Starting phenix.real_space_refine on Sun Apr 7 00:27:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar7_11875/04_2024/7ar7_11875_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar7_11875/04_2024/7ar7_11875.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar7_11875/04_2024/7ar7_11875_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar7_11875/04_2024/7ar7_11875_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar7_11875/04_2024/7ar7_11875_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar7_11875/04_2024/7ar7_11875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar7_11875/04_2024/7ar7_11875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar7_11875/04_2024/7ar7_11875_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ar7_11875/04_2024/7ar7_11875_updated.pdb" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 14 5.49 5 S 416 5.16 5 C 39193 2.51 5 N 10118 2.21 5 O 10835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 58": "OD1" <-> "OD2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 58": "OD1" <-> "OD2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C ASP 179": "OD1" <-> "OD2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "D PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 44": "OD1" <-> "OD2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 357": "OD1" <-> "OD2" Residue "G GLU 71": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 321": "OE1" <-> "OE2" Residue "G GLU 326": "OE1" <-> "OE2" Residue "G PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "H ASP 204": "OD1" <-> "OD2" Residue "H GLU 209": "OE1" <-> "OE2" Residue "H TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 36": "OE1" <-> "OE2" Residue "K ASP 54": "OD1" <-> "OD2" Residue "K PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 199": "OD1" <-> "OD2" Residue "M PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 357": "OD1" <-> "OD2" Residue "M PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 444": "OD1" <-> "OD2" Residue "N ASP 46": "OD1" <-> "OD2" Residue "N ASP 113": "OD1" <-> "OD2" Residue "N PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 358": "OD1" <-> "OD2" Residue "N TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 227": "OD1" <-> "OD2" Residue "P TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 112": "OE1" <-> "OE2" Residue "Q ASP 124": "OD1" <-> "OD2" Residue "Q ASP 142": "OD1" <-> "OD2" Residue "S GLU 13": "OE1" <-> "OE2" Residue "S GLU 52": "OE1" <-> "OE2" Residue "S GLU 69": "OE1" <-> "OE2" Residue "T PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 73": "OD1" <-> "OD2" Residue "V TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 147": "OE1" <-> "OE2" Residue "W GLU 21": "OE1" <-> "OE2" Residue "W ASP 28": "OD1" <-> "OD2" Residue "W TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 122": "OD1" <-> "OD2" Residue "X ASP 51": "OD1" <-> "OD2" Residue "X TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 90": "OD1" <-> "OD2" Residue "Z GLU 76": "OE1" <-> "OE2" Residue "Z GLU 93": "OE1" <-> "OE2" Residue "Z GLU 106": "OE1" <-> "OE2" Residue "a TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 5": "OE1" <-> "OE2" Residue "b GLU 14": "OE1" <-> "OE2" Residue "b ASP 39": "OD1" <-> "OD2" Residue "c PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 16": "OD1" <-> "OD2" Residue "e ASP 40": "OD1" <-> "OD2" Residue "f ASP 4": "OD1" <-> "OD2" Residue "f GLU 9": "OE1" <-> "OE2" Residue "f ASP 92": "OD1" <-> "OD2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "i PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 59": "OE1" <-> "OE2" Residue "q TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 119": "OE1" <-> "OE2" Residue "x TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 196": "OE1" <-> "OE2" Residue "y GLU 228": "OE1" <-> "OE2" Residue "z GLU 142": "OE1" <-> "OE2" Residue "z GLU 196": "OE1" <-> "OE2" Residue "z PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 60606 Number of models: 1 Model: "" Number of chains: 61 Chain: "A" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 785 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain breaks: 1 Chain: "B" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1244 Classifications: {'peptide': 157} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 146} Chain: "C" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1581 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "D" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3077 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 17, 'TRANS': 367} Chain: "E" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1500 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain: "F" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3368 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} Chain: "G" Number of atoms: 5252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5252 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 35, 'TRANS': 652} Chain: "H" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2536 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 18, 'TRANS': 305} Chain: "I" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1381 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 8, 'TRANS': 160} Chain: "J" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1093 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain breaks: 1 Chain: "K" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'TRANS': 87} Chain: "L" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4807 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 20, 'TRANS': 594} Chain: "M" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3887 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 17, 'TRANS': 469} Chain: "N" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3820 Classifications: {'peptide': 488} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 471} Chain: "P" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2556 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 21, 'TRANS': 309} Chain: "Q" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 939 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "R" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 482 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 6, 'TRANS': 55} Chain: "S" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 728 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "T" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "U" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 650 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "V" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1123 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "W" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 880 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain breaks: 1 Chain: "X" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 763 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "Z" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 10, 'TRANS': 114} Chain: "a" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 470 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "b" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 295 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "c" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 617 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 7, 'TRANS': 68} Chain: "d" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 592 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "e" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 546 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "f" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 752 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "g" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 586 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 7, 'TRANS': 64} Chain: "i" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 737 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "j" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 415 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "k" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 374 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "l" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 360 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 3, 'TRANS': 42} Chain: "m" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 565 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "n" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 911 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "o" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 657 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "p" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 778 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "q" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 520 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "r" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 87 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "u" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 150 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 30} Unresolved non-hydrogen planarities: 30 Chain: "v" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 226 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "x" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1659 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 14, 'TRANS': 199} Chain: "y" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2032 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain: "z" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 226} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" 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: "G" 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: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'UQ9': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1, 'UQ9:plan-7': 1, 'UQ9:plan-2': 1} Unresolved non-hydrogen planarities: 23 Chain: "I" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {'PTY': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 171 Unusual residues: {'LMN': 1, 'PC7': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC7': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {' ZN': 1, 'PGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "z" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'PSF': 1, 'T7X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1538 SG CYS B 158 68.301 97.047 98.410 1.00 50.30 S ATOM 1038 SG CYS B 94 69.862 96.211 91.775 1.00 36.00 S ATOM 1768 SG CYS B 188 67.952 91.628 96.003 1.00 50.30 S ATOM 1032 SG CYS B 93 73.247 94.021 95.077 1.00 30.31 S ATOM 7523 SG CYS E 135 38.817 27.156 116.357 1.00116.71 S ATOM 7796 SG CYS E 171 38.087 29.512 120.213 1.00108.16 S ATOM 7796 SG CYS E 171 38.087 29.512 120.213 1.00108.16 S ATOM 7820 SG CYS E 175 40.662 26.638 120.326 1.00115.43 S ATOM 10912 SG CYS F 405 50.364 51.236 128.059 1.00 39.02 S ATOM 10932 SG CYS F 408 49.039 47.151 124.807 1.00 39.42 S ATOM 10893 SG CYS F 402 43.983 48.547 128.525 1.00 26.36 S ATOM 11257 SG CYS F 448 48.700 45.504 130.945 1.00 37.85 S ATOM 11933 SG CYS G 106 50.165 61.213 131.581 1.00 41.87 S ATOM 12017 SG CYS G 117 51.530 60.826 128.566 1.00 39.92 S ATOM 12042 SG CYS G 120 55.908 60.797 133.404 1.00 38.63 S ATOM 12144 SG CYS G 134 52.742 60.742 135.089 1.00 30.86 S ATOM 12478 SG CYS G 179 51.278 69.816 118.714 1.00 35.25 S ATOM 12417 SG CYS G 170 52.458 69.250 112.019 1.00 50.30 S ATOM 12438 SG CYS G 173 46.945 71.366 114.737 1.00 50.30 S ATOM 12830 SG CYS G 224 39.431 65.160 126.331 1.00 50.30 S ATOM 12783 SG CYS G 218 42.350 62.798 121.148 1.00 50.30 S ATOM 12806 SG CYS G 221 45.876 64.316 126.515 1.00 50.30 S ATOM 13151 SG CYS G 268 43.863 68.610 122.851 1.00 40.69 S ATOM 20279 SG CYS I 168 58.419 83.110 98.123 1.00 50.30 S ATOM 20232 SG CYS I 162 60.281 88.869 96.438 1.00 50.30 S ATOM 20258 SG CYS I 165 64.230 84.919 99.684 1.00 50.30 S ATOM 20000 SG CYS I 133 59.480 87.786 102.739 1.00 50.30 S ATOM 20308 SG CYS I 172 53.900 77.792 99.642 1.00 50.30 S ATOM 19931 SG CYS I 123 47.686 80.511 100.692 1.00 50.30 S ATOM 19973 SG CYS I 129 53.511 82.466 102.472 1.00 50.30 S ATOM 19950 SG CYS I 126 51.837 77.180 105.039 1.00 50.30 S ATOM 38708 SG CYS R 72 42.684 63.905 98.554 1.00 31.13 S ATOM 38894 SG CYS R 97 42.270 66.545 101.338 1.00 31.71 S ATOM 38921 SG CYS R 100 43.738 67.547 97.914 1.00 34.32 S Time building chain proxies: 23.36, per 1000 atoms: 0.39 Number of scatterers: 60606 At special positions: 0 Unit cell: (216.783, 277.047, 188.325, 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 416 16.00 P 14 15.00 O 10835 8.00 N 10118 7.00 C 39193 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 174 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS N 336 " - pdb=" SG CYS N 420 " distance=2.03 Simple disulfide: pdb=" SG CYS X 71 " - pdb=" SG CYS X 103 " distance=2.03 Simple disulfide: pdb=" SG CYS e 24 " - pdb=" SG CYS e 34 " distance=2.03 Simple disulfide: pdb=" SG CYS o 30 " - pdb=" SG CYS o 61 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=15, symmetry=0 Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.94 Conformation dependent library (CDL) restraints added in 8.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 500 " pdb="FE2 FES E 500 " - pdb=" SG CYS E 171 " pdb="FE1 FES E 500 " - pdb=" SG CYS E 135 " pdb="FE2 FES E 500 " - pdb=" SG CYS E 175 " pdb=" FES G 801 " pdb="FE2 FES G 801 " - pdb=" SG CYS G 120 " pdb="FE1 FES G 801 " - pdb=" SG CYS G 106 " pdb="FE2 FES G 801 " - pdb=" SG CYS G 134 " pdb="FE1 FES G 801 " - pdb=" SG CYS G 117 " pdb=" SF4 B 500 " pdb="FE4 SF4 B 500 " - pdb=" SG CYS B 93 " pdb="FE1 SF4 B 500 " - pdb=" SG CYS B 158 " pdb="FE2 SF4 B 500 " - pdb=" SG CYS B 94 " pdb="FE3 SF4 B 500 " - pdb=" SG CYS B 188 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 408 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 405 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 448 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 402 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" NE2 HIS G 166 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 179 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 173 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 170 " pdb=" SF4 G 803 " pdb="FE4 SF4 G 803 " - pdb=" SG CYS G 268 " pdb="FE3 SF4 G 803 " - pdb=" SG CYS G 221 " pdb="FE1 SF4 G 803 " - pdb=" SG CYS G 224 " pdb="FE2 SF4 G 803 " - pdb=" SG CYS G 218 " pdb=" SF4 I 301 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 162 " pdb="FE3 SF4 I 301 " - pdb=" SG CYS I 165 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 133 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 168 " pdb=" SF4 I 302 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 172 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 126 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 129 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 123 " Number of angles added : 82 Zn2+ tetrahedral coordination pdb=" ZN R 200 " pdb="ZN ZN R 200 " - pdb=" NE2 HIS R 82 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 100 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 97 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 72 " pdb=" ZN y 301 " pdb="ZN ZN y 301 " - pdb=" ND1 HIS y 107 " Number of angles added : 3 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 289 helices and 34 sheets defined 50.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.62 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 Proline residue: A 7 - end of helix Processing helix chain 'A' and resid 25 through 28 No H-bonds generated for 'chain 'A' and resid 25 through 28' Processing helix chain 'A' and resid 59 through 83 removed outlier: 3.855A pdb=" N VAL A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) Proline residue: A 80 - end of helix removed outlier: 3.653A pdb=" N VAL A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 Processing helix chain 'B' and resid 63 through 82 removed outlier: 4.005A pdb=" N PHE B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 101 removed outlier: 3.658A pdb=" N GLU B 97 " --> pdb=" O CYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 133 through 144 Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 192 through 207 Processing helix chain 'B' and resid 211 through 217 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 38 through 47 Processing helix chain 'C' and resid 106 through 119 removed outlier: 3.568A pdb=" N GLY C 109 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP C 110 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE C 119 " --> pdb=" O TRP C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 51 through 57 removed outlier: 4.052A pdb=" N GLU D 56 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 68 removed outlier: 3.857A pdb=" N ASP D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 64 through 68' Processing helix chain 'D' and resid 75 through 90 removed outlier: 3.575A pdb=" N GLU D 79 " --> pdb=" O MET D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 125 Processing helix chain 'D' and resid 129 through 148 removed outlier: 4.286A pdb=" N LYS D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 192 removed outlier: 3.886A pdb=" N GLN D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA D 183 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N SER D 184 " --> pdb=" O GLN D 180 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 201 Processing helix chain 'D' and resid 211 through 216 Processing helix chain 'D' and resid 222 through 227 removed outlier: 4.062A pdb=" N SER D 227 " --> pdb=" O MET D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 259 through 281 Processing helix chain 'D' and resid 299 through 302 No H-bonds generated for 'chain 'D' and resid 299 through 302' Processing helix chain 'D' and resid 306 through 316 Processing helix chain 'D' and resid 358 through 369 removed outlier: 3.529A pdb=" N HIS D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP D 367 " --> pdb=" O SER D 363 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE D 368 " --> pdb=" O GLN D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 385 removed outlier: 4.143A pdb=" N VAL D 379 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N THR D 380 " --> pdb=" O ASP D 377 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 385 " --> pdb=" O ILE D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 392 No H-bonds generated for 'chain 'D' and resid 389 through 392' Processing helix chain 'E' and resid 51 through 63 removed outlier: 3.948A pdb=" N SER E 55 " --> pdb=" O GLU E 51 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS E 56 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR E 63 " --> pdb=" O GLU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 84 removed outlier: 4.247A pdb=" N ILE E 74 " --> pdb=" O SER E 71 " (cutoff:3.500A) Proline residue: E 75 - end of helix removed outlier: 3.532A pdb=" N ASN E 84 " --> pdb=" O GLN E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 100 Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.705A pdb=" N VAL E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 136 No H-bonds generated for 'chain 'E' and resid 133 through 136' Processing helix chain 'E' and resid 140 through 142 No H-bonds generated for 'chain 'E' and resid 140 through 142' Processing helix chain 'E' and resid 145 through 151 removed outlier: 3.680A pdb=" N LEU E 151 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 removed outlier: 3.530A pdb=" N VAL E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 81 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 118 through 124 Processing helix chain 'F' and resid 149 through 156 Processing helix chain 'F' and resid 158 through 171 Processing helix chain 'F' and resid 186 through 201 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 228 through 230 No H-bonds generated for 'chain 'F' and resid 228 through 230' Processing helix chain 'F' and resid 232 through 239 removed outlier: 3.948A pdb=" N LEU F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 260 No H-bonds generated for 'chain 'F' and resid 258 through 260' Processing helix chain 'F' and resid 268 through 280 removed outlier: 3.750A pdb=" N SER F 274 " --> pdb=" O THR F 270 " (cutoff:3.500A) Proline residue: F 275 - end of helix Processing helix chain 'F' and resid 282 through 287 removed outlier: 3.566A pdb=" N SER F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 325 Processing helix chain 'F' and resid 362 through 368 removed outlier: 3.866A pdb=" N VAL F 368 " --> pdb=" O ALA F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 Processing helix chain 'F' and resid 406 through 423 removed outlier: 4.483A pdb=" N GLY F 413 " --> pdb=" O ARG F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 442 removed outlier: 3.578A pdb=" N ILE F 432 " --> pdb=" O LEU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 482 Proline residue: F 457 - end of helix Proline residue: F 467 - end of helix Processing helix chain 'G' and resid 60 through 62 No H-bonds generated for 'chain 'G' and resid 60 through 62' Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 149 through 164 removed outlier: 3.791A pdb=" N ARG G 155 " --> pdb=" O ALA G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 187 removed outlier: 3.523A pdb=" N ALA G 187 " --> pdb=" O ASP G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 262 through 267 removed outlier: 3.788A pdb=" N ILE G 267 " --> pdb=" O VAL G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 333 No H-bonds generated for 'chain 'G' and resid 330 through 333' Processing helix chain 'G' and resid 336 through 340 Processing helix chain 'G' and resid 361 through 374 removed outlier: 3.791A pdb=" N HIS G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN G 374 " --> pdb=" O ASP G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 403 Processing helix chain 'G' and resid 432 through 436 removed outlier: 3.598A pdb=" N GLU G 435 " --> pdb=" O SER G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 465 removed outlier: 3.615A pdb=" N ALA G 456 " --> pdb=" O ALA G 452 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG G 457 " --> pdb=" O MET G 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 489 through 497 Processing helix chain 'G' and resid 501 through 507 Processing helix chain 'G' and resid 518 through 522 Processing helix chain 'G' and resid 526 through 540 Processing helix chain 'G' and resid 557 through 564 removed outlier: 4.819A pdb=" N ALA G 561 " --> pdb=" O ALA G 557 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA G 562 " --> pdb=" O ALA G 558 " (cutoff:3.500A) Processing helix chain 'G' and resid 623 through 625 No H-bonds generated for 'chain 'G' and resid 623 through 625' Processing helix chain 'G' and resid 653 through 664 Processing helix chain 'G' and resid 673 through 682 removed outlier: 3.922A pdb=" N SER G 682 " --> pdb=" O SER G 678 " (cutoff:3.500A) Processing helix chain 'G' and resid 685 through 688 Processing helix chain 'G' and resid 700 through 702 No H-bonds generated for 'chain 'G' and resid 700 through 702' Processing helix chain 'G' and resid 727 through 730 No H-bonds generated for 'chain 'G' and resid 727 through 730' Processing helix chain 'G' and resid 733 through 741 removed outlier: 3.936A pdb=" N VAL G 741 " --> pdb=" O GLN G 737 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 34 Proline residue: H 15 - end of helix Processing helix chain 'H' and resid 50 through 59 Processing helix chain 'H' and resid 73 through 89 Proline residue: H 78 - end of helix removed outlier: 4.505A pdb=" N TRP H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 116 Processing helix chain 'H' and resid 119 through 127 Processing helix chain 'H' and resid 133 through 162 removed outlier: 3.999A pdb=" N VAL H 149 " --> pdb=" O VAL H 145 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER H 150 " --> pdb=" O SER H 146 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS H 161 " --> pdb=" O THR H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 174 removed outlier: 3.683A pdb=" N GLN H 174 " --> pdb=" O ILE H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 196 Processing helix chain 'H' and resid 205 through 212 Processing helix chain 'H' and resid 225 through 246 removed outlier: 3.851A pdb=" N LEU H 242 " --> pdb=" O MET H 239 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS H 243 " --> pdb=" O SER H 240 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE H 246 " --> pdb=" O CYS H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 286 removed outlier: 3.643A pdb=" N SER H 270 " --> pdb=" O SER H 266 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS H 272 " --> pdb=" O TRP H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 301 removed outlier: 3.838A pdb=" N GLY H 297 " --> pdb=" O ASP H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 320 Processing helix chain 'I' and resid 60 through 69 removed outlier: 3.691A pdb=" N PHE I 64 " --> pdb=" O TRP I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 87 removed outlier: 3.730A pdb=" N LEU I 82 " --> pdb=" O ARG I 78 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR I 83 " --> pdb=" O GLY I 79 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU I 84 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR I 86 " --> pdb=" O LEU I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 132 Processing helix chain 'I' and resid 169 through 171 No H-bonds generated for 'chain 'I' and resid 169 through 171' Processing helix chain 'I' and resid 191 through 193 No H-bonds generated for 'chain 'I' and resid 191 through 193' Processing helix chain 'I' and resid 199 through 206 Processing helix chain 'I' and resid 208 through 218 removed outlier: 4.061A pdb=" N GLU I 213 " --> pdb=" O THR I 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 18 removed outlier: 3.683A pdb=" N VAL J 18 " --> pdb=" O GLY J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 44 removed outlier: 3.504A pdb=" N PHE J 34 " --> pdb=" O PHE J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 56 removed outlier: 3.933A pdb=" N LEU J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 70 Processing helix chain 'J' and resid 136 through 144 removed outlier: 3.702A pdb=" N LEU J 140 " --> pdb=" O ASN J 136 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU J 143 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 170 removed outlier: 3.588A pdb=" N ILE J 167 " --> pdb=" O MET J 163 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR J 170 " --> pdb=" O ALA J 166 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 23 Processing helix chain 'K' and resid 30 through 53 Processing helix chain 'K' and resid 57 through 86 removed outlier: 3.625A pdb=" N PHE K 61 " --> pdb=" O MET K 57 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU K 66 " --> pdb=" O ALA K 62 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL K 68 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL K 86 " --> pdb=" O ILE K 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 18 Proline residue: L 9 - end of helix Processing helix chain 'L' and resid 20 through 50 removed outlier: 6.323A pdb=" N SER L 25 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLU L 26 " --> pdb=" O PHE L 22 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA L 29 " --> pdb=" O SER L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 105 removed outlier: 3.670A pdb=" N VAL L 88 " --> pdb=" O VAL L 84 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE L 91 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER L 105 " --> pdb=" O ILE L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 129 Processing helix chain 'L' and resid 133 through 151 Processing helix chain 'L' and resid 158 through 189 Processing helix chain 'L' and resid 194 through 199 removed outlier: 3.609A pdb=" N ALA L 199 " --> pdb=" O SER L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 217 through 233 removed outlier: 4.675A pdb=" N GLY L 231 " --> pdb=" O ILE L 227 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS L 232 " --> pdb=" O GLY L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 247 removed outlier: 3.585A pdb=" N MET L 246 " --> pdb=" O LEU L 242 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLU L 247 " --> pdb=" O PRO L 243 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 255 Processing helix chain 'L' and resid 264 through 271 Processing helix chain 'L' and resid 273 through 276 No H-bonds generated for 'chain 'L' and resid 273 through 276' Processing helix chain 'L' and resid 280 through 302 removed outlier: 3.547A pdb=" N ILE L 284 " --> pdb=" O PRO L 280 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL L 285 " --> pdb=" O THR L 281 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA L 298 " --> pdb=" O SER L 294 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE L 302 " --> pdb=" O ALA L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 327 removed outlier: 4.099A pdb=" N ILE L 311 " --> pdb=" O LEU L 307 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA L 312 " --> pdb=" O LYS L 308 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR L 313 " --> pdb=" O ARG L 309 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER L 314 " --> pdb=" O VAL L 310 " (cutoff:3.500A) Processing helix chain 'L' and resid 331 through 358 removed outlier: 3.814A pdb=" N PHE L 343 " --> pdb=" O MET L 339 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE L 344 " --> pdb=" O ASN L 340 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA L 346 " --> pdb=" O ALA L 342 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 390 Proline residue: L 376 - end of helix removed outlier: 3.507A pdb=" N MET L 382 " --> pdb=" O TYR L 379 " (cutoff:3.500A) Processing helix chain 'L' and resid 398 through 410 removed outlier: 4.824A pdb=" N VAL L 403 " --> pdb=" O TYR L 399 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU L 405 " --> pdb=" O LYS L 401 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 440 removed outlier: 3.599A pdb=" N PHE L 418 " --> pdb=" O ILE L 414 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL L 427 " --> pdb=" O GLY L 423 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU L 428 " --> pdb=" O SER L 424 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE L 429 " --> pdb=" O VAL L 425 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU L 438 " --> pdb=" O SER L 434 " (cutoff:3.500A) Processing helix chain 'L' and resid 450 through 453 No H-bonds generated for 'chain 'L' and resid 450 through 453' Processing helix chain 'L' and resid 462 through 485 Proline residue: L 466 - end of helix removed outlier: 3.567A pdb=" N LEU L 475 " --> pdb=" O ALA L 471 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE L 476 " --> pdb=" O LEU L 472 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLY L 478 " --> pdb=" O SER L 474 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TYR L 479 " --> pdb=" O LEU L 475 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASP L 483 " --> pdb=" O TYR L 479 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET L 484 " --> pdb=" O LEU L 480 " (cutoff:3.500A) Processing helix chain 'L' and resid 507 through 512 removed outlier: 3.925A pdb=" N PHE L 511 " --> pdb=" O ALA L 507 " (cutoff:3.500A) Processing helix chain 'L' and resid 517 through 537 Proline residue: L 521 - end of helix Processing helix chain 'L' and resid 553 through 560 Processing helix chain 'L' and resid 565 through 583 removed outlier: 4.101A pdb=" N ASN L 570 " --> pdb=" O ASP L 566 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG L 575 " --> pdb=" O ASP L 571 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER L 576 " --> pdb=" O PHE L 572 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR L 582 " --> pdb=" O LEU L 578 " (cutoff:3.500A) Processing helix chain 'L' and resid 585 through 588 No H-bonds generated for 'chain 'L' and resid 585 through 588' Processing helix chain 'L' and resid 593 through 596 No H-bonds generated for 'chain 'L' and resid 593 through 596' Processing helix chain 'L' and resid 605 through 612 removed outlier: 4.755A pdb=" N GLU L 611 " --> pdb=" O ARG L 607 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ARG L 612 " --> pdb=" O ARG L 608 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 28 Proline residue: M 19 - end of helix Processing helix chain 'M' and resid 34 through 57 Processing helix chain 'M' and resid 88 through 107 removed outlier: 4.549A pdb=" N PHE M 92 " --> pdb=" O GLY M 88 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE M 93 " --> pdb=" O ILE M 89 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE M 101 " --> pdb=" O THR M 97 " (cutoff:3.500A) Proline residue: M 102 - end of helix Processing helix chain 'M' and resid 110 through 115 removed outlier: 4.533A pdb=" N ARG M 113 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 134 Processing helix chain 'M' and resid 139 through 146 Processing helix chain 'M' and resid 148 through 159 removed outlier: 3.731A pdb=" N ILE M 151 " --> pdb=" O SER M 148 " (cutoff:3.500A) Proline residue: M 152 - end of helix removed outlier: 4.049A pdb=" N VAL M 159 " --> pdb=" O ILE M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 176 Processing helix chain 'M' and resid 179 through 194 removed outlier: 3.650A pdb=" N ALA M 187 " --> pdb=" O PHE M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 204 Processing helix chain 'M' and resid 210 through 227 removed outlier: 4.254A pdb=" N ILE M 214 " --> pdb=" O GLU M 210 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE M 215 " --> pdb=" O ARG M 211 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER M 223 " --> pdb=" O ALA M 219 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL M 226 " --> pdb=" O ALA M 222 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS M 227 " --> pdb=" O SER M 223 " (cutoff:3.500A) Processing helix chain 'M' and resid 235 through 242 removed outlier: 3.728A pdb=" N GLU M 239 " --> pdb=" O ILE M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 252 Processing helix chain 'M' and resid 256 through 267 removed outlier: 4.282A pdb=" N GLY M 260 " --> pdb=" O LEU M 256 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR M 261 " --> pdb=" O LEU M 257 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 278 Processing helix chain 'M' and resid 280 through 300 removed outlier: 3.783A pdb=" N LEU M 299 " --> pdb=" O SER M 295 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG M 300 " --> pdb=" O LEU M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 323 removed outlier: 4.024A pdb=" N SER M 311 " --> pdb=" O ILE M 307 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR M 320 " --> pdb=" O MET M 316 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE M 321 " --> pdb=" O ASN M 317 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY M 322 " --> pdb=" O LEU M 318 " (cutoff:3.500A) Processing helix chain 'M' and resid 328 through 359 removed outlier: 3.819A pdb=" N SER M 346 " --> pdb=" O GLY M 342 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG M 358 " --> pdb=" O VAL M 354 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS M 359 " --> pdb=" O LEU M 355 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 388 Processing helix chain 'M' and resid 395 through 410 removed outlier: 4.073A pdb=" N GLY M 399 " --> pdb=" O SER M 395 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG M 410 " --> pdb=" O GLY M 406 " (cutoff:3.500A) Processing helix chain 'M' and resid 414 through 436 removed outlier: 3.694A pdb=" N MET M 422 " --> pdb=" O ALA M 418 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE M 423 " --> pdb=" O ALA M 419 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU M 424 " --> pdb=" O LEU M 420 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA M 427 " --> pdb=" O ILE M 423 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL M 436 " --> pdb=" O LEU M 432 " (cutoff:3.500A) Processing helix chain 'M' and resid 454 through 472 removed outlier: 4.214A pdb=" N PHE M 460 " --> pdb=" O GLU M 456 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE M 461 " --> pdb=" O VAL M 457 " (cutoff:3.500A) Proline residue: M 462 - end of helix Processing helix chain 'M' and resid 475 through 479 Processing helix chain 'M' and resid 482 through 490 Processing helix chain 'N' and resid 13 through 16 Processing helix chain 'N' and resid 20 through 39 removed outlier: 4.213A pdb=" N ILE N 25 " --> pdb=" O PRO N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 72 Processing helix chain 'N' and resid 91 through 109 removed outlier: 3.634A pdb=" N LEU N 102 " --> pdb=" O ILE N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 117 removed outlier: 3.914A pdb=" N ASP N 116 " --> pdb=" O PHE N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 141 removed outlier: 3.559A pdb=" N SER N 141 " --> pdb=" O LEU N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 163 removed outlier: 3.636A pdb=" N GLN N 155 " --> pdb=" O ALA N 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 170 through 201 removed outlier: 3.590A pdb=" N MET N 196 " --> pdb=" O PHE N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 212 removed outlier: 3.659A pdb=" N LYS N 211 " --> pdb=" O ASP N 207 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 240 Processing helix chain 'N' and resid 250 through 256 Processing helix chain 'N' and resid 259 through 264 Processing helix chain 'N' and resid 268 through 284 removed outlier: 3.629A pdb=" N SER N 272 " --> pdb=" O ALA N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 290 through 311 removed outlier: 3.502A pdb=" N CYS N 297 " --> pdb=" O ILE N 293 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET N 310 " --> pdb=" O ALA N 306 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ALA N 311 " --> pdb=" O LEU N 307 " (cutoff:3.500A) Processing helix chain 'N' and resid 316 through 335 removed outlier: 4.327A pdb=" N GLY N 333 " --> pdb=" O TYR N 329 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE N 334 " --> pdb=" O ILE N 330 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER N 335 " --> pdb=" O CYS N 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 339 through 369 removed outlier: 3.873A pdb=" N GLN N 368 " --> pdb=" O LEU N 364 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THR N 369 " --> pdb=" O ALA N 365 " (cutoff:3.500A) Processing helix chain 'N' and resid 380 through 383 No H-bonds generated for 'chain 'N' and resid 380 through 383' Processing helix chain 'N' and resid 385 through 399 Processing helix chain 'N' and resid 407 through 419 Processing helix chain 'N' and resid 423 through 448 removed outlier: 3.635A pdb=" N PHE N 438 " --> pdb=" O VAL N 434 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR N 439 " --> pdb=" O ILE N 435 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR N 440 " --> pdb=" O GLY N 436 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG N 446 " --> pdb=" O ARG N 442 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET N 447 " --> pdb=" O LEU N 443 " (cutoff:3.500A) Processing helix chain 'N' and resid 463 through 478 Processing helix chain 'N' and resid 484 through 497 removed outlier: 3.734A pdb=" N LEU N 497 " --> pdb=" O MET N 493 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 90 removed outlier: 3.775A pdb=" N GLN P 86 " --> pdb=" O ARG P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 134 Processing helix chain 'P' and resid 156 through 174 removed outlier: 3.983A pdb=" N HIS P 162 " --> pdb=" O ASP P 158 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE P 163 " --> pdb=" O ALA P 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 210 removed outlier: 3.917A pdb=" N LEU P 208 " --> pdb=" O GLU P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 231 through 239 Processing helix chain 'P' and resid 258 through 269 Processing helix chain 'P' and resid 290 through 301 removed outlier: 4.745A pdb=" N MET P 300 " --> pdb=" O ILE P 296 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE P 301 " --> pdb=" O MET P 297 " (cutoff:3.500A) Processing helix chain 'P' and resid 312 through 324 removed outlier: 3.762A pdb=" N ALA P 320 " --> pdb=" O LYS P 316 " (cutoff:3.500A) Proline residue: P 321 - end of helix Processing helix chain 'P' and resid 341 through 347 removed outlier: 3.628A pdb=" N ASN P 345 " --> pdb=" O LEU P 341 " (cutoff:3.500A) Processing helix chain 'P' and resid 361 through 363 No H-bonds generated for 'chain 'P' and resid 361 through 363' Processing helix chain 'P' and resid 373 through 378 removed outlier: 4.782A pdb=" N PHE P 377 " --> pdb=" O PRO P 374 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 43 Processing helix chain 'Q' and resid 47 through 49 No H-bonds generated for 'chain 'Q' and resid 47 through 49' Processing helix chain 'Q' and resid 101 through 104 No H-bonds generated for 'chain 'Q' and resid 101 through 104' Processing helix chain 'Q' and resid 111 through 120 Processing helix chain 'Q' and resid 140 through 143 Processing helix chain 'R' and resid 53 through 59 removed outlier: 4.195A pdb=" N SER R 58 " --> pdb=" O MET R 54 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU R 59 " --> pdb=" O GLU R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 80 No H-bonds generated for 'chain 'R' and resid 78 through 80' Processing helix chain 'S' and resid 26 through 34 removed outlier: 3.732A pdb=" N LYS S 34 " --> pdb=" O THR S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 42 removed outlier: 3.638A pdb=" N LEU S 42 " --> pdb=" O ASP S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 93 removed outlier: 3.598A pdb=" N GLY S 93 " --> pdb=" O LEU S 89 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 45 No H-bonds generated for 'chain 'T' and resid 43 through 45' Processing helix chain 'T' and resid 49 through 55 removed outlier: 3.834A pdb=" N VAL T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL T 54 " --> pdb=" O VAL T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 92 Processing helix chain 'T' and resid 99 through 102 No H-bonds generated for 'chain 'T' and resid 99 through 102' Processing helix chain 'T' and resid 108 through 117 removed outlier: 3.579A pdb=" N ILE T 112 " --> pdb=" O CYS T 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 59 removed outlier: 3.648A pdb=" N VAL U 57 " --> pdb=" O ARG U 53 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL U 58 " --> pdb=" O VAL U 54 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS U 59 " --> pdb=" O LEU U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 78 No H-bonds generated for 'chain 'U' and resid 75 through 78' Processing helix chain 'U' and resid 83 through 93 Processing helix chain 'U' and resid 103 through 105 No H-bonds generated for 'chain 'U' and resid 103 through 105' Processing helix chain 'U' and resid 112 through 120 Processing helix chain 'V' and resid 29 through 46 removed outlier: 3.681A pdb=" N ASP V 35 " --> pdb=" O ALA V 31 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU V 36 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR V 37 " --> pdb=" O LEU V 33 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER V 38 " --> pdb=" O ILE V 34 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN V 45 " --> pdb=" O LEU V 41 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA V 46 " --> pdb=" O LYS V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 70 removed outlier: 3.650A pdb=" N GLN V 63 " --> pdb=" O SER V 59 " (cutoff:3.500A) Processing helix chain 'V' and resid 74 through 81 Processing helix chain 'V' and resid 86 through 106 Processing helix chain 'V' and resid 140 through 150 removed outlier: 3.518A pdb=" N LEU V 146 " --> pdb=" O PHE V 142 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 35 Processing helix chain 'W' and resid 37 through 43 Processing helix chain 'W' and resid 52 through 66 removed outlier: 3.739A pdb=" N ARG W 56 " --> pdb=" O PRO W 52 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR W 57 " --> pdb=" O SER W 53 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN W 66 " --> pdb=" O GLN W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 90 Processing helix chain 'W' and resid 98 through 102 Processing helix chain 'W' and resid 122 through 127 Processing helix chain 'X' and resid 15 through 28 removed outlier: 4.728A pdb=" N LYS X 23 " --> pdb=" O THR X 19 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N HIS X 24 " --> pdb=" O ALA X 20 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET X 27 " --> pdb=" O LYS X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 30 through 42 Processing helix chain 'X' and resid 51 through 70 removed outlier: 3.780A pdb=" N ASP X 55 " --> pdb=" O LYS X 52 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL X 56 " --> pdb=" O GLY X 53 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS X 70 " --> pdb=" O LEU X 67 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 84 removed outlier: 3.776A pdb=" N ASP X 77 " --> pdb=" O LYS X 73 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 102 removed outlier: 4.080A pdb=" N VAL X 102 " --> pdb=" O ALA X 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 48 through 83 Processing helix chain 'Z' and resid 86 through 111 Processing helix chain 'a' and resid 5 through 34 Proline residue: a 11 - end of helix removed outlier: 3.501A pdb=" N ILE a 21 " --> pdb=" O MET a 18 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER a 25 " --> pdb=" O MET a 22 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS a 31 " --> pdb=" O TYR a 28 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR a 33 " --> pdb=" O HIS a 30 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS a 34 " --> pdb=" O LYS a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 59 Processing helix chain 'b' and resid 3 through 13 Processing helix chain 'b' and resid 15 through 39 Proline residue: b 31 - end of helix removed outlier: 4.385A pdb=" N ARG b 35 " --> pdb=" O PRO b 31 " (cutoff:3.500A) Proline residue: b 36 - end of helix Processing helix chain 'c' and resid 34 through 57 Proline residue: c 50 - end of helix Processing helix chain 'd' and resid 9 through 23 Processing helix chain 'd' and resid 32 through 74 removed outlier: 3.521A pdb=" N ARG d 73 " --> pdb=" O ALA d 69 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG d 74 " --> pdb=" O ALA d 70 " (cutoff:3.500A) Processing helix chain 'e' and resid 15 through 27 removed outlier: 3.881A pdb=" N HIS e 27 " --> pdb=" O GLU e 23 " (cutoff:3.500A) Processing helix chain 'e' and resid 35 through 46 Processing helix chain 'e' and resid 48 through 64 removed outlier: 3.977A pdb=" N LYS e 64 " --> pdb=" O GLU e 60 " (cutoff:3.500A) Processing helix chain 'f' and resid 22 through 27 Processing helix chain 'f' and resid 31 through 53 removed outlier: 3.983A pdb=" N ILE f 53 " --> pdb=" O TYR f 49 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 86 Processing helix chain 'f' and resid 92 through 99 removed outlier: 3.968A pdb=" N ALA f 96 " --> pdb=" O ASP f 92 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN f 99 " --> pdb=" O VAL f 95 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 47 No H-bonds generated for 'chain 'g' and resid 45 through 47' Processing helix chain 'g' and resid 63 through 83 removed outlier: 4.119A pdb=" N ASN g 82 " --> pdb=" O GLY g 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 89 through 101 Processing helix chain 'i' and resid 4 through 15 removed outlier: 4.288A pdb=" N ASN i 10 " --> pdb=" O GLU i 6 " (cutoff:3.500A) Processing helix chain 'i' and resid 19 through 45 removed outlier: 3.571A pdb=" N ALA i 45 " --> pdb=" O LYS i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 53 through 55 No H-bonds generated for 'chain 'i' and resid 53 through 55' Processing helix chain 'i' and resid 57 through 59 No H-bonds generated for 'chain 'i' and resid 57 through 59' Processing helix chain 'j' and resid 22 through 50 removed outlier: 4.464A pdb=" N THR j 27 " --> pdb=" O TRP j 23 " (cutoff:3.500A) Proline residue: j 48 - end of helix Processing helix chain 'k' and resid 9 through 15 removed outlier: 3.649A pdb=" N ARG k 15 " --> pdb=" O PHE k 11 " (cutoff:3.500A) Processing helix chain 'k' and resid 17 through 19 No H-bonds generated for 'chain 'k' and resid 17 through 19' Processing helix chain 'k' and resid 22 through 24 No H-bonds generated for 'chain 'k' and resid 22 through 24' Processing helix chain 'k' and resid 33 through 49 removed outlier: 3.969A pdb=" N GLY k 36 " --> pdb=" O PRO k 33 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE k 37 " --> pdb=" O GLY k 34 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY k 38 " --> pdb=" O ILE k 35 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL k 39 " --> pdb=" O GLY k 36 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU k 49 " --> pdb=" O LEU k 46 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 99 removed outlier: 3.800A pdb=" N TRP l 81 " --> pdb=" O GLU l 77 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU l 82 " --> pdb=" O ALA l 78 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 117 Processing helix chain 'm' and resid 11 through 21 removed outlier: 4.176A pdb=" N ASP m 15 " --> pdb=" O LYS m 11 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TRP m 16 " --> pdb=" O PHE m 12 " (cutoff:3.500A) Processing helix chain 'm' and resid 23 through 25 No H-bonds generated for 'chain 'm' and resid 23 through 25' Processing helix chain 'm' and resid 31 through 63 removed outlier: 3.509A pdb=" N PHE m 40 " --> pdb=" O LEU m 36 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LEU m 44 " --> pdb=" O PHE m 40 " (cutoff:3.500A) Proline residue: m 45 - end of helix removed outlier: 3.650A pdb=" N ALA m 63 " --> pdb=" O GLN m 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 10 through 34 removed outlier: 4.007A pdb=" N ALA n 15 " --> pdb=" O ALA n 11 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN n 16 " --> pdb=" O ARG n 12 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS n 17 " --> pdb=" O ARG n 13 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 52 removed outlier: 4.744A pdb=" N ARG n 43 " --> pdb=" O HIS n 39 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP n 44 " --> pdb=" O ILE n 40 " (cutoff:3.500A) Processing helix chain 'n' and resid 62 through 77 removed outlier: 4.384A pdb=" N LYS n 66 " --> pdb=" O ASP n 62 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU n 67 " --> pdb=" O ARG n 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS n 77 " --> pdb=" O ALA n 73 " (cutoff:3.500A) Processing helix chain 'o' and resid 15 through 19 Processing helix chain 'o' and resid 31 through 43 removed outlier: 3.645A pdb=" N ILE o 35 " --> pdb=" O HIS o 32 " (cutoff:3.500A) Proline residue: o 36 - end of helix removed outlier: 3.528A pdb=" N ARG o 41 " --> pdb=" O ASN o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 53 through 83 removed outlier: 3.838A pdb=" N VAL o 57 " --> pdb=" O ASP o 53 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR o 58 " --> pdb=" O GLU o 54 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU o 82 " --> pdb=" O GLU o 78 " (cutoff:3.500A) Processing helix chain 'p' and resid 23 through 25 No H-bonds generated for 'chain 'p' and resid 23 through 25' Processing helix chain 'p' and resid 30 through 62 removed outlier: 3.912A pdb=" N ARG p 60 " --> pdb=" O LYS p 56 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL p 61 " --> pdb=" O TRP p 57 " (cutoff:3.500A) Processing helix chain 'p' and resid 66 through 83 removed outlier: 3.683A pdb=" N CYS p 70 " --> pdb=" O HIS p 66 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG p 71 " --> pdb=" O TYR p 67 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N HIS p 72 " --> pdb=" O GLN p 68 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU p 73 " --> pdb=" O LYS p 69 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN p 75 " --> pdb=" O ARG p 71 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY p 83 " --> pdb=" O ASP p 79 " (cutoff:3.500A) Processing helix chain 'q' and resid 91 through 97 removed outlier: 3.827A pdb=" N GLY q 95 " --> pdb=" O ALA q 91 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TRP q 96 " --> pdb=" O GLU q 92 " (cutoff:3.500A) Processing helix chain 'u' and resid 2 through 25 Processing helix chain 'v' and resid 80 through 102 removed outlier: 4.007A pdb=" N TYR v 84 " --> pdb=" O LYS v 80 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA v 85 " --> pdb=" O ASN v 81 " (cutoff:3.500A) Processing helix chain 'x' and resid 211 through 234 removed outlier: 3.779A pdb=" N GLU x 216 " --> pdb=" O GLU x 212 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE x 217 " --> pdb=" O GLU x 213 " (cutoff:3.500A) Proline residue: x 218 - end of helix removed outlier: 3.629A pdb=" N SER x 233 " --> pdb=" O GLY x 229 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU x 234 " --> pdb=" O ASP x 230 " (cutoff:3.500A) Processing helix chain 'x' and resid 240 through 250 Processing helix chain 'y' and resid 3 through 29 Processing helix chain 'y' and resid 194 through 218 removed outlier: 3.714A pdb=" N ILE y 208 " --> pdb=" O ALA y 204 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN y 209 " --> pdb=" O LYS y 205 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN y 212 " --> pdb=" O ILE y 208 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE y 213 " --> pdb=" O ASN y 209 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS y 214 " --> pdb=" O LEU y 210 " (cutoff:3.500A) Processing helix chain 'y' and resid 222 through 234 removed outlier: 3.501A pdb=" N VAL y 227 " --> pdb=" O GLU y 223 " (cutoff:3.500A) Processing helix chain 'y' and resid 240 through 245 Processing helix chain 'y' and resid 254 through 256 No H-bonds generated for 'chain 'y' and resid 254 through 256' Processing helix chain 'y' and resid 260 through 262 No H-bonds generated for 'chain 'y' and resid 260 through 262' Processing helix chain 'z' and resid 3 through 30 Processing helix chain 'z' and resid 194 through 218 removed outlier: 3.531A pdb=" N ALA z 204 " --> pdb=" O ILE z 200 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR z 205 " --> pdb=" O SER z 201 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU z 217 " --> pdb=" O ALA z 213 " (cutoff:3.500A) Processing helix chain 'z' and resid 224 through 231 Processing sheet with id= A, first strand: chain 'B' and resid 124 through 128 removed outlier: 6.694A pdb=" N TRP B 151 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL B 127 " --> pdb=" O TRP B 151 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 153 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE B 183 " --> pdb=" O SER B 154 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 55 through 59 removed outlier: 3.563A pdb=" N VAL C 55 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN C 76 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE C 59 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL C 74 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASN C 29 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLN C 89 " --> pdb=" O ASN C 29 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE C 31 " --> pdb=" O GLN C 89 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N SER C 91 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N THR C 33 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 153 through 158 removed outlier: 3.503A pdb=" N GLU C 167 " --> pdb=" O GLN C 154 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG C 163 " --> pdb=" O ASP C 158 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 326 through 332 Processing sheet with id= E, first strand: chain 'D' and resid 28 through 32 Processing sheet with id= F, first strand: chain 'E' and resid 125 through 129 Processing sheet with id= G, first strand: chain 'E' and resid 181 through 184 Processing sheet with id= H, first strand: chain 'F' and resid 263 through 267 removed outlier: 7.237A pdb=" N TYR F 135 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N THR F 266 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL F 137 " --> pdb=" O THR F 266 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU F 136 " --> pdb=" O SER F 175 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA F 177 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL F 138 " --> pdb=" O ALA F 177 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE F 179 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU F 217 " --> pdb=" O ALA F 177 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE F 179 " --> pdb=" O GLU F 217 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR F 219 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE F 181 " --> pdb=" O TYR F 219 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N HIS F 221 " --> pdb=" O ILE F 181 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 296 through 298 Processing sheet with id= J, first strand: chain 'F' and resid 339 through 341 Processing sheet with id= K, first strand: chain 'G' and resid 74 through 77 Processing sheet with id= L, first strand: chain 'G' and resid 211 through 213 Processing sheet with id= M, first strand: chain 'G' and resid 238 through 240 Processing sheet with id= N, first strand: chain 'G' and resid 288 through 293 removed outlier: 3.577A pdb=" N THR G 292 " --> pdb=" O ILE G 303 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 348 through 350 Processing sheet with id= P, first strand: chain 'G' and resid 514 through 517 Processing sheet with id= Q, first strand: chain 'G' and resid 582 through 584 removed outlier: 6.320A pdb=" N VAL G 601 " --> pdb=" O LEU G 583 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 111 through 113 Processing sheet with id= S, first strand: chain 'I' and resid 138 through 144 removed outlier: 6.316A pdb=" N GLU I 143 " --> pdb=" O THR I 152 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N THR I 152 " --> pdb=" O GLU I 143 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 57 through 59 removed outlier: 3.735A pdb=" N LEU L 59 " --> pdb=" O PHE L 76 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'M' and resid 71 through 73 Processing sheet with id= V, first strand: chain 'P' and resid 71 through 74 removed outlier: 7.539A pdb=" N VAL P 140 " --> pdb=" O THR P 72 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N PHE P 74 " --> pdb=" O VAL P 140 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE P 142 " --> pdb=" O PHE P 74 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG P 179 " --> pdb=" O VAL P 141 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASN P 143 " --> pdb=" O ARG P 179 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE P 181 " --> pdb=" O ASN P 143 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 95 through 99 Processing sheet with id= X, first strand: chain 'Q' and resid 54 through 58 Processing sheet with id= Y, first strand: chain 'R' and resid 63 through 65 removed outlier: 3.508A pdb=" N VAL R 65 " --> pdb=" O VAL R 105 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'R' and resid 69 through 72 Processing sheet with id= AA, first strand: chain 'S' and resid 14 through 17 Processing sheet with id= AB, first strand: chain 'q' and resid 60 through 63 removed outlier: 3.658A pdb=" N TRP q 75 " --> pdb=" O TYR q 62 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'x' and resid 88 through 90 removed outlier: 6.031A pdb=" N ILE x 109 " --> pdb=" O THR x 89 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'x' and resid 196 through 199 removed outlier: 3.591A pdb=" N ARG x 207 " --> pdb=" O LEU x 197 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLY x 199 " --> pdb=" O PHE x 205 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N PHE x 205 " --> pdb=" O GLY x 199 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'y' and resid 66 through 69 removed outlier: 3.673A pdb=" N GLY y 87 " --> pdb=" O ILE y 68 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'y' and resid 71 through 73 removed outlier: 5.954A pdb=" N ILE y 92 " --> pdb=" O GLN y 72 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'z' and resid 92 through 94 removed outlier: 6.208A pdb=" N THR z 120 " --> pdb=" O SER z 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'z' and resid 105 through 107 2425 hydrogen bonds defined for protein. 6798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.52 Time building geometry restraints manager: 20.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 25184 1.40 - 1.62: 36151 1.62 - 1.84: 651 1.84 - 2.06: 0 2.06 - 2.28: 80 Bond restraints: 62066 Sorted by residual: bond pdb=" C3 UQ9 H 500 " pdb=" C4 UQ9 H 500 " ideal model delta sigma weight residual 1.340 1.534 -0.194 2.00e-02 2.50e+03 9.45e+01 bond pdb=" C1 UQ9 H 500 " pdb=" C6 UQ9 H 500 " ideal model delta sigma weight residual 1.345 1.534 -0.189 2.00e-02 2.50e+03 8.97e+01 bond pdb=" C1 LMN M 503 " pdb=" O5 LMN M 503 " ideal model delta sigma weight residual 1.403 1.535 -0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" CBS LMN M 503 " pdb=" CCM LMN M 503 " ideal model delta sigma weight residual 1.529 1.631 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C4 LMN M 503 " pdb=" O4 LMN M 503 " ideal model delta sigma weight residual 1.409 1.508 -0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 62061 not shown) Histogram of bond angle deviations from ideal: 73.56 - 85.67: 76 85.67 - 97.79: 4 97.79 - 109.90: 7912 109.90 - 122.01: 64730 122.01 - 134.13: 11324 Bond angle restraints: 84046 Sorted by residual: angle pdb=" CA PRO Q 46 " pdb=" N PRO Q 46 " pdb=" CD PRO Q 46 " ideal model delta sigma weight residual 112.00 102.72 9.28 1.40e+00 5.10e-01 4.39e+01 angle pdb=" C ILE L 461 " pdb=" CA ILE L 461 " pdb=" CB ILE L 461 " ideal model delta sigma weight residual 114.35 108.07 6.28 1.06e+00 8.90e-01 3.51e+01 angle pdb=" O11 PTY N 501 " pdb=" P1 PTY N 501 " pdb=" O14 PTY N 501 " ideal model delta sigma weight residual 92.90 109.88 -16.98 3.00e+00 1.11e-01 3.20e+01 angle pdb=" O11 PTY M 502 " pdb=" P1 PTY M 502 " pdb=" O14 PTY M 502 " ideal model delta sigma weight residual 92.90 109.86 -16.96 3.00e+00 1.11e-01 3.20e+01 angle pdb=" O3P PGT y 302 " pdb=" P PGT y 302 " pdb=" O4P PGT y 302 " ideal model delta sigma weight residual 92.82 109.66 -16.84 3.00e+00 1.11e-01 3.15e+01 ... (remaining 84041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 36061 35.00 - 70.00: 825 70.00 - 105.00: 112 105.00 - 140.00: 17 140.00 - 175.00: 3 Dihedral angle restraints: 37018 sinusoidal: 15128 harmonic: 21890 Sorted by residual: dihedral pdb=" C10 FMN F 500 " pdb=" C1' FMN F 500 " pdb=" N10 FMN F 500 " pdb=" C2' FMN F 500 " ideal model delta sinusoidal sigma weight residual 257.59 82.59 175.00 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" CA PHE L 210 " pdb=" C PHE L 210 " pdb=" N CYS L 211 " pdb=" CA CYS L 211 " ideal model delta harmonic sigma weight residual 180.00 154.11 25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ALA H 201 " pdb=" C ALA H 201 " pdb=" N PRO H 202 " pdb=" CA PRO H 202 " ideal model delta harmonic sigma weight residual 180.00 154.70 25.30 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 37015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.970: 9313 0.970 - 1.940: 0 1.940 - 2.910: 0 2.910 - 3.881: 0 3.881 - 4.851: 1 Chirality restraints: 9314 Sorted by residual: chirality pdb=" C1 T7X z 302 " pdb=" C2 T7X z 302 " pdb=" C6 T7X z 302 " pdb=" O1 T7X z 302 " both_signs ideal model delta sigma weight residual False -2.42 2.43 -4.85 2.00e-01 2.50e+01 5.88e+02 chirality pdb=" CB ILE f 5 " pdb=" CA ILE f 5 " pdb=" CG1 ILE f 5 " pdb=" CG2 ILE f 5 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB ILE E 143 " pdb=" CA ILE E 143 " pdb=" CG1 ILE E 143 " pdb=" CG2 ILE E 143 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 9311 not shown) Planarity restraints: 10573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE Q 45 " 0.085 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO Q 46 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO Q 46 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO Q 46 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 62 " 0.066 5.00e-02 4.00e+02 9.92e-02 1.58e+01 pdb=" N PRO L 63 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO L 63 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO L 63 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO x 237 " -0.016 2.00e-02 2.50e+03 3.10e-02 9.63e+00 pdb=" C PRO x 237 " 0.054 2.00e-02 2.50e+03 pdb=" O PRO x 237 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR x 238 " -0.018 2.00e-02 2.50e+03 ... (remaining 10570 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 2 2.05 - 2.77: 10829 2.77 - 3.48: 88139 3.48 - 4.19: 142714 4.19 - 4.90: 260087 Nonbonded interactions: 501771 Sorted by model distance: nonbonded pdb=" CB GLU V 118 " pdb=" NH2 ARG r 86 " model vdw 1.343 3.520 nonbonded pdb=" CG GLU V 118 " pdb=" NH2 ARG r 86 " model vdw 1.933 3.520 nonbonded pdb=" OG1 THR X 14 " pdb=" OD1 ASP a 53 " model vdw 2.099 2.440 nonbonded pdb=" O LEU M 413 " pdb=" OG1 THR M 416 " model vdw 2.116 2.440 nonbonded pdb=" OH TYR x 148 " pdb=" O ASN z 103 " model vdw 2.136 2.440 ... (remaining 501766 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 9.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 41.040 Check model and map are aligned: 0.680 Set scattering table: 0.410 Process input model: 129.660 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.170 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 185.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 : 0.004 0.194 62066 Z= 0.278 Angle : 0.723 16.976 84046 Z= 0.348 Chirality : 0.066 4.851 9314 Planarity : 0.005 0.122 10573 Dihedral : 15.714 175.004 22929 Min Nonbonded Distance : 1.343 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.51 % Favored : 93.47 % Rotamer: Outliers : 0.03 % Allowed : 0.39 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % 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: -0.26 (0.10), residues: 7468 helix: 1.01 (0.09), residues: 3772 sheet: -1.15 (0.26), residues: 437 loop : -1.47 (0.11), residues: 3259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 154 HIS 0.010 0.001 HIS L 239 PHE 0.029 0.001 PHE M 408 TYR 0.039 0.001 TYR o 63 ARG 0.010 0.000 ARG M 435 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1339 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1337 time to evaluate : 5.020 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: D 31 GLU cc_start: 0.7143 (pt0) cc_final: 0.6910 (mt-10) REVERT: D 146 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7868 (tm-30) REVERT: F 315 MET cc_start: 0.7249 (tpt) cc_final: 0.6976 (tpt) REVERT: H 211 GLU cc_start: 0.8475 (pp20) cc_final: 0.7665 (pp20) REVERT: H 223 MET cc_start: 0.7313 (ptm) cc_final: 0.6963 (ptt) REVERT: I 196 ASP cc_start: 0.7829 (p0) cc_final: 0.7562 (p0) REVERT: J 1 MET cc_start: 0.6475 (ppp) cc_final: 0.6216 (ppp) REVERT: J 167 ILE cc_start: 0.8811 (mm) cc_final: 0.8435 (mm) REVERT: K 75 ILE cc_start: 0.9186 (mm) cc_final: 0.8962 (mm) REVERT: L 103 TYR cc_start: 0.6297 (t80) cc_final: 0.5947 (t80) REVERT: L 113 PHE cc_start: 0.7972 (t80) cc_final: 0.7558 (t80) REVERT: N 207 ASP cc_start: 0.8141 (t0) cc_final: 0.7941 (t0) REVERT: N 368 GLN cc_start: 0.6422 (mm110) cc_final: 0.6048 (mm110) REVERT: X 97 GLU cc_start: 0.7275 (pm20) cc_final: 0.6963 (pm20) REVERT: c 44 VAL cc_start: 0.7955 (t) cc_final: 0.7606 (p) REVERT: d 68 ARG cc_start: 0.8213 (ttm110) cc_final: 0.8004 (mtm-85) REVERT: g 46 MET cc_start: 0.6932 (mtt) cc_final: 0.6447 (mtt) REVERT: g 47 ASN cc_start: 0.7511 (m110) cc_final: 0.6910 (p0) REVERT: k 18 TRP cc_start: 0.4560 (p-90) cc_final: 0.4136 (p-90) REVERT: k 28 MET cc_start: 0.3204 (mmt) cc_final: 0.1534 (ptp) REVERT: m 50 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7637 (mmmt) REVERT: p 33 MET cc_start: 0.7616 (tpp) cc_final: 0.7327 (tpt) REVERT: x 167 ILE cc_start: 0.7734 (mm) cc_final: 0.7038 (mm) REVERT: y 202 GLN cc_start: 0.8059 (tp-100) cc_final: 0.7635 (tm-30) REVERT: y 241 ASP cc_start: 0.7914 (m-30) cc_final: 0.7436 (m-30) outliers start: 2 outliers final: 0 residues processed: 1338 average time/residue: 0.5583 time to fit residues: 1264.3653 Evaluate side-chains 1060 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1060 time to evaluate : 5.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 624 optimal weight: 6.9990 chunk 560 optimal weight: 4.9990 chunk 310 optimal weight: 3.9990 chunk 191 optimal weight: 0.4980 chunk 377 optimal weight: 0.9990 chunk 299 optimal weight: 3.9990 chunk 579 optimal weight: 0.6980 chunk 224 optimal weight: 1.9990 chunk 352 optimal weight: 0.5980 chunk 431 optimal weight: 0.7980 chunk 671 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 23 HIS ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 320 ASN G 479 ASN ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 447 ASN L 560 ASN M 317 ASN M 329 GLN N 91 ASN ** P 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 291 HIS Q 86 ASN S 81 GLN ** S 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 77 ASN a 39 HIS c 60 GLN ** d 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 71 GLN ** k 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 37 HIS p 68 GLN ** v 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 112 ASN ** z 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 171 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 62066 Z= 0.210 Angle : 0.602 12.876 84046 Z= 0.300 Chirality : 0.042 0.301 9314 Planarity : 0.005 0.066 10573 Dihedral : 10.259 175.096 8787 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.76 % Favored : 93.20 % Rotamer: Outliers : 1.29 % Allowed : 11.23 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % 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: -0.22 (0.10), residues: 7468 helix: 1.03 (0.09), residues: 3816 sheet: -1.09 (0.25), residues: 437 loop : -1.46 (0.11), residues: 3215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 140 HIS 0.008 0.001 HIS L 357 PHE 0.038 0.002 PHE M 384 TYR 0.028 0.001 TYR L 321 ARG 0.006 0.000 ARG r 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1178 time to evaluate : 5.113 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: D 31 GLU cc_start: 0.7240 (pt0) cc_final: 0.7007 (mt-10) REVERT: F 315 MET cc_start: 0.7280 (tpt) cc_final: 0.6932 (tpt) REVERT: G 394 MET cc_start: 0.7655 (tpp) cc_final: 0.7438 (tpp) REVERT: H 211 GLU cc_start: 0.8809 (pp20) cc_final: 0.8577 (pp20) REVERT: H 223 MET cc_start: 0.7196 (ptm) cc_final: 0.6890 (ptt) REVERT: J 1 MET cc_start: 0.6346 (ppp) cc_final: 0.6002 (ppp) REVERT: K 75 ILE cc_start: 0.9158 (mm) cc_final: 0.8926 (mm) REVERT: L 113 PHE cc_start: 0.8001 (t80) cc_final: 0.7725 (t80) REVERT: L 268 MET cc_start: 0.7683 (tmm) cc_final: 0.7477 (tmm) REVERT: L 608 ARG cc_start: 0.4113 (mpp80) cc_final: 0.2166 (tpt170) REVERT: M 323 MET cc_start: 0.7900 (ttp) cc_final: 0.7690 (ttp) REVERT: N 119 ARG cc_start: 0.7028 (tpp-160) cc_final: 0.6611 (tpp-160) REVERT: N 121 ASP cc_start: 0.6956 (p0) cc_final: 0.6377 (p0) REVERT: N 207 ASP cc_start: 0.8176 (t0) cc_final: 0.7924 (t0) REVERT: N 304 LEU cc_start: 0.8715 (tt) cc_final: 0.7977 (mt) REVERT: N 332 ILE cc_start: 0.7978 (mm) cc_final: 0.7469 (mm) REVERT: N 368 GLN cc_start: 0.6374 (mm110) cc_final: 0.6111 (mm110) REVERT: N 412 TYR cc_start: 0.8276 (t80) cc_final: 0.7947 (t80) REVERT: U 91 MET cc_start: 0.7793 (ttm) cc_final: 0.7559 (tpp) REVERT: Z 94 ASP cc_start: 0.8274 (m-30) cc_final: 0.8061 (m-30) REVERT: c 60 GLN cc_start: 0.6081 (mm110) cc_final: 0.5717 (pt0) REVERT: g 46 MET cc_start: 0.6871 (mtt) cc_final: 0.6538 (mtt) REVERT: g 47 ASN cc_start: 0.7460 (m110) cc_final: 0.6892 (p0) REVERT: k 18 TRP cc_start: 0.4477 (p-90) cc_final: 0.4154 (p-90) REVERT: k 28 MET cc_start: 0.3047 (mmt) cc_final: 0.1473 (ptp) REVERT: l 114 TYR cc_start: 0.6492 (m-80) cc_final: 0.5950 (m-80) REVERT: x 167 ILE cc_start: 0.7686 (mm) cc_final: 0.7455 (mm) REVERT: y 147 MET cc_start: 0.6192 (mtt) cc_final: 0.5758 (mtp) REVERT: y 196 GLU cc_start: 0.7669 (tt0) cc_final: 0.7411 (tt0) REVERT: y 202 GLN cc_start: 0.8055 (tp-100) cc_final: 0.7665 (tm-30) REVERT: y 226 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7933 (mt-10) REVERT: y 241 ASP cc_start: 0.7917 (m-30) cc_final: 0.7452 (m-30) outliers start: 83 outliers final: 60 residues processed: 1212 average time/residue: 0.5630 time to fit residues: 1164.2369 Evaluate side-chains 1143 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1083 time to evaluate : 5.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 601 VAL Chi-restraints excluded: chain H residue 267 ILE Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 550 THR Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 380 ILE Chi-restraints excluded: chain M residue 452 LEU Chi-restraints excluded: chain N residue 22 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 180 LEU Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 331 CYS Chi-restraints excluded: chain N residue 411 PHE Chi-restraints excluded: chain N residue 462 ASP Chi-restraints excluded: chain P residue 162 HIS Chi-restraints excluded: chain P residue 276 MET Chi-restraints excluded: chain P residue 286 ASP Chi-restraints excluded: chain P residue 343 GLN Chi-restraints excluded: chain P residue 366 VAL Chi-restraints excluded: chain Q residue 124 ASP Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 91 ASP Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain b residue 20 SER Chi-restraints excluded: chain c residue 78 PHE Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 38 SER Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain l residue 76 TYR Chi-restraints excluded: chain q residue 65 LEU Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 105 ASP Chi-restraints excluded: chain x residue 211 ASN Chi-restraints excluded: chain z residue 171 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 372 optimal weight: 0.0980 chunk 208 optimal weight: 0.9980 chunk 558 optimal weight: 3.9990 chunk 456 optimal weight: 0.7980 chunk 185 optimal weight: 0.5980 chunk 672 optimal weight: 3.9990 chunk 726 optimal weight: 5.9990 chunk 598 optimal weight: 0.7980 chunk 666 optimal weight: 7.9990 chunk 229 optimal weight: 0.0070 chunk 539 optimal weight: 3.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 ASN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 ASN ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 ASN f 2 ASN ** k 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 83 ASN x 59 GLN ** x 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 112 ASN ** z 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 62066 Z= 0.172 Angle : 0.565 11.780 84046 Z= 0.281 Chirality : 0.041 0.314 9314 Planarity : 0.004 0.070 10573 Dihedral : 9.371 174.515 8787 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.32 % Favored : 93.65 % Rotamer: Outliers : 1.99 % Allowed : 14.11 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % 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: -0.15 (0.10), residues: 7468 helix: 1.08 (0.09), residues: 3813 sheet: -1.10 (0.25), residues: 442 loop : -1.41 (0.11), residues: 3213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 56 HIS 0.007 0.001 HIS o 56 PHE 0.032 0.001 PHE L 559 TYR 0.040 0.001 TYR M 428 ARG 0.005 0.000 ARG r 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1293 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1165 time to evaluate : 5.129 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: C 3 ASN cc_start: 0.7413 (t0) cc_final: 0.7137 (t0) REVERT: F 315 MET cc_start: 0.7271 (tpt) cc_final: 0.6924 (tpt) REVERT: G 156 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: G 394 MET cc_start: 0.7644 (tpp) cc_final: 0.7435 (tpp) REVERT: H 86 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8636 (mm) REVERT: H 204 ASP cc_start: 0.8706 (t0) cc_final: 0.8429 (t0) REVERT: H 223 MET cc_start: 0.7181 (ptm) cc_final: 0.6911 (ptt) REVERT: K 56 MET cc_start: 0.9057 (tpp) cc_final: 0.8798 (tpt) REVERT: L 113 PHE cc_start: 0.8119 (t80) cc_final: 0.7860 (t80) REVERT: L 608 ARG cc_start: 0.4181 (mpp80) cc_final: 0.2182 (tpt170) REVERT: N 138 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7722 (m-10) REVERT: N 207 ASP cc_start: 0.8163 (t0) cc_final: 0.7864 (t0) REVERT: N 255 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7547 (tm-30) REVERT: N 304 LEU cc_start: 0.8638 (tt) cc_final: 0.7956 (mt) REVERT: N 332 ILE cc_start: 0.7880 (mm) cc_final: 0.7355 (mm) REVERT: N 412 TYR cc_start: 0.8291 (t80) cc_final: 0.8062 (t80) REVERT: P 226 GLU cc_start: 0.7703 (pm20) cc_final: 0.7017 (tm-30) REVERT: W 41 MET cc_start: 0.6639 (tpp) cc_final: 0.6222 (tpp) REVERT: X 76 ASP cc_start: 0.7247 (m-30) cc_final: 0.6880 (m-30) REVERT: X 97 GLU cc_start: 0.7244 (pm20) cc_final: 0.7029 (pm20) REVERT: c 34 ARG cc_start: 0.5983 (ptt180) cc_final: 0.5626 (mtm110) REVERT: c 60 GLN cc_start: 0.6133 (mm110) cc_final: 0.5765 (pt0) REVERT: g 46 MET cc_start: 0.6799 (mtt) cc_final: 0.6525 (mtt) REVERT: g 47 ASN cc_start: 0.7469 (m110) cc_final: 0.6920 (p0) REVERT: g 57 ARG cc_start: 0.6525 (mtp85) cc_final: 0.6054 (ttm170) REVERT: k 18 TRP cc_start: 0.4450 (p-90) cc_final: 0.4072 (p-90) REVERT: k 28 MET cc_start: 0.2959 (mmt) cc_final: 0.1404 (ptp) REVERT: p 30 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.7111 (ttp) REVERT: x 167 ILE cc_start: 0.7622 (mm) cc_final: 0.7356 (mm) REVERT: y 147 MET cc_start: 0.6196 (mtt) cc_final: 0.5905 (mtp) REVERT: y 196 GLU cc_start: 0.7597 (tt0) cc_final: 0.6727 (tt0) REVERT: y 202 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7653 (tm-30) REVERT: y 241 ASP cc_start: 0.7875 (m-30) cc_final: 0.7421 (m-30) outliers start: 128 outliers final: 86 residues processed: 1226 average time/residue: 0.5591 time to fit residues: 1165.2146 Evaluate side-chains 1161 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1071 time to evaluate : 5.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 419 MET Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 601 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 228 PHE Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 267 ILE Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain H residue 294 GLN Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 550 THR Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 380 ILE Chi-restraints excluded: chain M residue 452 LEU Chi-restraints excluded: chain N residue 22 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 138 PHE Chi-restraints excluded: chain N residue 180 LEU Chi-restraints excluded: chain N residue 224 SER Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 331 CYS Chi-restraints excluded: chain N residue 411 PHE Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 162 HIS Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 276 MET Chi-restraints excluded: chain P residue 286 ASP Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 343 GLN Chi-restraints excluded: chain P residue 366 VAL Chi-restraints excluded: chain Q residue 124 ASP Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain a residue 10 LEU Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 56 LEU Chi-restraints excluded: chain e residue 16 ASP Chi-restraints excluded: chain f residue 2 ASN Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 38 SER Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain l residue 76 TYR Chi-restraints excluded: chain o residue 61 CYS Chi-restraints excluded: chain p residue 30 MET Chi-restraints excluded: chain p residue 55 VAL Chi-restraints excluded: chain q residue 65 LEU Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 105 ASP Chi-restraints excluded: chain x residue 114 CYS Chi-restraints excluded: chain x residue 168 LEU Chi-restraints excluded: chain x residue 211 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 664 optimal weight: 8.9990 chunk 505 optimal weight: 0.6980 chunk 348 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 320 optimal weight: 4.9990 chunk 451 optimal weight: 2.9990 chunk 674 optimal weight: 1.9990 chunk 714 optimal weight: 5.9990 chunk 352 optimal weight: 2.9990 chunk 639 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 ASN ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 560 ASN N 291 GLN P 291 HIS ** S 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 82 ASN ** k 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 59 GLN ** x 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 112 ASN ** z 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 62066 Z= 0.247 Angle : 0.584 12.305 84046 Z= 0.292 Chirality : 0.043 0.342 9314 Planarity : 0.004 0.065 10573 Dihedral : 8.951 175.109 8787 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.87 % Favored : 93.09 % Rotamer: Outliers : 2.69 % Allowed : 15.46 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % 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: -0.19 (0.10), residues: 7468 helix: 1.05 (0.09), residues: 3818 sheet: -1.14 (0.25), residues: 456 loop : -1.43 (0.11), residues: 3194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 140 HIS 0.004 0.001 HIS L 239 PHE 0.025 0.002 PHE M 384 TYR 0.033 0.001 TYR L 321 ARG 0.008 0.000 ARG W 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1280 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1107 time to evaluate : 5.319 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: E 148 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6957 (tp) REVERT: F 58 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7402 (tp) REVERT: F 315 MET cc_start: 0.7383 (tpt) cc_final: 0.6802 (tpp) REVERT: G 156 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: G 394 MET cc_start: 0.7778 (tpp) cc_final: 0.7542 (tpp) REVERT: G 493 LYS cc_start: 0.8727 (pttt) cc_final: 0.8426 (ttmm) REVERT: H 169 GLU cc_start: 0.7589 (tp30) cc_final: 0.7311 (tp30) REVERT: H 254 ILE cc_start: 0.7407 (pt) cc_final: 0.7088 (mt) REVERT: K 1 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6388 (ppp) REVERT: L 268 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7722 (ppp) REVERT: L 349 PHE cc_start: 0.6927 (OUTLIER) cc_final: 0.6630 (m-80) REVERT: L 381 MET cc_start: 0.6625 (mmp) cc_final: 0.6420 (mmp) REVERT: L 608 ARG cc_start: 0.4223 (mpp80) cc_final: 0.2242 (tpt170) REVERT: N 207 ASP cc_start: 0.8176 (t0) cc_final: 0.7876 (t0) REVERT: N 304 LEU cc_start: 0.8680 (tt) cc_final: 0.8062 (mp) REVERT: N 332 ILE cc_start: 0.7928 (mm) cc_final: 0.7370 (mm) REVERT: N 412 TYR cc_start: 0.8382 (t80) cc_final: 0.8044 (t80) REVERT: P 226 GLU cc_start: 0.7681 (pm20) cc_final: 0.7036 (tm-30) REVERT: S 18 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8487 (pp) REVERT: W 41 MET cc_start: 0.6779 (tpp) cc_final: 0.6351 (tpp) REVERT: Z 94 ASP cc_start: 0.8263 (m-30) cc_final: 0.8005 (m-30) REVERT: g 47 ASN cc_start: 0.7688 (m110) cc_final: 0.7031 (p0) REVERT: g 57 ARG cc_start: 0.6557 (mtp85) cc_final: 0.6104 (ttm170) REVERT: k 18 TRP cc_start: 0.4469 (p-90) cc_final: 0.4121 (p-90) REVERT: k 28 MET cc_start: 0.3165 (mmt) cc_final: 0.1553 (ptp) REVERT: x 167 ILE cc_start: 0.7699 (mm) cc_final: 0.7322 (mm) REVERT: y 147 MET cc_start: 0.6344 (mtt) cc_final: 0.6037 (mtp) REVERT: y 162 MET cc_start: 0.6875 (ptm) cc_final: 0.6231 (ptm) REVERT: y 196 GLU cc_start: 0.7565 (tt0) cc_final: 0.7106 (tt0) REVERT: y 202 GLN cc_start: 0.8073 (tp-100) cc_final: 0.7709 (tm-30) REVERT: y 241 ASP cc_start: 0.7887 (m-30) cc_final: 0.7474 (m-30) outliers start: 173 outliers final: 118 residues processed: 1193 average time/residue: 0.5646 time to fit residues: 1145.8969 Evaluate side-chains 1164 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1039 time to evaluate : 5.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 601 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 228 PHE Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 267 ILE Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain H residue 294 GLN Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 268 MET Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 349 PHE Chi-restraints excluded: chain L residue 550 THR Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 380 ILE Chi-restraints excluded: chain M residue 452 LEU Chi-restraints excluded: chain N residue 22 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 180 LEU Chi-restraints excluded: chain N residue 224 SER Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 331 CYS Chi-restraints excluded: chain N residue 411 PHE Chi-restraints excluded: chain N residue 462 ASP Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 162 HIS Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 276 MET Chi-restraints excluded: chain P residue 286 ASP Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 343 GLN Chi-restraints excluded: chain P residue 366 VAL Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 124 ASP Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 18 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain Z residue 21 LEU Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain a residue 10 LEU Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain b residue 20 SER Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 56 LEU Chi-restraints excluded: chain e residue 16 ASP Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 24 LYS Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 38 SER Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 58 LYS Chi-restraints excluded: chain g residue 69 THR Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain l residue 76 TYR Chi-restraints excluded: chain o residue 61 CYS Chi-restraints excluded: chain p residue 55 VAL Chi-restraints excluded: chain q residue 65 LEU Chi-restraints excluded: chain q residue 87 SER Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 105 ASP Chi-restraints excluded: chain x residue 108 LYS Chi-restraints excluded: chain x residue 114 CYS Chi-restraints excluded: chain x residue 168 LEU Chi-restraints excluded: chain x residue 211 ASN Chi-restraints excluded: chain x residue 228 SER Chi-restraints excluded: chain z residue 13 PHE Chi-restraints excluded: chain z residue 27 CYS Chi-restraints excluded: chain z residue 94 VAL Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 171 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 594 optimal weight: 0.9980 chunk 405 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 531 optimal weight: 0.6980 chunk 294 optimal weight: 7.9990 chunk 609 optimal weight: 1.9990 chunk 493 optimal weight: 0.0040 chunk 0 optimal weight: 3.9990 chunk 364 optimal weight: 3.9990 chunk 641 optimal weight: 0.9980 chunk 180 optimal weight: 0.5980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 ASN K 27 ASN ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 447 ASN P 291 HIS ** S 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 2 ASN ** k 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 59 GLN ** x 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 112 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 62066 Z= 0.180 Angle : 0.557 10.623 84046 Z= 0.279 Chirality : 0.041 0.335 9314 Planarity : 0.004 0.065 10573 Dihedral : 8.638 179.805 8787 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.41 % Favored : 93.55 % Rotamer: Outliers : 2.87 % Allowed : 16.36 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % 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: -0.11 (0.10), residues: 7468 helix: 1.12 (0.09), residues: 3813 sheet: -0.98 (0.26), residues: 432 loop : -1.43 (0.11), residues: 3223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 140 HIS 0.005 0.001 HIS L 239 PHE 0.025 0.001 PHE M 384 TYR 0.034 0.001 TYR L 321 ARG 0.006 0.000 ARG d 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1318 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1133 time to evaluate : 5.160 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: E 148 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6809 (tp) REVERT: F 61 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6925 (pm20) REVERT: F 315 MET cc_start: 0.7326 (tpt) cc_final: 0.6785 (tpp) REVERT: G 156 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: G 394 MET cc_start: 0.7731 (tpp) cc_final: 0.7495 (tpp) REVERT: H 169 GLU cc_start: 0.7577 (tp30) cc_final: 0.7293 (tp30) REVERT: H 204 ASP cc_start: 0.8580 (t0) cc_final: 0.8367 (t0) REVERT: H 223 MET cc_start: 0.7150 (ptm) cc_final: 0.6882 (ptt) REVERT: H 254 ILE cc_start: 0.7406 (pt) cc_final: 0.7167 (mt) REVERT: H 290 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.6783 (t80) REVERT: K 1 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6449 (ppp) REVERT: L 213 MET cc_start: 0.3775 (mmm) cc_final: 0.3437 (mmm) REVERT: L 268 MET cc_start: 0.8172 (tmm) cc_final: 0.7609 (ppp) REVERT: L 349 PHE cc_start: 0.6851 (OUTLIER) cc_final: 0.6541 (m-80) REVERT: L 595 GLU cc_start: 0.5576 (tp30) cc_final: 0.5154 (tp30) REVERT: L 608 ARG cc_start: 0.4269 (mpp80) cc_final: 0.2333 (tpt170) REVERT: M 250 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8701 (p) REVERT: M 428 TYR cc_start: 0.6592 (t80) cc_final: 0.6039 (t80) REVERT: N 207 ASP cc_start: 0.8157 (t0) cc_final: 0.7854 (t0) REVERT: N 304 LEU cc_start: 0.8658 (tt) cc_final: 0.7944 (mt) REVERT: N 332 ILE cc_start: 0.7830 (mm) cc_final: 0.7259 (mm) REVERT: N 412 TYR cc_start: 0.8363 (t80) cc_final: 0.8020 (t80) REVERT: P 226 GLU cc_start: 0.7669 (pm20) cc_final: 0.7041 (tm-30) REVERT: S 18 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8467 (pp) REVERT: T 87 MET cc_start: 0.2654 (tpp) cc_final: 0.1942 (tpt) REVERT: V 70 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: W 41 MET cc_start: 0.6775 (tpp) cc_final: 0.6329 (tpp) REVERT: g 47 ASN cc_start: 0.7633 (m110) cc_final: 0.7011 (p0) REVERT: g 57 ARG cc_start: 0.6530 (mtp85) cc_final: 0.6262 (ttm170) REVERT: k 18 TRP cc_start: 0.4475 (p-90) cc_final: 0.4136 (p-90) REVERT: k 28 MET cc_start: 0.3089 (mmt) cc_final: 0.1544 (ptp) REVERT: r 85 ARG cc_start: 0.6653 (ptt90) cc_final: 0.6427 (ptt90) REVERT: x 138 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7835 (pp) REVERT: x 167 ILE cc_start: 0.7618 (mm) cc_final: 0.7204 (mm) REVERT: y 147 MET cc_start: 0.6318 (mtt) cc_final: 0.5960 (mtp) REVERT: y 162 MET cc_start: 0.6598 (ptm) cc_final: 0.6056 (ptm) REVERT: y 196 GLU cc_start: 0.7515 (tt0) cc_final: 0.7060 (tt0) REVERT: y 202 GLN cc_start: 0.8079 (tp-100) cc_final: 0.7704 (tm-30) REVERT: y 241 ASP cc_start: 0.7879 (m-30) cc_final: 0.7485 (m-30) outliers start: 185 outliers final: 132 residues processed: 1232 average time/residue: 0.5776 time to fit residues: 1219.7560 Evaluate side-chains 1205 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1063 time to evaluate : 5.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain D residue 14 ASN Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 601 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 228 PHE Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 267 ILE Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 140 TRP Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 349 PHE Chi-restraints excluded: chain L residue 550 THR Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 328 ILE Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 380 ILE Chi-restraints excluded: chain M residue 452 LEU Chi-restraints excluded: chain M residue 456 GLU Chi-restraints excluded: chain N residue 22 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 174 GLU Chi-restraints excluded: chain N residue 180 LEU Chi-restraints excluded: chain N residue 224 SER Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 331 CYS Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 398 TYR Chi-restraints excluded: chain N residue 411 PHE Chi-restraints excluded: chain N residue 462 ASP Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 162 HIS Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 276 MET Chi-restraints excluded: chain P residue 286 ASP Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 343 GLN Chi-restraints excluded: chain P residue 366 VAL Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 124 ASP Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 92 ASN Chi-restraints excluded: chain S residue 18 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 20 SER Chi-restraints excluded: chain d residue 56 LEU Chi-restraints excluded: chain e residue 16 ASP Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 24 LYS Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 38 SER Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 58 LYS Chi-restraints excluded: chain g residue 69 THR Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain i residue 6 GLU Chi-restraints excluded: chain i residue 28 GLU Chi-restraints excluded: chain l residue 76 TYR Chi-restraints excluded: chain o residue 61 CYS Chi-restraints excluded: chain p residue 55 VAL Chi-restraints excluded: chain q residue 65 LEU Chi-restraints excluded: chain q residue 87 SER Chi-restraints excluded: chain v residue 76 VAL Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 105 ASP Chi-restraints excluded: chain x residue 108 LYS Chi-restraints excluded: chain x residue 114 CYS Chi-restraints excluded: chain x residue 138 LEU Chi-restraints excluded: chain x residue 211 ASN Chi-restraints excluded: chain z residue 13 PHE Chi-restraints excluded: chain z residue 27 CYS Chi-restraints excluded: chain z residue 108 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 240 optimal weight: 0.8980 chunk 643 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 419 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 715 optimal weight: 4.9990 chunk 593 optimal weight: 0.9990 chunk 331 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 236 optimal weight: 0.7980 chunk 375 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 ASN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 447 ASN M 434 ASN N 312 GLN P 291 HIS ** S 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 60 GLN f 2 ASN ** k 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 59 GLN ** x 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 112 ASN ** y 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 112 ASN ** z 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 171 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 62066 Z= 0.255 Angle : 0.587 11.765 84046 Z= 0.293 Chirality : 0.043 0.373 9314 Planarity : 0.004 0.067 10573 Dihedral : 8.498 175.190 8787 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.04 % Favored : 92.92 % Rotamer: Outliers : 3.64 % Allowed : 17.07 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % 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: -0.16 (0.10), residues: 7468 helix: 1.10 (0.09), residues: 3809 sheet: -1.03 (0.26), residues: 445 loop : -1.45 (0.11), residues: 3214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP L 154 HIS 0.007 0.001 HIS L 239 PHE 0.031 0.002 PHE M 384 TYR 0.031 0.001 TYR L 321 ARG 0.009 0.000 ARG n 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1351 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1117 time to evaluate : 5.141 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: D 146 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7802 (tm-30) REVERT: E 148 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6816 (tp) REVERT: F 58 LEU cc_start: 0.7682 (tp) cc_final: 0.7473 (tp) REVERT: F 61 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6881 (pm20) REVERT: F 315 MET cc_start: 0.7392 (tpt) cc_final: 0.6834 (tpp) REVERT: G 394 MET cc_start: 0.7837 (tpp) cc_final: 0.7580 (tpp) REVERT: G 493 LYS cc_start: 0.8688 (pttt) cc_final: 0.8402 (ttmm) REVERT: G 530 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8287 (tt) REVERT: H 119 TYR cc_start: 0.8121 (m-80) cc_final: 0.7897 (m-80) REVERT: H 169 GLU cc_start: 0.7608 (tp30) cc_final: 0.7330 (tp30) REVERT: H 207 GLU cc_start: 0.8006 (pp20) cc_final: 0.7768 (pp20) REVERT: H 254 ILE cc_start: 0.7615 (pt) cc_final: 0.7385 (mt) REVERT: H 290 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.6979 (t80) REVERT: J 171 MET cc_start: 0.8293 (tpt) cc_final: 0.8055 (tpt) REVERT: K 1 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6516 (ppp) REVERT: K 77 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8976 (mm) REVERT: L 154 TRP cc_start: 0.3261 (OUTLIER) cc_final: 0.2966 (m-10) REVERT: L 213 MET cc_start: 0.3548 (mmm) cc_final: 0.3304 (mmm) REVERT: L 268 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7675 (ppp) REVERT: L 349 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.6516 (m-80) REVERT: L 486 ILE cc_start: 0.4936 (OUTLIER) cc_final: 0.3962 (tp) REVERT: L 595 GLU cc_start: 0.5587 (tp30) cc_final: 0.5165 (tp30) REVERT: L 608 ARG cc_start: 0.4244 (mpp80) cc_final: 0.2385 (tpt170) REVERT: M 112 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.6175 (mmm) REVERT: N 120 PHE cc_start: 0.8523 (t80) cc_final: 0.8010 (t80) REVERT: N 207 ASP cc_start: 0.8202 (t0) cc_final: 0.7852 (t0) REVERT: N 304 LEU cc_start: 0.8674 (tt) cc_final: 0.8015 (mp) REVERT: N 332 ILE cc_start: 0.7853 (mm) cc_final: 0.7240 (mm) REVERT: P 226 GLU cc_start: 0.7711 (pm20) cc_final: 0.7044 (tm-30) REVERT: S 18 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8414 (pp) REVERT: T 87 MET cc_start: 0.2668 (tpp) cc_final: 0.1865 (tpt) REVERT: V 70 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: W 41 MET cc_start: 0.6813 (tpp) cc_final: 0.6332 (tpp) REVERT: Z 94 ASP cc_start: 0.8177 (m-30) cc_final: 0.7965 (m-30) REVERT: g 46 MET cc_start: 0.6946 (mtt) cc_final: 0.6706 (mtt) REVERT: g 47 ASN cc_start: 0.7730 (m110) cc_final: 0.7100 (p0) REVERT: g 57 ARG cc_start: 0.6568 (mtp85) cc_final: 0.6213 (ttm170) REVERT: k 18 TRP cc_start: 0.4399 (p-90) cc_final: 0.4074 (p-90) REVERT: k 28 MET cc_start: 0.3274 (mmt) cc_final: 0.1717 (ptp) REVERT: x 138 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7863 (pp) REVERT: x 167 ILE cc_start: 0.7630 (mm) cc_final: 0.7115 (mm) REVERT: y 147 MET cc_start: 0.6451 (mtt) cc_final: 0.6003 (mtp) REVERT: y 153 ASP cc_start: 0.6148 (OUTLIER) cc_final: 0.5942 (p0) REVERT: y 162 MET cc_start: 0.6646 (ptm) cc_final: 0.6098 (ptm) REVERT: y 196 GLU cc_start: 0.7498 (tt0) cc_final: 0.7014 (tt0) REVERT: y 202 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7714 (tm-30) REVERT: y 241 ASP cc_start: 0.7885 (m-30) cc_final: 0.7523 (m-30) outliers start: 234 outliers final: 169 residues processed: 1245 average time/residue: 0.5592 time to fit residues: 1192.7677 Evaluate side-chains 1249 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1065 time to evaluate : 6.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 14 ASN Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 72 HIS Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 530 LEU Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 601 VAL Chi-restraints excluded: chain G residue 611 VAL Chi-restraints excluded: chain G residue 718 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 228 PHE Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 267 ILE Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 294 GLN Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 140 TRP Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 154 TRP Chi-restraints excluded: chain L residue 268 MET Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 349 PHE Chi-restraints excluded: chain L residue 476 PHE Chi-restraints excluded: chain L residue 486 ILE Chi-restraints excluded: chain L residue 550 THR Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain M residue 380 ILE Chi-restraints excluded: chain M residue 391 LEU Chi-restraints excluded: chain M residue 452 LEU Chi-restraints excluded: chain M residue 456 GLU Chi-restraints excluded: chain N residue 22 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 138 PHE Chi-restraints excluded: chain N residue 174 GLU Chi-restraints excluded: chain N residue 180 LEU Chi-restraints excluded: chain N residue 224 SER Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 331 CYS Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 395 MET Chi-restraints excluded: chain N residue 411 PHE Chi-restraints excluded: chain N residue 462 ASP Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 162 HIS Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 276 MET Chi-restraints excluded: chain P residue 286 ASP Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 343 GLN Chi-restraints excluded: chain P residue 366 VAL Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 124 ASP Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 92 ASN Chi-restraints excluded: chain S residue 18 LEU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain Z residue 21 LEU Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain a residue 10 LEU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 40 ILE Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 20 SER Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 56 LEU Chi-restraints excluded: chain e residue 16 ASP Chi-restraints excluded: chain f residue 2 ASN Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 24 LYS Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 38 SER Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 58 LYS Chi-restraints excluded: chain g residue 69 THR Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain i residue 28 GLU Chi-restraints excluded: chain j residue 31 LEU Chi-restraints excluded: chain l residue 76 TYR Chi-restraints excluded: chain o residue 61 CYS Chi-restraints excluded: chain p residue 55 VAL Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain q residue 65 LEU Chi-restraints excluded: chain q residue 87 SER Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain v residue 76 VAL Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 105 ASP Chi-restraints excluded: chain x residue 108 LYS Chi-restraints excluded: chain x residue 114 CYS Chi-restraints excluded: chain x residue 138 LEU Chi-restraints excluded: chain x residue 211 ASN Chi-restraints excluded: chain x residue 252 LEU Chi-restraints excluded: chain y residue 150 THR Chi-restraints excluded: chain y residue 153 ASP Chi-restraints excluded: chain y residue 261 ASN Chi-restraints excluded: chain z residue 13 PHE Chi-restraints excluded: chain z residue 27 CYS Chi-restraints excluded: chain z residue 94 VAL Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 171 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 689 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 chunk 407 optimal weight: 1.9990 chunk 522 optimal weight: 0.7980 chunk 404 optimal weight: 2.9990 chunk 601 optimal weight: 1.9990 chunk 399 optimal weight: 0.7980 chunk 712 optimal weight: 0.6980 chunk 445 optimal weight: 0.8980 chunk 434 optimal weight: 0.9980 chunk 328 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 ASN I 190 HIS ** K 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 447 ASN P 291 HIS ** S 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 59 GLN ** x 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 112 ASN ** y 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 171 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 62066 Z= 0.201 Angle : 0.577 11.524 84046 Z= 0.288 Chirality : 0.042 0.401 9314 Planarity : 0.004 0.070 10573 Dihedral : 8.315 174.799 8787 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.44 % Favored : 93.52 % Rotamer: Outliers : 3.22 % Allowed : 18.24 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % 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: -0.08 (0.10), residues: 7468 helix: 1.16 (0.09), residues: 3794 sheet: -1.08 (0.26), residues: 460 loop : -1.39 (0.11), residues: 3214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP M 431 HIS 0.006 0.001 HIS L 239 PHE 0.030 0.001 PHE M 384 TYR 0.043 0.001 TYR M 428 ARG 0.007 0.000 ARG d 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1118 time to evaluate : 6.596 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: D 15 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7030 (m-80) REVERT: E 148 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6820 (tp) REVERT: F 58 LEU cc_start: 0.7703 (tp) cc_final: 0.7495 (tp) REVERT: F 61 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6852 (pm20) REVERT: F 315 MET cc_start: 0.7349 (tpt) cc_final: 0.6772 (tpp) REVERT: G 394 MET cc_start: 0.7826 (tpp) cc_final: 0.7543 (tpp) REVERT: G 493 LYS cc_start: 0.8698 (pttt) cc_final: 0.8388 (ttmm) REVERT: G 530 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8275 (tt) REVERT: H 169 GLU cc_start: 0.7590 (tp30) cc_final: 0.7302 (tp30) REVERT: H 223 MET cc_start: 0.7211 (ptm) cc_final: 0.6889 (ptt) REVERT: H 254 ILE cc_start: 0.7645 (pt) cc_final: 0.7410 (mt) REVERT: H 290 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.6869 (t80) REVERT: J 171 MET cc_start: 0.8249 (tpt) cc_final: 0.7977 (tpt) REVERT: K 1 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6561 (ppp) REVERT: K 77 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8972 (mm) REVERT: L 101 ILE cc_start: 0.6868 (mt) cc_final: 0.6626 (mt) REVERT: L 268 MET cc_start: 0.8258 (tmm) cc_final: 0.7697 (ppp) REVERT: L 349 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.6678 (m-80) REVERT: L 486 ILE cc_start: 0.4923 (OUTLIER) cc_final: 0.3959 (tp) REVERT: L 595 GLU cc_start: 0.5593 (tp30) cc_final: 0.5205 (tp30) REVERT: L 608 ARG cc_start: 0.4287 (mpp80) cc_final: 0.2204 (tmt-80) REVERT: M 112 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6236 (mmm) REVERT: N 119 ARG cc_start: 0.6616 (tpp80) cc_final: 0.6374 (tpp80) REVERT: N 138 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7946 (m-10) REVERT: N 207 ASP cc_start: 0.8202 (t0) cc_final: 0.7857 (t0) REVERT: N 304 LEU cc_start: 0.8656 (tt) cc_final: 0.8034 (mm) REVERT: N 332 ILE cc_start: 0.7795 (mm) cc_final: 0.7200 (mm) REVERT: P 226 GLU cc_start: 0.7712 (pm20) cc_final: 0.7037 (tm-30) REVERT: S 18 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8405 (pp) REVERT: T 87 MET cc_start: 0.2657 (tpp) cc_final: 0.2088 (tpt) REVERT: V 70 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: W 41 MET cc_start: 0.6803 (tpp) cc_final: 0.6335 (tpp) REVERT: g 46 MET cc_start: 0.6908 (mtt) cc_final: 0.6683 (mtt) REVERT: g 47 ASN cc_start: 0.7744 (m110) cc_final: 0.7079 (p0) REVERT: g 57 ARG cc_start: 0.6557 (mtp85) cc_final: 0.6178 (ttm170) REVERT: k 18 TRP cc_start: 0.4419 (p-90) cc_final: 0.4096 (p-90) REVERT: k 28 MET cc_start: 0.3243 (mmt) cc_final: 0.1781 (ptp) REVERT: r 85 ARG cc_start: 0.6809 (ptt90) cc_final: 0.6373 (ptt90) REVERT: x 138 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7861 (pp) REVERT: x 167 ILE cc_start: 0.7485 (mm) cc_final: 0.6970 (mm) REVERT: y 147 MET cc_start: 0.6374 (mtt) cc_final: 0.5910 (mtp) REVERT: y 153 ASP cc_start: 0.6185 (OUTLIER) cc_final: 0.5972 (p0) REVERT: y 162 MET cc_start: 0.6685 (ptm) cc_final: 0.6138 (ptm) REVERT: y 196 GLU cc_start: 0.7501 (tt0) cc_final: 0.7007 (tt0) REVERT: y 202 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7706 (tm-30) REVERT: y 241 ASP cc_start: 0.7934 (m-30) cc_final: 0.7628 (m-30) REVERT: z 124 ASP cc_start: 0.6113 (t70) cc_final: 0.5723 (t70) outliers start: 207 outliers final: 155 residues processed: 1229 average time/residue: 0.5595 time to fit residues: 1175.8218 Evaluate side-chains 1248 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1078 time to evaluate : 5.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 72 HIS Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 530 LEU Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 601 VAL Chi-restraints excluded: chain G residue 611 VAL Chi-restraints excluded: chain G residue 718 VAL Chi-restraints excluded: chain G residue 743 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 228 PHE Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 267 ILE Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 140 TRP Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 349 PHE Chi-restraints excluded: chain L residue 476 PHE Chi-restraints excluded: chain L residue 486 ILE Chi-restraints excluded: chain L residue 550 THR Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 328 ILE Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain M residue 380 ILE Chi-restraints excluded: chain M residue 452 LEU Chi-restraints excluded: chain M residue 456 GLU Chi-restraints excluded: chain N residue 22 GLU Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 138 PHE Chi-restraints excluded: chain N residue 180 LEU Chi-restraints excluded: chain N residue 224 SER Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 331 CYS Chi-restraints excluded: chain N residue 338 THR Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 411 PHE Chi-restraints excluded: chain N residue 462 ASP Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 162 HIS Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 276 MET Chi-restraints excluded: chain P residue 286 ASP Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 343 GLN Chi-restraints excluded: chain P residue 366 VAL Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 124 ASP Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 92 ASN Chi-restraints excluded: chain S residue 18 LEU Chi-restraints excluded: chain S residue 59 GLN Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain a residue 10 LEU Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain b residue 20 SER Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 56 LEU Chi-restraints excluded: chain e residue 16 ASP Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 24 LYS Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 38 SER Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 58 LYS Chi-restraints excluded: chain g residue 69 THR Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain i residue 6 GLU Chi-restraints excluded: chain i residue 28 GLU Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain j residue 31 LEU Chi-restraints excluded: chain l residue 76 TYR Chi-restraints excluded: chain o residue 61 CYS Chi-restraints excluded: chain p residue 55 VAL Chi-restraints excluded: chain q residue 65 LEU Chi-restraints excluded: chain v residue 76 VAL Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 105 ASP Chi-restraints excluded: chain x residue 108 LYS Chi-restraints excluded: chain x residue 114 CYS Chi-restraints excluded: chain x residue 138 LEU Chi-restraints excluded: chain x residue 211 ASN Chi-restraints excluded: chain x residue 252 LEU Chi-restraints excluded: chain y residue 112 ASN Chi-restraints excluded: chain y residue 150 THR Chi-restraints excluded: chain y residue 153 ASP Chi-restraints excluded: chain y residue 261 ASN Chi-restraints excluded: chain z residue 13 PHE Chi-restraints excluded: chain z residue 27 CYS Chi-restraints excluded: chain z residue 108 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 440 optimal weight: 0.5980 chunk 284 optimal weight: 8.9990 chunk 425 optimal weight: 0.3980 chunk 214 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 137 optimal weight: 0.0060 chunk 452 optimal weight: 3.9990 chunk 485 optimal weight: 1.9990 chunk 352 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 559 optimal weight: 0.0070 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 ASN ** K 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 112 ASN ** y 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 62066 Z= 0.163 Angle : 0.569 10.534 84046 Z= 0.284 Chirality : 0.041 0.415 9314 Planarity : 0.004 0.076 10573 Dihedral : 8.028 174.120 8787 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.47 % Favored : 93.51 % Rotamer: Outliers : 2.83 % Allowed : 19.02 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % 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: 0.00 (0.10), residues: 7468 helix: 1.22 (0.09), residues: 3806 sheet: -1.02 (0.26), residues: 460 loop : -1.35 (0.11), residues: 3202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP M 431 HIS 0.005 0.001 HIS L 337 PHE 0.030 0.001 PHE M 384 TYR 0.040 0.001 TYR M 428 ARG 0.008 0.000 ARG d 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1145 time to evaluate : 5.117 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: E 148 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6658 (tp) REVERT: F 58 LEU cc_start: 0.7684 (tp) cc_final: 0.7456 (tp) REVERT: F 61 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6817 (pm20) REVERT: F 143 SER cc_start: 0.7057 (OUTLIER) cc_final: 0.6516 (p) REVERT: F 315 MET cc_start: 0.7198 (tpt) cc_final: 0.6725 (tpp) REVERT: G 156 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: G 394 MET cc_start: 0.7725 (tpp) cc_final: 0.7499 (tpp) REVERT: G 493 LYS cc_start: 0.8700 (pttt) cc_final: 0.8411 (ttmm) REVERT: G 530 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8274 (tt) REVERT: H 169 GLU cc_start: 0.7593 (tp30) cc_final: 0.7330 (tp30) REVERT: H 207 GLU cc_start: 0.7782 (pp20) cc_final: 0.7334 (pp20) REVERT: H 223 MET cc_start: 0.7135 (ptm) cc_final: 0.6857 (ptt) REVERT: H 290 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.6769 (t80) REVERT: J 171 MET cc_start: 0.8187 (tpt) cc_final: 0.7943 (tpt) REVERT: K 1 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6530 (ppp) REVERT: K 56 MET cc_start: 0.9213 (tpt) cc_final: 0.8841 (mmt) REVERT: K 77 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8989 (mm) REVERT: L 101 ILE cc_start: 0.6889 (mt) cc_final: 0.6648 (mt) REVERT: L 268 MET cc_start: 0.8212 (tmm) cc_final: 0.7656 (ppp) REVERT: L 349 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6798 (m-80) REVERT: L 486 ILE cc_start: 0.4758 (OUTLIER) cc_final: 0.3811 (tp) REVERT: L 595 GLU cc_start: 0.5647 (tp30) cc_final: 0.5268 (tp30) REVERT: L 608 ARG cc_start: 0.4145 (mpp80) cc_final: 0.2104 (tmt-80) REVERT: M 112 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6442 (mmm) REVERT: M 299 LEU cc_start: 0.8706 (pp) cc_final: 0.8399 (pp) REVERT: N 119 ARG cc_start: 0.6460 (tpp80) cc_final: 0.6258 (tpp80) REVERT: N 207 ASP cc_start: 0.8195 (t0) cc_final: 0.7809 (t0) REVERT: N 296 PHE cc_start: 0.8370 (t80) cc_final: 0.8157 (t80) REVERT: N 304 LEU cc_start: 0.8618 (tt) cc_final: 0.8018 (mm) REVERT: N 332 ILE cc_start: 0.7734 (mm) cc_final: 0.7147 (mm) REVERT: N 447 MET cc_start: 0.8126 (ttp) cc_final: 0.7917 (tmm) REVERT: P 226 GLU cc_start: 0.7732 (pm20) cc_final: 0.7052 (tm-30) REVERT: T 87 MET cc_start: 0.2651 (tpp) cc_final: 0.2097 (tpt) REVERT: V 70 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: W 41 MET cc_start: 0.6861 (tpp) cc_final: 0.6401 (tpp) REVERT: a 54 LYS cc_start: 0.8492 (tmmt) cc_final: 0.7777 (tttp) REVERT: c 60 GLN cc_start: 0.5802 (mm-40) cc_final: 0.5417 (pt0) REVERT: g 47 ASN cc_start: 0.7686 (m110) cc_final: 0.7035 (p0) REVERT: g 57 ARG cc_start: 0.6554 (mtp85) cc_final: 0.6204 (ttm170) REVERT: k 18 TRP cc_start: 0.4468 (p-90) cc_final: 0.4125 (p-90) REVERT: k 28 MET cc_start: 0.3157 (mmt) cc_final: 0.1699 (ptp) REVERT: p 57 TRP cc_start: 0.5279 (m100) cc_final: 0.4808 (m100) REVERT: x 138 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7920 (pp) REVERT: y 147 MET cc_start: 0.6355 (mtt) cc_final: 0.5994 (mtp) REVERT: y 162 MET cc_start: 0.6681 (ptm) cc_final: 0.6182 (ptm) REVERT: y 196 GLU cc_start: 0.7511 (tt0) cc_final: 0.7014 (tt0) REVERT: y 202 GLN cc_start: 0.8040 (tp-100) cc_final: 0.7680 (tm-30) REVERT: y 241 ASP cc_start: 0.7899 (m-30) cc_final: 0.7609 (m-30) REVERT: z 124 ASP cc_start: 0.6095 (t70) cc_final: 0.5710 (t70) outliers start: 182 outliers final: 142 residues processed: 1243 average time/residue: 0.5488 time to fit residues: 1164.6349 Evaluate side-chains 1242 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1087 time to evaluate : 5.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 14 ASN Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 530 LEU Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 601 VAL Chi-restraints excluded: chain G residue 718 VAL Chi-restraints excluded: chain G residue 743 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 228 PHE Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 267 ILE Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 69 MET Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 140 TRP Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 349 PHE Chi-restraints excluded: chain L residue 486 ILE Chi-restraints excluded: chain L residue 550 THR Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 328 ILE Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain M residue 380 ILE Chi-restraints excluded: chain M residue 456 GLU Chi-restraints excluded: chain N residue 22 GLU Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 174 GLU Chi-restraints excluded: chain N residue 180 LEU Chi-restraints excluded: chain N residue 224 SER Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 331 CYS Chi-restraints excluded: chain N residue 338 THR Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 398 TYR Chi-restraints excluded: chain N residue 411 PHE Chi-restraints excluded: chain N residue 462 ASP Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 162 HIS Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 276 MET Chi-restraints excluded: chain P residue 343 GLN Chi-restraints excluded: chain P residue 366 VAL Chi-restraints excluded: chain P residue 375 VAL Chi-restraints excluded: chain Q residue 124 ASP Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 92 ASN Chi-restraints excluded: chain S residue 59 GLN Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain a residue 10 LEU Chi-restraints excluded: chain a residue 15 ILE Chi-restraints excluded: chain a residue 40 ILE Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 56 LEU Chi-restraints excluded: chain e residue 16 ASP Chi-restraints excluded: chain e residue 42 LEU Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 24 LYS Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 38 SER Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 58 LYS Chi-restraints excluded: chain g residue 69 THR Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain i residue 6 GLU Chi-restraints excluded: chain i residue 28 GLU Chi-restraints excluded: chain j residue 31 LEU Chi-restraints excluded: chain l residue 76 TYR Chi-restraints excluded: chain m residue 23 LEU Chi-restraints excluded: chain o residue 61 CYS Chi-restraints excluded: chain p residue 30 MET Chi-restraints excluded: chain p residue 55 VAL Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain q residue 65 LEU Chi-restraints excluded: chain v residue 76 VAL Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 105 ASP Chi-restraints excluded: chain x residue 114 CYS Chi-restraints excluded: chain x residue 138 LEU Chi-restraints excluded: chain x residue 211 ASN Chi-restraints excluded: chain y residue 112 ASN Chi-restraints excluded: chain y residue 150 THR Chi-restraints excluded: chain y residue 261 ASN Chi-restraints excluded: chain z residue 13 PHE Chi-restraints excluded: chain z residue 27 CYS Chi-restraints excluded: chain z residue 108 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 647 optimal weight: 2.9990 chunk 682 optimal weight: 2.9990 chunk 622 optimal weight: 4.9990 chunk 663 optimal weight: 8.9990 chunk 399 optimal weight: 0.5980 chunk 289 optimal weight: 0.0970 chunk 521 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 chunk 599 optimal weight: 0.5980 chunk 627 optimal weight: 0.6980 chunk 661 optimal weight: 5.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 ASN ** K 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 536 ASN ** S 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 14 GLN ** v 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 59 GLN ** x 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 112 ASN ** y 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 62066 Z= 0.188 Angle : 0.579 10.887 84046 Z= 0.288 Chirality : 0.042 0.503 9314 Planarity : 0.004 0.074 10573 Dihedral : 7.907 174.217 8787 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.47 % Favored : 93.51 % Rotamer: Outliers : 2.83 % Allowed : 19.42 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % 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: 0.00 (0.10), residues: 7468 helix: 1.20 (0.09), residues: 3815 sheet: -1.04 (0.26), residues: 450 loop : -1.33 (0.11), residues: 3203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP L 154 HIS 0.005 0.001 HIS L 239 PHE 0.036 0.001 PHE n 52 TYR 0.033 0.001 TYR L 321 ARG 0.009 0.000 ARG n 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1109 time to evaluate : 5.077 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: E 148 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6612 (tp) REVERT: E 158 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8409 (t) REVERT: F 58 LEU cc_start: 0.7678 (tp) cc_final: 0.7431 (tp) REVERT: F 61 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6824 (pm20) REVERT: F 143 SER cc_start: 0.7012 (OUTLIER) cc_final: 0.6492 (p) REVERT: F 315 MET cc_start: 0.7227 (tpt) cc_final: 0.6749 (tpp) REVERT: G 156 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: G 394 MET cc_start: 0.7794 (tpp) cc_final: 0.7507 (tpp) REVERT: G 493 LYS cc_start: 0.8726 (pttt) cc_final: 0.8443 (ttmm) REVERT: G 530 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8272 (tt) REVERT: H 169 GLU cc_start: 0.7604 (tp30) cc_final: 0.7311 (tp30) REVERT: H 223 MET cc_start: 0.7095 (ptm) cc_final: 0.6835 (ptt) REVERT: H 290 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.6768 (t80) REVERT: J 171 MET cc_start: 0.8156 (tpt) cc_final: 0.7870 (tpt) REVERT: K 1 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6502 (ppp) REVERT: K 77 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8999 (mm) REVERT: L 91 PHE cc_start: 0.7072 (t80) cc_final: 0.6862 (t80) REVERT: L 101 ILE cc_start: 0.6967 (mt) cc_final: 0.6751 (mt) REVERT: L 268 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7657 (ppp) REVERT: L 311 ILE cc_start: 0.6417 (mt) cc_final: 0.5933 (mm) REVERT: L 349 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6588 (m-80) REVERT: L 486 ILE cc_start: 0.4702 (OUTLIER) cc_final: 0.3925 (tp) REVERT: L 595 GLU cc_start: 0.5769 (tp30) cc_final: 0.5409 (tp30) REVERT: L 608 ARG cc_start: 0.4091 (mpp80) cc_final: 0.2279 (tpt170) REVERT: N 138 PHE cc_start: 0.7996 (m-10) cc_final: 0.7594 (m-10) REVERT: N 207 ASP cc_start: 0.8206 (t0) cc_final: 0.7810 (t0) REVERT: N 296 PHE cc_start: 0.8387 (t80) cc_final: 0.8172 (t80) REVERT: N 304 LEU cc_start: 0.8633 (tt) cc_final: 0.8026 (mm) REVERT: N 332 ILE cc_start: 0.7729 (mm) cc_final: 0.7143 (mm) REVERT: P 226 GLU cc_start: 0.7713 (pm20) cc_final: 0.7048 (tm-30) REVERT: T 87 MET cc_start: 0.2668 (tpp) cc_final: 0.2108 (tpt) REVERT: V 70 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: W 41 MET cc_start: 0.6842 (tpp) cc_final: 0.6366 (tpp) REVERT: a 54 LYS cc_start: 0.8517 (tmmt) cc_final: 0.7752 (tttp) REVERT: g 46 MET cc_start: 0.6860 (mtt) cc_final: 0.6303 (mtt) REVERT: g 47 ASN cc_start: 0.7329 (m110) cc_final: 0.6862 (p0) REVERT: k 18 TRP cc_start: 0.4425 (p-90) cc_final: 0.4102 (p-90) REVERT: k 28 MET cc_start: 0.3114 (mmt) cc_final: 0.1675 (ptp) REVERT: p 16 ASP cc_start: 0.6410 (p0) cc_final: 0.5913 (m-30) REVERT: x 138 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7897 (pp) REVERT: y 147 MET cc_start: 0.6328 (mtt) cc_final: 0.5987 (mtp) REVERT: y 162 MET cc_start: 0.6697 (ptm) cc_final: 0.6165 (ptm) REVERT: y 196 GLU cc_start: 0.7497 (tt0) cc_final: 0.7005 (tt0) REVERT: y 202 GLN cc_start: 0.8052 (tp-100) cc_final: 0.7690 (tm-30) REVERT: y 241 ASP cc_start: 0.7860 (m-30) cc_final: 0.7532 (m-30) REVERT: z 124 ASP cc_start: 0.6045 (t70) cc_final: 0.5658 (t70) outliers start: 182 outliers final: 152 residues processed: 1204 average time/residue: 0.5789 time to fit residues: 1195.4483 Evaluate side-chains 1237 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1071 time to evaluate : 5.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 14 ASN Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 422 MET Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 530 LEU Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 601 VAL Chi-restraints excluded: chain G residue 718 VAL Chi-restraints excluded: chain G residue 743 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 228 PHE Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 267 ILE Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 69 MET Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 140 TRP Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 268 MET Chi-restraints excluded: chain L residue 349 PHE Chi-restraints excluded: chain L residue 486 ILE Chi-restraints excluded: chain L residue 550 THR Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 328 ILE Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 380 ILE Chi-restraints excluded: chain M residue 445 PHE Chi-restraints excluded: chain M residue 456 GLU Chi-restraints excluded: chain N residue 22 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 174 GLU Chi-restraints excluded: chain N residue 180 LEU Chi-restraints excluded: chain N residue 224 SER Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 331 CYS Chi-restraints excluded: chain N residue 338 THR Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 395 MET Chi-restraints excluded: chain N residue 398 TYR Chi-restraints excluded: chain N residue 411 PHE Chi-restraints excluded: chain N residue 462 ASP Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 162 HIS Chi-restraints excluded: chain P residue 276 MET Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 343 GLN Chi-restraints excluded: chain P residue 366 VAL Chi-restraints excluded: chain P residue 375 VAL Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 124 ASP Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 92 ASN Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain a residue 10 LEU Chi-restraints excluded: chain a residue 15 ILE Chi-restraints excluded: chain a residue 40 ILE Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 56 LEU Chi-restraints excluded: chain e residue 16 ASP Chi-restraints excluded: chain e residue 42 LEU Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 24 LYS Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 38 SER Chi-restraints excluded: chain g residue 58 LYS Chi-restraints excluded: chain g residue 69 THR Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain i residue 28 GLU Chi-restraints excluded: chain i residue 32 GLU Chi-restraints excluded: chain j residue 31 LEU Chi-restraints excluded: chain l residue 76 TYR Chi-restraints excluded: chain m residue 23 LEU Chi-restraints excluded: chain o residue 61 CYS Chi-restraints excluded: chain p residue 30 MET Chi-restraints excluded: chain p residue 55 VAL Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain q residue 65 LEU Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain v residue 76 VAL Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 105 ASP Chi-restraints excluded: chain x residue 108 LYS Chi-restraints excluded: chain x residue 114 CYS Chi-restraints excluded: chain x residue 138 LEU Chi-restraints excluded: chain x residue 211 ASN Chi-restraints excluded: chain x residue 252 LEU Chi-restraints excluded: chain y residue 112 ASN Chi-restraints excluded: chain y residue 150 THR Chi-restraints excluded: chain y residue 261 ASN Chi-restraints excluded: chain z residue 13 PHE Chi-restraints excluded: chain z residue 27 CYS Chi-restraints excluded: chain z residue 108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 435 optimal weight: 0.8980 chunk 701 optimal weight: 0.7980 chunk 428 optimal weight: 2.9990 chunk 332 optimal weight: 7.9990 chunk 487 optimal weight: 0.9980 chunk 736 optimal weight: 0.8980 chunk 677 optimal weight: 4.9990 chunk 586 optimal weight: 0.0040 chunk 60 optimal weight: 2.9990 chunk 452 optimal weight: 0.9990 chunk 359 optimal weight: 0.9980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 ASN ** K 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 83 ASN x 59 GLN ** x 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 112 ASN ** y 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 62066 Z= 0.203 Angle : 0.590 11.910 84046 Z= 0.293 Chirality : 0.043 0.407 9314 Planarity : 0.004 0.075 10573 Dihedral : 7.825 174.320 8787 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.59 % Favored : 93.37 % Rotamer: Outliers : 2.70 % Allowed : 19.62 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % 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: 0.00 (0.10), residues: 7468 helix: 1.20 (0.09), residues: 3813 sheet: -1.02 (0.26), residues: 450 loop : -1.33 (0.11), residues: 3205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP M 431 HIS 0.006 0.001 HIS L 239 PHE 0.032 0.001 PHE M 384 TYR 0.041 0.001 TYR M 428 ARG 0.009 0.000 ARG I 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14936 Ramachandran restraints generated. 7468 Oldfield, 0 Emsley, 7468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1272 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1098 time to evaluate : 5.124 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: E 148 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6605 (tp) REVERT: E 158 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8415 (t) REVERT: F 58 LEU cc_start: 0.7709 (tp) cc_final: 0.7455 (tp) REVERT: F 61 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6812 (pm20) REVERT: F 315 MET cc_start: 0.7241 (tpt) cc_final: 0.6731 (tpp) REVERT: G 156 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: G 394 MET cc_start: 0.7799 (tpp) cc_final: 0.7560 (tpp) REVERT: G 493 LYS cc_start: 0.8723 (pttt) cc_final: 0.8442 (ttmm) REVERT: G 530 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8254 (tt) REVERT: H 223 MET cc_start: 0.7134 (ptm) cc_final: 0.6869 (ptt) REVERT: H 290 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.6791 (t80) REVERT: K 1 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6559 (ppp) REVERT: K 77 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.9002 (mm) REVERT: L 101 ILE cc_start: 0.6980 (mt) cc_final: 0.6777 (mt) REVERT: L 226 PHE cc_start: 0.8020 (t80) cc_final: 0.7483 (t80) REVERT: L 268 MET cc_start: 0.8204 (tmm) cc_final: 0.7659 (ppp) REVERT: L 311 ILE cc_start: 0.6413 (mt) cc_final: 0.5947 (mm) REVERT: L 349 PHE cc_start: 0.6997 (OUTLIER) cc_final: 0.6555 (m-80) REVERT: L 595 GLU cc_start: 0.5751 (tp30) cc_final: 0.5398 (tp30) REVERT: L 608 ARG cc_start: 0.4015 (mpp80) cc_final: 0.2349 (tpt170) REVERT: N 138 PHE cc_start: 0.8027 (m-10) cc_final: 0.7616 (m-10) REVERT: N 207 ASP cc_start: 0.8211 (t0) cc_final: 0.7814 (t0) REVERT: N 304 LEU cc_start: 0.8644 (tt) cc_final: 0.8027 (mm) REVERT: N 332 ILE cc_start: 0.7742 (mm) cc_final: 0.7145 (mm) REVERT: P 226 GLU cc_start: 0.7707 (pm20) cc_final: 0.7035 (tm-30) REVERT: P 300 MET cc_start: 0.8064 (ptp) cc_final: 0.7384 (pmm) REVERT: T 87 MET cc_start: 0.2696 (tpp) cc_final: 0.2076 (tpt) REVERT: V 70 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: W 41 MET cc_start: 0.6865 (tpp) cc_final: 0.6406 (tpp) REVERT: a 54 LYS cc_start: 0.8521 (tmmt) cc_final: 0.7796 (tttp) REVERT: d 68 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7962 (mtm-85) REVERT: j 51 MET cc_start: 0.4228 (mmp) cc_final: 0.3977 (mmt) REVERT: k 18 TRP cc_start: 0.4474 (p-90) cc_final: 0.4156 (p-90) REVERT: k 28 MET cc_start: 0.2975 (mmt) cc_final: 0.1613 (ptp) REVERT: l 104 LYS cc_start: 0.2210 (ptpt) cc_final: 0.1688 (ptmm) REVERT: n 113 LEU cc_start: 0.7418 (pt) cc_final: 0.7199 (mm) REVERT: p 16 ASP cc_start: 0.6458 (p0) cc_final: 0.5885 (m-30) REVERT: x 138 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7913 (pp) REVERT: y 147 MET cc_start: 0.6314 (mtt) cc_final: 0.5961 (mtp) REVERT: y 153 ASP cc_start: 0.6118 (OUTLIER) cc_final: 0.5904 (p0) REVERT: y 162 MET cc_start: 0.6726 (ptm) cc_final: 0.6134 (ptm) REVERT: y 196 GLU cc_start: 0.7489 (tt0) cc_final: 0.6992 (tt0) REVERT: y 202 GLN cc_start: 0.8034 (tp-100) cc_final: 0.7679 (tm-30) REVERT: y 241 ASP cc_start: 0.7837 (m-30) cc_final: 0.7552 (m-30) REVERT: z 124 ASP cc_start: 0.5961 (OUTLIER) cc_final: 0.5571 (t70) outliers start: 174 outliers final: 150 residues processed: 1193 average time/residue: 0.5610 time to fit residues: 1149.9994 Evaluate side-chains 1236 residues out of total 6437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1073 time to evaluate : 5.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 14 ASN Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 422 MET Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 530 LEU Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 601 VAL Chi-restraints excluded: chain G residue 718 VAL Chi-restraints excluded: chain G residue 743 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 228 PHE Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 267 ILE Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 69 MET Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 140 TRP Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 349 PHE Chi-restraints excluded: chain L residue 550 THR Chi-restraints excluded: chain M residue 68 PHE Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 328 ILE Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 380 ILE Chi-restraints excluded: chain M residue 445 PHE Chi-restraints excluded: chain M residue 456 GLU Chi-restraints excluded: chain N residue 22 GLU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 174 GLU Chi-restraints excluded: chain N residue 180 LEU Chi-restraints excluded: chain N residue 224 SER Chi-restraints excluded: chain N residue 257 SER Chi-restraints excluded: chain N residue 331 CYS Chi-restraints excluded: chain N residue 338 THR Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 395 MET Chi-restraints excluded: chain N residue 411 PHE Chi-restraints excluded: chain N residue 462 ASP Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 162 HIS Chi-restraints excluded: chain P residue 276 MET Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 343 GLN Chi-restraints excluded: chain P residue 366 VAL Chi-restraints excluded: chain P residue 375 VAL Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 124 ASP Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 92 ASN Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 130 SER Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain a residue 10 LEU Chi-restraints excluded: chain a residue 15 ILE Chi-restraints excluded: chain a residue 40 ILE Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 56 LEU Chi-restraints excluded: chain e residue 16 ASP Chi-restraints excluded: chain e residue 42 LEU Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 24 LYS Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 38 SER Chi-restraints excluded: chain g residue 58 LYS Chi-restraints excluded: chain g residue 69 THR Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain i residue 28 GLU Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain j residue 31 LEU Chi-restraints excluded: chain l residue 76 TYR Chi-restraints excluded: chain m residue 23 LEU Chi-restraints excluded: chain o residue 61 CYS Chi-restraints excluded: chain p residue 55 VAL Chi-restraints excluded: chain p residue 93 ILE Chi-restraints excluded: chain q residue 65 LEU Chi-restraints excluded: chain q residue 87 SER Chi-restraints excluded: chain r residue 90 THR Chi-restraints excluded: chain v residue 76 VAL Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 105 ASP Chi-restraints excluded: chain x residue 108 LYS Chi-restraints excluded: chain x residue 114 CYS Chi-restraints excluded: chain x residue 138 LEU Chi-restraints excluded: chain x residue 211 ASN Chi-restraints excluded: chain x residue 252 LEU Chi-restraints excluded: chain y residue 112 ASN Chi-restraints excluded: chain y residue 150 THR Chi-restraints excluded: chain y residue 153 ASP Chi-restraints excluded: chain y residue 261 ASN Chi-restraints excluded: chain z residue 13 PHE Chi-restraints excluded: chain z residue 27 CYS Chi-restraints excluded: chain z residue 108 VAL Chi-restraints excluded: chain z residue 124 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 739 random chunks: chunk 465 optimal weight: 3.9990 chunk 624 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 540 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 162 optimal weight: 0.0020 chunk 587 optimal weight: 0.3980 chunk 245 optimal weight: 0.7980 chunk 602 optimal weight: 0.0070 chunk 74 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 overall best weight: 0.3806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 ASN ** K 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 305 ASN ** S 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 110 ASN o 42 GLN ** v 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 59 GLN ** x 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 112 ASN ** y 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.130773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.101424 restraints weight = 115768.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099884 restraints weight = 113411.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.101031 restraints weight = 98928.384| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 62066 Z= 0.168 Angle : 0.579 10.724 84046 Z= 0.288 Chirality : 0.042 0.324 9314 Planarity : 0.004 0.073 10573 Dihedral : 7.659 173.732 8787 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.39 % Favored : 93.60 % Rotamer: Outliers : 2.52 % Allowed : 20.09 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % 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: 0.05 (0.10), residues: 7468 helix: 1.24 (0.09), residues: 3813 sheet: -0.97 (0.26), residues: 450 loop : -1.32 (0.11), residues: 3205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP M 431 HIS 0.005 0.000 HIS L 239 PHE 0.029 0.001 PHE M 384 TYR 0.028 0.001 TYR L 321 ARG 0.009 0.000 ARG I 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17533.42 seconds wall clock time: 305 minutes 36.81 seconds (18336.81 seconds total)