final: 0.2270 (m-10) REVERT: E 87 MET cc_start: 0.8416 (tmm) cc_final: 0.8011 (tmm) REVERT: E 141 LYS cc_start: 0.7741 (ttpt) cc_final: 0.7066 (mptt) REVERT: E 205 LYS cc_start: 0.5634 (OUTLIER) cc_final: 0.5357 (pttt) REVERT: D 116 TYR cc_start: 0.3037 (m-80) cc_final: 0.2691 (m-10) REVERT: X 96 ARG cc_start: 0.7004 (ttp80) cc_final: 0.6219 (ptt-90) REVERT: Q 61 TRP cc_start: 0.3564 (m100) cc_final: 0.3290 (m-90) REVERT: o 172 THR cc_start: 0.7777 (OUTLIER) cc_final: 0.7447 (p) REVERT: o 246 LYS cc_start: 0.5819 (mmpt) cc_final: 0.5158 (mmtm) REVERT: q 57 LYS cc_start: 0.4424 (mmtt) cc_final: 0.2956 (tttp) REVERT: q 141 ASP cc_start: 0.4643 (t0) cc_final: 0.4328 (m-30) REVERT: p 192 LEU cc_start: 0.0369 (OUTLIER) cc_final: 0.0090 (mp) REVERT: p 194 ASP cc_start: 0.5665 (m-30) cc_final: 0.5345 (m-30) REVERT: z 182 LYS cc_start: 0.0511 (OUTLIER) cc_final: -0.0003 (pttt) REVERT: z 307 ASN cc_start: 0.3069 (p0) cc_final: 0.2403 (p0) REVERT: z 370 TYR cc_start: 0.2079 (t80) cc_final: 0.1433 (t80) REVERT: z 415 GLN cc_start: 0.6435 (mm110) cc_final: 0.5511 (tt0) REVERT: z 516 MET cc_start: 0.0922 (ppp) cc_final: 0.0426 (pmm) outliers start: 351 outliers final: 218 residues processed: 1137 average time/residue: 0.5808 time to fit residues: 1110.1262 Evaluate side-chains 1026 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 794 time to evaluate : 6.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain I residue 247 HIS Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 298 SER Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 336 CYS 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 486 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 161 CYS Chi-restraints excluded: chain H residue 178 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 42 HIS Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain S residue 34 GLU Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 61 SER Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain G residue 370 SER Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 654 TRP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 77 THR Chi-restraints excluded: chain T residue 95 VAL Chi-restraints excluded: chain T residue 118 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 286 ASP Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 344 ILE Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 75 ASP Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 41 THR Chi-restraints excluded: chain c residue 57 ILE Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 80 LEU Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 133 THR Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 172 THR Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 10 SER Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 175 ILE Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain q residue 201 SER Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 99 ASN Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 VAL Chi-restraints excluded: chain p residue 125 ASN Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain p residue 175 ILE Chi-restraints excluded: chain p residue 192 LEU Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 112 VAL Chi-restraints excluded: chain z residue 182 LYS Chi-restraints excluded: chain z residue 183 GLU Chi-restraints excluded: chain z residue 255 ILE Chi-restraints excluded: chain z residue 284 LEU Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 393 THR Chi-restraints excluded: chain z residue 403 ASP Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 409 HIS Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 446 VAL Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 540 THR Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 489 optimal weight: 4.9990 chunk 333 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 437 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 chunk 501 optimal weight: 9.9990 chunk 406 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 300 optimal weight: 20.0000 chunk 527 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 464 ASN N 22 ASN N 142 ASN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 ASN ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 35 HIS ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 373 HIS ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 538 GLN ** 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 86 GLN ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 ASN ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 GLN ** 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 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 110 HIS z 388 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.253 50643 Z= 0.627 Angle : 1.751 51.091 68619 Z= 1.116 Chirality : 0.327 6.410 7612 Planarity : 0.006 0.053 8730 Dihedral : 8.580 179.038 7052 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 31.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.49 % Favored : 90.42 % Rotamer: Outliers : 6.82 % Allowed : 24.20 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.32 % Twisted General : 0.00 % 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: -2.43 (0.10), residues: 6177 helix: -0.76 (0.09), residues: 2707 sheet: -2.19 (0.26), residues: 373 loop : -2.36 (0.10), residues: 3097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP p 80 HIS 0.010 0.002 HIS U 138 PHE 0.042 0.002 PHE N 49 TYR 0.036 0.002 TYR I 143 ARG 0.012 0.001 ARG E 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1230 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 361 poor density : 869 time to evaluate : 6.955 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: I 209 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.6937 (tt) REVERT: I 290 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7571 (pt) REVERT: I 310 MET cc_start: 0.3107 (OUTLIER) cc_final: 0.2683 (mpp) REVERT: J 2 MET cc_start: 0.2486 (tmm) cc_final: 0.2178 (ttt) REVERT: J 8 ILE cc_start: 0.4524 (pt) cc_final: 0.4221 (pt) REVERT: N 3 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5604 (mm) REVERT: N 53 PHE cc_start: 0.6282 (m-80) cc_final: 0.5983 (m-80) REVERT: K 40 LEU cc_start: 0.4277 (tt) cc_final: 0.3872 (tt) REVERT: K 64 LEU cc_start: 0.8409 (mm) cc_final: 0.8132 (mm) REVERT: Y 27 MET cc_start: 0.6870 (mmt) cc_final: 0.5530 (ptp) REVERT: Z 49 MET cc_start: 0.2701 (tpp) cc_final: 0.2277 (tpp) REVERT: S 100 GLU cc_start: 0.8343 (tt0) cc_final: 0.7843 (tm-30) REVERT: i 19 TYR cc_start: 0.4950 (OUTLIER) cc_final: 0.4095 (p90) REVERT: j 25 MET cc_start: 0.7589 (tpp) cc_final: 0.7128 (tpp) REVERT: G 47 LEU cc_start: 0.7725 (tp) cc_final: 0.7449 (tp) REVERT: G 314 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6739 (mm-30) REVERT: C 632 ASN cc_start: 0.7338 (p0) cc_final: 0.7014 (p0) REVERT: C 742 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6278 (mp) REVERT: T 180 TYR cc_start: 0.4797 (OUTLIER) cc_final: 0.4362 (t80) REVERT: T 344 ILE cc_start: 0.6694 (OUTLIER) cc_final: 0.6329 (mt) REVERT: F 18 TRP cc_start: 0.6525 (m-10) cc_final: 0.6251 (m-10) REVERT: F 70 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7090 (mtp85) REVERT: B 132 THR cc_start: 0.5388 (OUTLIER) cc_final: 0.5113 (m) REVERT: B 180 MET cc_start: 0.5593 (tmm) cc_final: 0.5260 (tmm) REVERT: O 131 ASN cc_start: 0.7101 (m110) cc_final: 0.6867 (m-40) REVERT: P 100 CYS cc_start: 0.5947 (t) cc_final: 0.4795 (t) REVERT: E 87 MET cc_start: 0.8432 (tmm) cc_final: 0.8200 (tmm) REVERT: D 80 LEU cc_start: 0.6804 (mt) cc_final: 0.6157 (tp) REVERT: D 100 LYS cc_start: 0.3765 (mttp) cc_final: 0.3456 (mmtt) REVERT: D 122 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.6171 (mtt180) REVERT: D 155 TYR cc_start: 0.5157 (t80) cc_final: 0.4848 (t80) REVERT: X 96 ARG cc_start: 0.6953 (ttp80) cc_final: 0.6175 (ptt-90) REVERT: k 87 MET cc_start: 0.0912 (ptt) cc_final: 0.0672 (ptt) REVERT: o 246 LYS cc_start: 0.5948 (mmpt) cc_final: 0.5296 (mmtm) REVERT: q 57 LYS cc_start: 0.4710 (mmtt) cc_final: 0.3156 (tttp) REVERT: q 141 ASP cc_start: 0.4765 (t0) cc_final: 0.4311 (m-30) REVERT: z 182 LYS cc_start: 0.0485 (OUTLIER) cc_final: 0.0111 (pttp) REVERT: z 370 TYR cc_start: 0.2127 (t80) cc_final: 0.1378 (t80) REVERT: z 415 GLN cc_start: 0.6569 (mm110) cc_final: 0.5495 (tt0) outliers start: 361 outliers final: 249 residues processed: 1121 average time/residue: 0.5981 time to fit residues: 1136.9049 Evaluate side-chains 1054 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 793 time to evaluate : 6.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 298 SER Chi-restraints excluded: chain I residue 310 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 336 CYS 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 486 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 148 TYR Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 161 CYS Chi-restraints excluded: chain H residue 178 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 194 CYS Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain K residue 2 ASP Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 42 HIS Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain S residue 34 GLU Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 73 HIS Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain G residue 14 ASN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain G residue 370 SER Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 410 CYS Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 472 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 553 LEU Chi-restraints excluded: chain C residue 654 TRP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 77 THR Chi-restraints excluded: chain T residue 83 TYR Chi-restraints excluded: chain T residue 95 VAL Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 118 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 180 TYR Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 211 LEU Chi-restraints excluded: chain T residue 286 ASP Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 344 ILE Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain F residue 9 TYR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 75 ASP Chi-restraints excluded: chain P residue 97 CYS Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 41 THR Chi-restraints excluded: chain c residue 57 ILE Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 38 ASP Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain n residue 94 VAL Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 133 THR Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 172 THR Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 10 SER Chi-restraints excluded: chain q residue 39 LEU Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 122 ILE Chi-restraints excluded: chain q residue 147 MET Chi-restraints excluded: chain q residue 175 ILE Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain q residue 201 SER Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 67 VAL Chi-restraints excluded: chain p residue 91 THR Chi-restraints excluded: chain p residue 99 ASN Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 VAL Chi-restraints excluded: chain p residue 125 ASN Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain p residue 135 HIS Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain p residue 175 ILE Chi-restraints excluded: chain p residue 209 ASN Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 112 VAL Chi-restraints excluded: chain z residue 182 LYS Chi-restraints excluded: chain z residue 183 GLU Chi-restraints excluded: chain z residue 242 VAL Chi-restraints excluded: chain z residue 255 ILE Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 393 THR Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 409 HIS Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 446 VAL Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 540 THR Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 197 optimal weight: 6.9990 chunk 529 optimal weight: 20.0000 chunk 116 optimal weight: 0.9990 chunk 345 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 588 optimal weight: 8.9990 chunk 488 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 308 optimal weight: 0.0470 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 384 ASN ** N 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 ASN ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 68 ASN ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 HIS i 35 HIS j 47 HIS G 48 HIS ** G 80 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 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 538 GLN ** 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 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 GLN ** 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 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 317 HIS z 388 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5996 moved from start: 0.7269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.255 50643 Z= 0.627 Angle : 1.750 51.082 68619 Z= 1.114 Chirality : 0.326 6.393 7612 Planarity : 0.006 0.083 8730 Dihedral : 8.614 175.836 7052 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 31.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.78 % Favored : 90.14 % Rotamer: Outliers : 6.70 % Allowed : 25.20 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.32 % Twisted General : 0.00 % 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: -2.43 (0.10), residues: 6177 helix: -0.75 (0.09), residues: 2687 sheet: -2.23 (0.25), residues: 383 loop : -2.35 (0.10), residues: 3107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP K 19 HIS 0.015 0.002 HIS z 317 PHE 0.054 0.003 PHE D 185 TYR 0.025 0.002 TYR E 106 ARG 0.009 0.001 ARG G 352 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1210 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 855 time to evaluate : 5.907 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: A 172 MET cc_start: 0.5775 (ttp) cc_final: 0.5217 (ttp) REVERT: A 354 ILE cc_start: 0.3469 (OUTLIER) cc_final: 0.2839 (tp) REVERT: A 366 LYS cc_start: 0.4263 (mmtm) cc_final: 0.3832 (mtpp) REVERT: A 417 MET cc_start: 0.3413 (mmm) cc_final: 0.2421 (mmt) REVERT: I 209 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6890 (tt) REVERT: I 248 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6599 (ptp) REVERT: I 290 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7619 (pt) REVERT: I 298 SER cc_start: 0.7095 (OUTLIER) cc_final: 0.6649 (m) REVERT: I 401 ILE cc_start: 0.7565 (mm) cc_final: 0.7301 (mm) REVERT: I 471 MET cc_start: 0.6392 (mtm) cc_final: 0.6066 (mtm) REVERT: H 27 GLU cc_start: 0.6525 (mm-30) cc_final: 0.6069 (mm-30) REVERT: H 74 PHE cc_start: 0.4750 (p90) cc_final: 0.3981 (p90) REVERT: H 289 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6901 (mtp85) REVERT: H 293 ASP cc_start: 0.7915 (t0) cc_final: 0.7690 (t0) REVERT: K 64 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8244 (mm) REVERT: W 4 MET cc_start: 0.3009 (tmm) cc_final: 0.2804 (tmm) REVERT: S 100 GLU cc_start: 0.8277 (tt0) cc_final: 0.7645 (pt0) REVERT: i 19 TYR cc_start: 0.4959 (OUTLIER) cc_final: 0.4199 (p90) REVERT: j 25 MET cc_start: 0.7592 (tpp) cc_final: 0.7191 (tpp) REVERT: G 44 ILE cc_start: 0.7504 (mm) cc_final: 0.6905 (mm) REVERT: G 47 LEU cc_start: 0.7748 (tp) cc_final: 0.7446 (tp) REVERT: C 53 ILE cc_start: 0.7022 (mm) cc_final: 0.6395 (mt) REVERT: C 632 ASN cc_start: 0.7405 (p0) cc_final: 0.7152 (p0) REVERT: C 634 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7560 (tt0) REVERT: C 742 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6371 (mp) REVERT: T 180 TYR cc_start: 0.4653 (OUTLIER) cc_final: 0.4026 (t80) REVERT: T 300 MET cc_start: 0.6514 (OUTLIER) cc_final: 0.5906 (ttp) REVERT: T 344 ILE cc_start: 0.6684 (OUTLIER) cc_final: 0.6349 (mt) REVERT: T 373 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: T 378 LEU cc_start: 0.7480 (mt) cc_final: 0.6264 (pp) REVERT: F 18 TRP cc_start: 0.6680 (m-10) cc_final: 0.6413 (m-10) REVERT: B 132 THR cc_start: 0.5348 (OUTLIER) cc_final: 0.5120 (m) REVERT: B 239 THR cc_start: 0.5014 (OUTLIER) cc_final: 0.4450 (t) REVERT: O 68 SER cc_start: 0.8139 (OUTLIER) cc_final: 0.7720 (p) REVERT: P 89 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6491 (mt) REVERT: E 87 MET cc_start: 0.8473 (tmm) cc_final: 0.7842 (tmm) REVERT: E 141 LYS cc_start: 0.7698 (ttpt) cc_final: 0.7174 (mptt) REVERT: D 80 LEU cc_start: 0.6928 (mt) cc_final: 0.6329 (tp) REVERT: D 122 ARG cc_start: 0.6731 (OUTLIER) cc_final: 0.6019 (mtt180) REVERT: D 182 ASN cc_start: 0.3610 (m-40) cc_final: 0.3375 (t0) REVERT: X 80 PHE cc_start: 0.7273 (m-80) cc_final: 0.6932 (m-10) REVERT: X 96 ARG cc_start: 0.6966 (ttp80) cc_final: 0.6253 (ptt-90) REVERT: Q 79 GLU cc_start: 0.2735 (tm-30) cc_final: 0.2208 (mp0) REVERT: o 246 LYS cc_start: 0.6383 (mmpt) cc_final: 0.5520 (mttp) REVERT: q 57 LYS cc_start: 0.4574 (mmtt) cc_final: 0.2952 (tttp) REVERT: q 141 ASP cc_start: 0.4856 (t0) cc_final: 0.4436 (m-30) REVERT: p 199 PHE cc_start: 0.5386 (t80) cc_final: 0.4841 (t80) REVERT: z 415 GLN cc_start: 0.6577 (mm110) cc_final: 0.5519 (tt0) outliers start: 355 outliers final: 246 residues processed: 1108 average time/residue: 0.5821 time to fit residues: 1088.7841 Evaluate side-chains 1053 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 788 time to evaluate : 5.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain I residue 248 MET Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 298 SER Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 336 CYS Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 461 MET Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain I residue 486 LEU Chi-restraints excluded: chain J residue 10 ILE Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 148 TYR Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 161 CYS Chi-restraints excluded: chain H residue 178 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 194 CYS Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 42 HIS Chi-restraints excluded: chain V residue 46 ASP Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 73 HIS Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain j residue 45 LEU Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain G residue 14 ASN Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 145 TYR Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain G residue 370 SER Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 472 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 634 GLU Chi-restraints excluded: chain C residue 654 TRP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 77 THR Chi-restraints excluded: chain T residue 83 TYR Chi-restraints excluded: chain T residue 95 VAL Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 118 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 TYR Chi-restraints excluded: chain T residue 286 ASP Chi-restraints excluded: chain T residue 300 MET Chi-restraints excluded: chain T residue 307 TYR Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 344 ILE Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 97 CYS Chi-restraints excluded: chain R residue 103 MET Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain U residue 36 ASP Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 41 THR Chi-restraints excluded: chain c residue 57 ILE Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 ASP Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain n residue 94 VAL Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 133 THR Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 10 SER Chi-restraints excluded: chain q residue 39 LEU Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 122 ILE Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain q residue 201 SER Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 67 VAL Chi-restraints excluded: chain p residue 91 THR Chi-restraints excluded: chain p residue 99 ASN Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 VAL Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain p residue 175 ILE Chi-restraints excluded: chain p residue 209 ASN Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 112 VAL Chi-restraints excluded: chain z residue 183 GLU Chi-restraints excluded: chain z residue 242 VAL Chi-restraints excluded: chain z residue 255 ILE Chi-restraints excluded: chain z residue 284 LEU Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 393 THR Chi-restraints excluded: chain z residue 403 ASP Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 409 HIS Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 446 VAL Chi-restraints excluded: chain z residue 485 ILE Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 540 THR Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 567 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 335 optimal weight: 4.9990 chunk 429 optimal weight: 0.8980 chunk 332 optimal weight: 5.9990 chunk 495 optimal weight: 9.9990 chunk 328 optimal weight: 8.9990 chunk 586 optimal weight: 20.0000 chunk 366 optimal weight: 0.8980 chunk 357 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN K 45 ASN ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 HIS ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 35 HIS ** G 80 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 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 GLN ** 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 254 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 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 80 ASN k 118 HIS ** o 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 GLN ** 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 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 218 ASN z 592 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 moved from start: 0.7535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.254 50643 Z= 0.590 Angle : 1.730 50.925 68619 Z= 1.104 Chirality : 0.326 6.359 7612 Planarity : 0.005 0.091 8730 Dihedral : 8.408 175.391 7048 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 28.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.69 % Favored : 91.23 % Rotamer: Outliers : 5.66 % Allowed : 26.66 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.22 (0.10), residues: 6177 helix: -0.54 (0.10), residues: 2680 sheet: -2.23 (0.24), residues: 399 loop : -2.25 (0.11), residues: 3098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP K 19 HIS 0.008 0.001 HIS U 138 PHE 0.043 0.002 PHE D 185 TYR 0.051 0.002 TYR D 155 ARG 0.014 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1153 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 853 time to evaluate : 5.743 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: A 172 MET cc_start: 0.5689 (ttp) cc_final: 0.5140 (ttp) REVERT: A 354 ILE cc_start: 0.3393 (OUTLIER) cc_final: 0.2907 (tp) REVERT: A 417 MET cc_start: 0.3358 (mmm) cc_final: 0.2497 (mmt) REVERT: I 209 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6876 (tt) REVERT: I 290 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7654 (pt) REVERT: I 298 SER cc_start: 0.7032 (OUTLIER) cc_final: 0.6583 (m) REVERT: I 401 ILE cc_start: 0.7310 (mm) cc_final: 0.6771 (tp) REVERT: I 471 MET cc_start: 0.6364 (mtm) cc_final: 0.6137 (mtm) REVERT: H 27 GLU cc_start: 0.6255 (mm-30) cc_final: 0.6044 (mm-30) REVERT: H 74 PHE cc_start: 0.4517 (p90) cc_final: 0.3726 (p90) REVERT: H 289 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6867 (mtp85) REVERT: H 293 ASP cc_start: 0.8054 (t0) cc_final: 0.7443 (t0) REVERT: K 31 MET cc_start: 0.5565 (tpt) cc_final: 0.4720 (tpt) REVERT: K 64 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8167 (mm) REVERT: V 18 MET cc_start: 0.4456 (mtp) cc_final: 0.4176 (ttp) REVERT: V 49 MET cc_start: 0.4159 (ptt) cc_final: 0.3851 (ttm) REVERT: S 34 GLU cc_start: 0.6644 (mp0) cc_final: 0.6117 (mt-10) REVERT: S 100 GLU cc_start: 0.7972 (tt0) cc_final: 0.7698 (pt0) REVERT: i 19 TYR cc_start: 0.5121 (OUTLIER) cc_final: 0.4215 (p90) REVERT: j 25 MET cc_start: 0.7592 (tpp) cc_final: 0.7213 (tpp) REVERT: G 44 ILE cc_start: 0.7577 (mm) cc_final: 0.6902 (mm) REVERT: G 223 MET cc_start: 0.6284 (mtt) cc_final: 0.6068 (mtt) REVERT: C 53 ILE cc_start: 0.7073 (mm) cc_final: 0.6489 (mt) REVERT: C 348 MET cc_start: 0.3187 (mmm) cc_final: 0.2924 (mmm) REVERT: C 742 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6231 (mp) REVERT: T 180 TYR cc_start: 0.4349 (OUTLIER) cc_final: 0.3398 (t80) REVERT: T 300 MET cc_start: 0.6282 (OUTLIER) cc_final: 0.5394 (ttt) REVERT: T 312 PHE cc_start: 0.3235 (m-80) cc_final: 0.2840 (m-10) REVERT: T 344 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.6416 (mt) REVERT: T 373 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.7030 (m-80) REVERT: F 18 TRP cc_start: 0.6777 (m-10) cc_final: 0.6512 (m-10) REVERT: F 116 TRP cc_start: 0.7405 (t60) cc_final: 0.6840 (t60) REVERT: F 118 MET cc_start: 0.7799 (mmp) cc_final: 0.7426 (mmt) REVERT: B 132 THR cc_start: 0.5091 (OUTLIER) cc_final: 0.4876 (m) REVERT: O 68 SER cc_start: 0.8016 (OUTLIER) cc_final: 0.7667 (p) REVERT: P 89 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6473 (mt) REVERT: E 87 MET cc_start: 0.8370 (tmm) cc_final: 0.7667 (tmm) REVERT: E 120 ARG cc_start: 0.6717 (mmt180) cc_final: 0.5395 (mtt90) REVERT: E 141 LYS cc_start: 0.7712 (ttpt) cc_final: 0.7151 (mptt) REVERT: E 203 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7070 (tt0) REVERT: E 205 LYS cc_start: 0.6230 (OUTLIER) cc_final: 0.6026 (pttt) REVERT: X 54 GLN cc_start: 0.5806 (pp30) cc_final: 0.5461 (mm-40) REVERT: X 55 LEU cc_start: 0.4308 (OUTLIER) cc_final: 0.3751 (mm) REVERT: X 80 PHE cc_start: 0.7299 (m-80) cc_final: 0.6994 (m-10) REVERT: X 96 ARG cc_start: 0.6773 (ttp80) cc_final: 0.6117 (ptt-90) REVERT: Q 79 GLU cc_start: 0.2978 (tm-30) cc_final: 0.2586 (mp0) REVERT: n 91 VAL cc_start: 0.8610 (t) cc_final: 0.8387 (p) REVERT: o 246 LYS cc_start: 0.6623 (mmpt) cc_final: 0.5815 (mttp) REVERT: q 141 ASP cc_start: 0.4677 (t70) cc_final: 0.4447 (m-30) REVERT: p 199 PHE cc_start: 0.5104 (t80) cc_final: 0.4461 (t80) REVERT: z 415 GLN cc_start: 0.6571 (mm110) cc_final: 0.5511 (tt0) outliers start: 300 outliers final: 225 residues processed: 1068 average time/residue: 0.5829 time to fit residues: 1053.1886 Evaluate side-chains 1018 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 775 time to evaluate : 6.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 298 SER Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 459 GLU Chi-restraints excluded: chain I residue 461 MET Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain I residue 486 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 148 TYR Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 161 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 194 CYS Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain Y residue 32 GLU Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 42 HIS Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain S residue 73 HIS Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain j residue 45 LEU Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain G residue 14 ASN Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 370 SER Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 654 TRP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 77 THR Chi-restraints excluded: chain T residue 83 TYR Chi-restraints excluded: chain T residue 95 VAL Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 118 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 180 TYR Chi-restraints excluded: chain T residue 286 ASP Chi-restraints excluded: chain T residue 300 MET Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 344 ILE Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 75 ASP Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 97 CYS Chi-restraints excluded: chain R residue 103 MET Chi-restraints excluded: chain U residue 36 ASP Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain X residue 55 LEU Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 57 ILE Chi-restraints excluded: chain c residue 75 MET Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 ASP Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain n residue 94 VAL Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 133 THR Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 39 LEU Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 122 ILE Chi-restraints excluded: chain q residue 131 SER Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain q residue 201 SER Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 91 THR Chi-restraints excluded: chain p residue 99 ASN Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 VAL Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain p residue 155 VAL Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain p residue 175 ILE Chi-restraints excluded: chain p residue 209 ASN Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 112 VAL Chi-restraints excluded: chain z residue 183 GLU Chi-restraints excluded: chain z residue 242 VAL Chi-restraints excluded: chain z residue 284 LEU Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 333 THR Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 403 ASP Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 409 HIS Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 446 VAL Chi-restraints excluded: chain z residue 475 GLU Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 540 THR Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 362 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 349 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 372 optimal weight: 9.9990 chunk 399 optimal weight: 0.1980 chunk 289 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 460 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 ASN Y 10 ASN ** Y 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 35 HIS ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 HIS ** C 559 GLN ** 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 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN ** X 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 118 HIS o 55 GLN ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 GLN ** 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 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 592 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 moved from start: 0.7694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.255 50643 Z= 0.580 Angle : 1.722 50.833 68619 Z= 1.100 Chirality : 0.326 6.344 7612 Planarity : 0.005 0.089 8730 Dihedral : 8.170 174.930 7048 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 26.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.39 % Favored : 91.53 % Rotamer: Outliers : 4.87 % Allowed : 27.58 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.06 (0.10), residues: 6177 helix: -0.39 (0.10), residues: 2687 sheet: -2.29 (0.24), residues: 407 loop : -2.15 (0.11), residues: 3083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP K 19 HIS 0.017 0.001 HIS U 138 PHE 0.031 0.002 PHE D 185 TYR 0.030 0.002 TYR D 86 ARG 0.015 0.001 ARG Q 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 850 time to evaluate : 5.414 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: A 122 TRP cc_start: 0.5245 (m-10) cc_final: 0.4827 (m-10) REVERT: A 125 MET cc_start: 0.5034 (mmm) cc_final: 0.4820 (mmm) REVERT: A 172 MET cc_start: 0.5537 (ttp) cc_final: 0.5111 (ttp) REVERT: A 354 ILE cc_start: 0.3542 (OUTLIER) cc_final: 0.3199 (tp) REVERT: I 209 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6919 (tt) REVERT: I 290 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7584 (pt) REVERT: I 298 SER cc_start: 0.7006 (OUTLIER) cc_final: 0.6552 (m) REVERT: I 471 MET cc_start: 0.6404 (mtm) cc_final: 0.6155 (mtm) REVERT: N 171 MET cc_start: 0.4524 (OUTLIER) cc_final: 0.4011 (tmm) REVERT: H 74 PHE cc_start: 0.4268 (p90) cc_final: 0.3586 (p90) REVERT: K 31 MET cc_start: 0.5692 (tpt) cc_final: 0.4927 (tpt) REVERT: K 64 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8212 (mm) REVERT: V 18 MET cc_start: 0.4242 (mtp) cc_final: 0.3754 (ttp) REVERT: V 28 TYR cc_start: 0.6762 (OUTLIER) cc_final: 0.5143 (m-80) REVERT: V 49 MET cc_start: 0.4309 (ptt) cc_final: 0.3849 (ttm) REVERT: S 34 GLU cc_start: 0.6708 (mp0) cc_final: 0.6170 (mt-10) REVERT: S 100 GLU cc_start: 0.7996 (tt0) cc_final: 0.7723 (pt0) REVERT: i 19 TYR cc_start: 0.4967 (OUTLIER) cc_final: 0.4079 (p90) REVERT: j 25 MET cc_start: 0.7647 (tpp) cc_final: 0.7279 (tpp) REVERT: G 14 ASN cc_start: 0.8294 (m-40) cc_final: 0.7862 (t0) REVERT: G 44 ILE cc_start: 0.7582 (mm) cc_final: 0.6929 (mm) REVERT: G 197 ARG cc_start: 0.5532 (mtm110) cc_final: 0.5121 (mtm110) REVERT: G 223 MET cc_start: 0.6264 (mtt) cc_final: 0.5486 (mtt) REVERT: G 314 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6661 (mm-30) REVERT: C 53 ILE cc_start: 0.7216 (mm) cc_final: 0.6725 (mt) REVERT: C 373 HIS cc_start: 0.2980 (OUTLIER) cc_final: 0.2749 (m-70) REVERT: C 742 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6180 (mp) REVERT: T 180 TYR cc_start: 0.4070 (OUTLIER) cc_final: 0.3088 (t80) REVERT: T 300 MET cc_start: 0.6259 (OUTLIER) cc_final: 0.5324 (ttp) REVERT: T 312 PHE cc_start: 0.3290 (m-80) cc_final: 0.2916 (m-10) REVERT: T 344 ILE cc_start: 0.6611 (OUTLIER) cc_final: 0.6347 (mt) REVERT: F 70 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7254 (mtp85) REVERT: F 116 TRP cc_start: 0.7315 (t60) cc_final: 0.6841 (t60) REVERT: B 132 THR cc_start: 0.4693 (OUTLIER) cc_final: 0.4449 (m) REVERT: O 68 SER cc_start: 0.8025 (OUTLIER) cc_final: 0.7635 (p) REVERT: P 89 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7023 (mt) REVERT: E 87 MET cc_start: 0.8214 (tmm) cc_final: 0.7420 (tmm) REVERT: E 141 LYS cc_start: 0.7703 (ttpt) cc_final: 0.7193 (mptt) REVERT: E 205 LYS cc_start: 0.6526 (OUTLIER) cc_final: 0.6185 (pttp) REVERT: D 122 ARG cc_start: 0.6500 (OUTLIER) cc_final: 0.5973 (mtt180) REVERT: X 54 GLN cc_start: 0.5997 (pp30) cc_final: 0.5793 (mm-40) REVERT: X 55 LEU cc_start: 0.4272 (OUTLIER) cc_final: 0.3860 (mm) REVERT: X 80 PHE cc_start: 0.7387 (m-80) cc_final: 0.7036 (m-10) REVERT: X 96 ARG cc_start: 0.6737 (ttp80) cc_final: 0.5984 (ptt-90) REVERT: c 64 THR cc_start: 0.6702 (p) cc_final: 0.6481 (p) REVERT: Q 79 GLU cc_start: 0.3004 (tm-30) cc_final: 0.2537 (mp0) REVERT: o 246 LYS cc_start: 0.6621 (mmpt) cc_final: 0.5801 (mttp) REVERT: p 199 PHE cc_start: 0.5046 (t80) cc_final: 0.4405 (t80) REVERT: z 415 GLN cc_start: 0.6592 (mm110) cc_final: 0.5512 (tt0) outliers start: 258 outliers final: 198 residues processed: 1030 average time/residue: 0.5839 time to fit residues: 1014.8892 Evaluate side-chains 1000 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 782 time to evaluate : 6.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 298 SER Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 332 ILE Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 461 MET Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain I residue 486 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 148 TYR Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 161 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain Y residue 32 GLU Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain V residue 28 TYR Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 42 HIS Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain S residue 73 HIS Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain j residue 45 LEU Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 373 HIS Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 472 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 611 VAL Chi-restraints excluded: chain C residue 654 TRP Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 83 TYR Chi-restraints excluded: chain T residue 95 VAL Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 118 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain T residue 180 TYR Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 286 ASP Chi-restraints excluded: chain T residue 300 MET Chi-restraints excluded: chain T residue 307 TYR Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 344 ILE Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 169 GLN Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain X residue 55 LEU Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain c residue 75 MET Chi-restraints excluded: chain Q residue 38 ASP Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 80 LEU Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 133 THR Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 39 LEU Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 122 ILE Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain q residue 201 SER Chi-restraints excluded: chain p residue 91 THR Chi-restraints excluded: chain p residue 99 ASN Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 VAL Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain p residue 155 VAL Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain p residue 175 ILE Chi-restraints excluded: chain p residue 209 ASN Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 112 VAL Chi-restraints excluded: chain z residue 242 VAL Chi-restraints excluded: chain z residue 255 ILE Chi-restraints excluded: chain z residue 284 LEU Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 333 THR Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 403 ASP Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 409 HIS Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 540 THR Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 533 optimal weight: 20.0000 chunk 561 optimal weight: 3.9990 chunk 512 optimal weight: 20.0000 chunk 546 optimal weight: 8.9990 chunk 328 optimal weight: 6.9990 chunk 237 optimal weight: 2.9990 chunk 428 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 493 optimal weight: 4.9990 chunk 516 optimal weight: 5.9990 chunk 544 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 ASN ** Y 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 HIS ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 320 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 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 GLN ** 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 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 592 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.7943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.253 50643 Z= 0.595 Angle : 1.740 50.911 68619 Z= 1.107 Chirality : 0.326 6.381 7612 Planarity : 0.005 0.097 8730 Dihedral : 8.181 175.108 7047 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 28.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.23 % Favored : 90.69 % Rotamer: Outliers : 5.17 % Allowed : 27.51 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.06 (0.10), residues: 6177 helix: -0.41 (0.10), residues: 2661 sheet: -2.19 (0.24), residues: 405 loop : -2.14 (0.11), residues: 3111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP O 74 HIS 0.019 0.001 HIS G 312 PHE 0.036 0.002 PHE N 49 TYR 0.030 0.002 TYR c 34 ARG 0.011 0.001 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 787 time to evaluate : 5.967 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: A 172 MET cc_start: 0.5573 (ttp) cc_final: 0.5101 (ttp) REVERT: A 354 ILE cc_start: 0.3397 (OUTLIER) cc_final: 0.3048 (tp) REVERT: A 417 MET cc_start: 0.2758 (mmm) cc_final: 0.2205 (ptm) REVERT: I 209 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6931 (tt) REVERT: I 298 SER cc_start: 0.6954 (OUTLIER) cc_final: 0.6477 (m) REVERT: I 469 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8017 (tp) REVERT: I 471 MET cc_start: 0.6480 (mtm) cc_final: 0.6214 (mtm) REVERT: N 171 MET cc_start: 0.4446 (OUTLIER) cc_final: 0.3452 (ttp) REVERT: H 27 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6737 (mm-30) REVERT: H 74 PHE cc_start: 0.4371 (p90) cc_final: 0.3521 (p90) REVERT: H 144 MET cc_start: 0.7194 (mmm) cc_final: 0.6884 (mmm) REVERT: K 64 LEU cc_start: 0.8518 (mm) cc_final: 0.8256 (mm) REVERT: Z 34 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.6115 (ptp90) REVERT: V 28 TYR cc_start: 0.6839 (OUTLIER) cc_final: 0.5202 (m-80) REVERT: S 34 GLU cc_start: 0.6715 (mp0) cc_final: 0.6404 (mp0) REVERT: S 100 GLU cc_start: 0.7968 (tt0) cc_final: 0.7539 (pt0) REVERT: i 19 TYR cc_start: 0.5077 (OUTLIER) cc_final: 0.4186 (p90) REVERT: j 25 MET cc_start: 0.7721 (tpp) cc_final: 0.7467 (tpp) REVERT: G 14 ASN cc_start: 0.8479 (m-40) cc_final: 0.7907 (t0) REVERT: G 44 ILE cc_start: 0.7593 (mm) cc_final: 0.6962 (mm) REVERT: G 197 ARG cc_start: 0.5599 (mtm110) cc_final: 0.5004 (mmm160) REVERT: C 53 ILE cc_start: 0.7195 (mm) cc_final: 0.6788 (mt) REVERT: C 89 PHE cc_start: 0.6668 (OUTLIER) cc_final: 0.6465 (t80) REVERT: C 394 MET cc_start: 0.6323 (OUTLIER) cc_final: 0.4930 (ttp) REVERT: C 742 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6261 (mp) REVERT: T 180 TYR cc_start: 0.4326 (OUTLIER) cc_final: 0.3301 (t80) REVERT: T 300 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.5405 (ttp) REVERT: T 312 PHE cc_start: 0.2850 (m-80) cc_final: 0.2637 (m-10) REVERT: T 325 MET cc_start: 0.2320 (mmp) cc_final: 0.1977 (mmp) REVERT: T 344 ILE cc_start: 0.6740 (OUTLIER) cc_final: 0.6473 (mt) REVERT: T 373 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6863 (m-80) REVERT: F 70 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7178 (mtp85) REVERT: F 116 TRP cc_start: 0.7366 (t60) cc_final: 0.6968 (t60) REVERT: B 132 THR cc_start: 0.4894 (OUTLIER) cc_final: 0.4640 (m) REVERT: O 68 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7696 (p) REVERT: O 82 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7117 (pp) REVERT: P 89 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6603 (mt) REVERT: R 122 ASN cc_start: 0.7230 (t0) cc_final: 0.6897 (t0) REVERT: U 100 ILE cc_start: 0.2114 (OUTLIER) cc_final: 0.1832 (pt) REVERT: E 87 MET cc_start: 0.8352 (tmm) cc_final: 0.7385 (tmm) REVERT: E 120 ARG cc_start: 0.6696 (mmt180) cc_final: 0.5401 (mtt90) REVERT: E 141 LYS cc_start: 0.7704 (ttpt) cc_final: 0.7201 (mptt) REVERT: E 203 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7190 (tt0) REVERT: D 105 PRO cc_start: 0.4207 (Cg_exo) cc_final: 0.3864 (Cg_endo) REVERT: X 80 PHE cc_start: 0.7360 (m-80) cc_final: 0.7055 (m-10) REVERT: X 96 ARG cc_start: 0.6906 (ttp80) cc_final: 0.6098 (ptt-90) REVERT: Q 79 GLU cc_start: 0.3177 (tm-30) cc_final: 0.2641 (mp0) REVERT: n 91 VAL cc_start: 0.8651 (t) cc_final: 0.8424 (p) REVERT: o 246 LYS cc_start: 0.6645 (mmpt) cc_final: 0.5809 (mttp) REVERT: p 199 PHE cc_start: 0.5206 (t80) cc_final: 0.4471 (t80) outliers start: 274 outliers final: 215 residues processed: 981 average time/residue: 0.5840 time to fit residues: 964.0820 Evaluate side-chains 995 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 758 time to evaluate : 5.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 298 SER Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 332 ILE Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 459 GLU Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain I residue 486 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 148 TYR Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 161 CYS Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 178 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain K residue 2 ASP Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 45 ASN Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 34 ARG Chi-restraints excluded: chain V residue 28 TYR Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 42 HIS Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 73 HIS Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain j residue 45 LEU Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 145 TYR Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 472 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 611 VAL Chi-restraints excluded: chain C residue 654 TRP Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 83 TYR Chi-restraints excluded: chain T residue 95 VAL Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 118 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain T residue 180 TYR Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 286 ASP Chi-restraints excluded: chain T residue 300 MET Chi-restraints excluded: chain T residue 307 TYR Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 344 ILE Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 75 ASP Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 169 GLN Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 75 MET Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 38 ASP Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain n residue 94 VAL Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 80 LEU Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 133 THR Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 39 LEU Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 122 ILE Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain q residue 201 SER Chi-restraints excluded: chain p residue 91 THR Chi-restraints excluded: chain p residue 99 ASN Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 VAL Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain p residue 155 VAL Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain p residue 175 ILE Chi-restraints excluded: chain p residue 209 ASN Chi-restraints excluded: chain z residue 112 VAL Chi-restraints excluded: chain z residue 183 GLU Chi-restraints excluded: chain z residue 242 VAL Chi-restraints excluded: chain z residue 284 LEU Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 333 THR Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 393 THR Chi-restraints excluded: chain z residue 403 ASP Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 409 HIS Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 540 THR Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 358 optimal weight: 3.9990 chunk 577 optimal weight: 10.0000 chunk 352 optimal weight: 0.0370 chunk 273 optimal weight: 6.9990 chunk 401 optimal weight: 5.9990 chunk 605 optimal weight: 10.0000 chunk 557 optimal weight: 9.9990 chunk 482 optimal weight: 0.3980 chunk 50 optimal weight: 10.0000 chunk 372 optimal weight: 6.9990 chunk 295 optimal weight: 10.0000 overall best weight: 3.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 35 HIS ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 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** ** C 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 GLN ** 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 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 592 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 0.8242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.253 50643 Z= 0.607 Angle : 1.754 51.019 68619 Z= 1.113 Chirality : 0.326 6.397 7612 Planarity : 0.006 0.100 8730 Dihedral : 8.214 174.805 7044 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 30.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.76 % Favored : 90.14 % Rotamer: Outliers : 4.87 % Allowed : 27.98 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -2.16 (0.10), residues: 6177 helix: -0.49 (0.10), residues: 2650 sheet: -2.03 (0.25), residues: 383 loop : -2.23 (0.11), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP O 74 HIS 0.042 0.002 HIS G 23 PHE 0.038 0.002 PHE N 49 TYR 0.049 0.002 TYR c 34 ARG 0.009 0.001 ARG R 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 778 time to evaluate : 5.853 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 122 TRP cc_start: 0.5283 (m-10) cc_final: 0.4699 (m-10) REVERT: A 172 MET cc_start: 0.5541 (ttp) cc_final: 0.5061 (ttp) REVERT: A 354 ILE cc_start: 0.3414 (OUTLIER) cc_final: 0.3017 (tp) REVERT: A 417 MET cc_start: 0.3077 (mmm) cc_final: 0.2573 (ptm) REVERT: I 209 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6948 (tt) REVERT: I 469 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8063 (tp) REVERT: I 471 MET cc_start: 0.6579 (mtm) cc_final: 0.6285 (mtm) REVERT: J 2 MET cc_start: 0.3040 (ttp) cc_final: 0.2653 (ttp) REVERT: N 171 MET cc_start: 0.4546 (OUTLIER) cc_final: 0.3532 (ttp) REVERT: H 144 MET cc_start: 0.7381 (mmm) cc_final: 0.7167 (mmm) REVERT: K 64 LEU cc_start: 0.8599 (mm) cc_final: 0.8350 (mm) REVERT: Z 34 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6305 (ptp90) REVERT: S 34 GLU cc_start: 0.6739 (mp0) cc_final: 0.6481 (mp0) REVERT: i 19 TYR cc_start: 0.5236 (OUTLIER) cc_final: 0.4309 (p90) REVERT: G 14 ASN cc_start: 0.8461 (m-40) cc_final: 0.7841 (t0) REVERT: G 123 MET cc_start: 0.8246 (mmm) cc_final: 0.7853 (mmm) REVERT: G 314 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7074 (mm-30) REVERT: C 53 ILE cc_start: 0.7439 (mm) cc_final: 0.7132 (mt) REVERT: C 394 MET cc_start: 0.6446 (OUTLIER) cc_final: 0.5010 (ttp) REVERT: C 609 LYS cc_start: 0.6650 (mtmt) cc_final: 0.6131 (mmmm) REVERT: C 742 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.5989 (mt) REVERT: T 180 TYR cc_start: 0.4420 (OUTLIER) cc_final: 0.3595 (t80) REVERT: T 300 MET cc_start: 0.6296 (OUTLIER) cc_final: 0.5420 (ttp) REVERT: T 312 PHE cc_start: 0.3094 (m-80) cc_final: 0.2876 (m-10) REVERT: T 325 MET cc_start: 0.2232 (mmp) cc_final: 0.1871 (mmp) REVERT: T 344 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6382 (mt) REVERT: T 373 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.7021 (m-80) REVERT: F 116 TRP cc_start: 0.7451 (t60) cc_final: 0.7188 (t60) REVERT: B 132 THR cc_start: 0.4970 (OUTLIER) cc_final: 0.4651 (m) REVERT: O 68 SER cc_start: 0.8142 (OUTLIER) cc_final: 0.7772 (p) REVERT: P 89 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.6993 (mt) REVERT: R 122 ASN cc_start: 0.7277 (t0) cc_final: 0.6937 (t0) REVERT: U 100 ILE cc_start: 0.2270 (OUTLIER) cc_final: 0.1919 (pt) REVERT: E 107 ASP cc_start: 0.5171 (OUTLIER) cc_final: 0.4878 (p0) REVERT: E 120 ARG cc_start: 0.6706 (mmt180) cc_final: 0.5378 (mtt90) REVERT: E 141 LYS cc_start: 0.7781 (ttpt) cc_final: 0.7254 (mptt) REVERT: E 203 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: D 76 MET cc_start: 0.5283 (mpp) cc_final: 0.4292 (mtt) REVERT: D 122 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.5826 (mtt180) REVERT: X 80 PHE cc_start: 0.7224 (m-80) cc_final: 0.6958 (m-10) REVERT: X 96 ARG cc_start: 0.6946 (ttp80) cc_final: 0.6113 (ptt-90) REVERT: Q 79 GLU cc_start: 0.3689 (tm-30) cc_final: 0.2989 (mp0) REVERT: k 116 TYR cc_start: 0.4465 (t80) cc_final: 0.4135 (t80) REVERT: o 246 LYS cc_start: 0.6486 (mmpt) cc_final: 0.5655 (mttp) REVERT: q 6 ARG cc_start: 0.5684 (OUTLIER) cc_final: 0.3986 (ptt90) REVERT: p 199 PHE cc_start: 0.5206 (t80) cc_final: 0.4476 (t80) REVERT: z 420 PHE cc_start: 0.0977 (m-80) cc_final: 0.0335 (m-10) outliers start: 258 outliers final: 220 residues processed: 968 average time/residue: 0.5878 time to fit residues: 958.0034 Evaluate side-chains 992 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 751 time to evaluate : 5.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 298 SER Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 332 ILE Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 459 GLU Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain I residue 486 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 148 TYR Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 161 CYS Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain K residue 2 ASP Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 85 TYR Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 34 ARG Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 42 HIS Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain S residue 30 CYS Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 73 HIS Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain j residue 45 LEU Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 145 TYR Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 314 GLU Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain G residue 370 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 654 TRP Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 83 TYR Chi-restraints excluded: chain T residue 95 VAL Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 118 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 170 VAL Chi-restraints excluded: chain T residue 180 TYR Chi-restraints excluded: chain T residue 300 MET Chi-restraints excluded: chain T residue 307 TYR Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 344 ILE Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain T residue 373 TYR Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 75 ASP Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain U residue 46 ASN Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 169 GLN Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 75 MET Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 38 ASP Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain n residue 94 VAL Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 80 LEU Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 133 THR Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 6 ARG Chi-restraints excluded: chain q residue 39 LEU Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 122 ILE Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain q residue 201 SER Chi-restraints excluded: chain p residue 91 THR Chi-restraints excluded: chain p residue 99 ASN Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 VAL Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain p residue 175 ILE Chi-restraints excluded: chain p residue 209 ASN Chi-restraints excluded: chain z residue 112 VAL Chi-restraints excluded: chain z residue 183 GLU Chi-restraints excluded: chain z residue 242 VAL Chi-restraints excluded: chain z residue 255 ILE Chi-restraints excluded: chain z residue 284 LEU Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 333 THR Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 393 THR Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 409 HIS Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 540 THR Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 383 optimal weight: 2.9990 chunk 513 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 444 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 483 optimal weight: 20.0000 chunk 202 optimal weight: 9.9990 chunk 496 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 88 optimal weight: 0.0010 overall best weight: 2.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 GLN ** I 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 ASN ** Y 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 HIS ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 HIS k 118 HIS ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 171 GLN ** q 202 GLN ** 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 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 592 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.174733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.156725 restraints weight = 127057.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.157352 restraints weight = 111328.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.157947 restraints weight = 75031.439| |-----------------------------------------------------------------------------| r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.8406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.253 50643 Z= 0.589 Angle : 1.740 50.911 68619 Z= 1.107 Chirality : 0.326 6.370 7612 Planarity : 0.005 0.093 8730 Dihedral : 8.072 175.077 7044 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 28.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.15 % Favored : 90.76 % Rotamer: Outliers : 4.72 % Allowed : 28.39 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -2.05 (0.10), residues: 6177 helix: -0.39 (0.10), residues: 2647 sheet: -1.97 (0.25), residues: 367 loop : -2.18 (0.11), residues: 3163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP O 74 HIS 0.014 0.001 HIS U 138 PHE 0.035 0.002 PHE H 278 TYR 0.032 0.002 TYR c 34 ARG 0.011 0.001 ARG Y 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16220.45 seconds wall clock time: 290 minutes 6.04 seconds (17406.04 seconds total)