Starting phenix.real_space_refine on Mon Mar 11 08:58:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6t_10105/03_2024/6s6t_10105_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6t_10105/03_2024/6s6t_10105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6t_10105/03_2024/6s6t_10105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6t_10105/03_2024/6s6t_10105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6t_10105/03_2024/6s6t_10105_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6t_10105/03_2024/6s6t_10105_updated.pdb" } resolution = 4.1 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= 0.018 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: 6 Type Number sf(0) Gaussians Fe 36 7.16 5 P 10 5.49 5 S 331 5.16 5 C 35335 2.51 5 N 10164 2.21 5 O 10667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 84": "OD1" <-> "OD2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 441": "OD1" <-> "OD2" Residue "A ASP 481": "OD1" <-> "OD2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A ARG 556": "NH1" <-> "NH2" Residue "A ARG 782": "NH1" <-> "NH2" Residue "A ASP 805": "OD1" <-> "OD2" Residue "A GLU 815": "OE1" <-> "OE2" Residue "A GLU 830": "OE1" <-> "OE2" Residue "A ARG 893": "NH1" <-> "NH2" Residue "A GLU 927": "OE1" <-> "OE2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "A ASP 1070": "OD1" <-> "OD2" Residue "A ARG 1156": "NH1" <-> "NH2" Residue "A GLU 1160": "OE1" <-> "OE2" Residue "A ARG 1173": "NH1" <-> "NH2" Residue "A ASP 1179": "OD1" <-> "OD2" Residue "A ARG 1186": "NH1" <-> "NH2" Residue "A TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1214": "NH1" <-> "NH2" Residue "A GLU 1225": "OE1" <-> "OE2" Residue "A ARG 1252": "NH1" <-> "NH2" Residue "A ASP 1294": "OD1" <-> "OD2" Residue "A ARG 1345": "NH1" <-> "NH2" Residue "A ARG 1449": "NH1" <-> "NH2" Residue "A GLU 1450": "OE1" <-> "OE2" Residue "A ARG 1465": "NH1" <-> "NH2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ASP 166": "OD1" <-> "OD2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B ARG 556": "NH1" <-> "NH2" Residue "B ASP 584": "OD1" <-> "OD2" Residue "B GLU 760": "OE1" <-> "OE2" Residue "B ARG 782": "NH1" <-> "NH2" Residue "B ASP 786": "OD1" <-> "OD2" Residue "B GLU 830": "OE1" <-> "OE2" Residue "B GLU 866": "OE1" <-> "OE2" Residue "B ASP 883": "OD1" <-> "OD2" Residue "B ARG 893": "NH1" <-> "NH2" Residue "B PHE 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 951": "OE1" <-> "OE2" Residue "B ASP 993": "OD1" <-> "OD2" Residue "B ASP 1078": "OD1" <-> "OD2" Residue "B ARG 1156": "NH1" <-> "NH2" Residue "B GLU 1160": "OE1" <-> "OE2" Residue "B ARG 1173": "NH1" <-> "NH2" Residue "B ARG 1186": "NH1" <-> "NH2" Residue "B GLU 1194": "OE1" <-> "OE2" Residue "B ARG 1214": "NH1" <-> "NH2" Residue "B ARG 1252": "NH1" <-> "NH2" Residue "B GLU 1344": "OE1" <-> "OE2" Residue "B ARG 1345": "NH1" <-> "NH2" Residue "B GLU 1358": "OE1" <-> "OE2" Residue "B ASP 1398": "OD1" <-> "OD2" Residue "B GLU 1434": "OE1" <-> "OE2" Residue "B GLU 1442": "OE1" <-> "OE2" Residue "B ARG 1449": "NH1" <-> "NH2" Residue "B GLU 1450": "OE1" <-> "OE2" Residue "B ARG 1465": "NH1" <-> "NH2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C ASP 147": "OD1" <-> "OD2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ASP 262": "OD1" <-> "OD2" Residue "C GLU 389": "OE1" <-> "OE2" Residue "C ASP 460": "OD1" <-> "OD2" Residue "C PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C ARG 556": "NH1" <-> "NH2" Residue "C GLU 769": "OE1" <-> "OE2" Residue "C ARG 782": "NH1" <-> "NH2" Residue "C GLU 815": "OE1" <-> "OE2" Residue "C ARG 893": "NH1" <-> "NH2" Residue "C GLU 927": "OE1" <-> "OE2" Residue "C GLU 951": "OE1" <-> "OE2" Residue "C ASP 1078": "OD1" <-> "OD2" Residue "C ARG 1156": "NH1" <-> "NH2" Residue "C ARG 1173": "NH1" <-> "NH2" Residue "C ASP 1179": "OD1" <-> "OD2" Residue "C ARG 1186": "NH1" <-> "NH2" Residue "C ARG 1214": "NH1" <-> "NH2" Residue "C ARG 1252": "NH1" <-> "NH2" Residue "C ARG 1345": "NH1" <-> "NH2" Residue "C ASP 1407": "OD1" <-> "OD2" Residue "C ARG 1449": "NH1" <-> "NH2" Residue "C GLU 1450": "OE1" <-> "OE2" Residue "C ARG 1465": "NH1" <-> "NH2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D ASP 115": "OD1" <-> "OD2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D ASP 443": "OD1" <-> "OD2" Residue "D PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 556": "NH1" <-> "NH2" Residue "D GLU 726": "OE1" <-> "OE2" Residue "D ARG 782": "NH1" <-> "NH2" Residue "D GLU 815": "OE1" <-> "OE2" Residue "D ASP 890": "OD1" <-> "OD2" Residue "D ARG 893": "NH1" <-> "NH2" Residue "D GLU 927": "OE1" <-> "OE2" Residue "D GLU 951": "OE1" <-> "OE2" Residue "D ARG 1156": "NH1" <-> "NH2" Residue "D ARG 1173": "NH1" <-> "NH2" Residue "D GLU 1176": "OE1" <-> "OE2" Residue "D ARG 1186": "NH1" <-> "NH2" Residue "D GLU 1206": "OE1" <-> "OE2" Residue "D ARG 1214": "NH1" <-> "NH2" Residue "D ARG 1252": "NH1" <-> "NH2" Residue "D ASP 1291": "OD1" <-> "OD2" Residue "D ARG 1345": "NH1" <-> "NH2" Residue "D GLU 1358": "OE1" <-> "OE2" Residue "D GLU 1442": "OE1" <-> "OE2" Residue "D ARG 1449": "NH1" <-> "NH2" Residue "D GLU 1450": "OE1" <-> "OE2" Residue "D ARG 1465": "NH1" <-> "NH2" Residue "E ARG 5": "NH1" <-> "NH2" Residue "E ARG 47": "NH1" <-> "NH2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E ARG 103": "NH1" <-> "NH2" Residue "E ARG 179": "NH1" <-> "NH2" Residue "E ARG 204": "NH1" <-> "NH2" Residue "E ARG 223": "NH1" <-> "NH2" Residue "E ARG 232": "NH1" <-> "NH2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "E ARG 311": "NH1" <-> "NH2" Residue "E ARG 325": "NH1" <-> "NH2" Residue "E ARG 333": "NH1" <-> "NH2" Residue "E ARG 364": "NH1" <-> "NH2" Residue "E ARG 367": "NH1" <-> "NH2" Residue "E GLU 415": "OE1" <-> "OE2" Residue "E ARG 420": "NH1" <-> "NH2" Residue "E ARG 429": "NH1" <-> "NH2" Residue "E ASP 460": "OD1" <-> "OD2" Residue "E GLU 474": "OE1" <-> "OE2" Residue "F ARG 5": "NH1" <-> "NH2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F ARG 47": "NH1" <-> "NH2" Residue "F ARG 77": "NH1" <-> "NH2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F ARG 103": "NH1" <-> "NH2" Residue "F TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 179": "NH1" <-> "NH2" Residue "F GLU 202": "OE1" <-> "OE2" Residue "F ARG 204": "NH1" <-> "NH2" Residue "F ARG 223": "NH1" <-> "NH2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "F ARG 311": "NH1" <-> "NH2" Residue "F ARG 325": "NH1" <-> "NH2" Residue "F ARG 333": "NH1" <-> "NH2" Residue "F ARG 364": "NH1" <-> "NH2" Residue "F ARG 367": "NH1" <-> "NH2" Residue "F ARG 420": "NH1" <-> "NH2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "F GLU 474": "OE1" <-> "OE2" Residue "G ARG 5": "NH1" <-> "NH2" Residue "G ARG 47": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G ARG 103": "NH1" <-> "NH2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G ARG 179": "NH1" <-> "NH2" Residue "G ASP 181": "OD1" <-> "OD2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "G ARG 223": "NH1" <-> "NH2" Residue "G ARG 232": "NH1" <-> "NH2" Residue "G ARG 247": "NH1" <-> "NH2" Residue "G ASP 304": "OD1" <-> "OD2" Residue "G ARG 311": "NH1" <-> "NH2" Residue "G ARG 325": "NH1" <-> "NH2" Residue "G ARG 333": "NH1" <-> "NH2" Residue "G GLU 344": "OE1" <-> "OE2" Residue "G ARG 364": "NH1" <-> "NH2" Residue "G ARG 367": "NH1" <-> "NH2" Residue "G ASP 374": "OD1" <-> "OD2" Residue "G GLU 403": "OE1" <-> "OE2" Residue "G GLU 415": "OE1" <-> "OE2" Residue "G ARG 420": "NH1" <-> "NH2" Residue "G ARG 429": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 56543 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "B" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "C" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "D" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "E" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3612 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3612 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3612 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8585 SG CYS A1113 58.027 148.354 67.636 1.00 48.66 S ATOM 8499 SG CYS A1102 61.549 144.976 67.678 1.00 46.01 S ATOM 8548 SG CYS A1108 62.702 149.858 69.310 1.00 55.93 S ATOM 19922 SG CYS B1113 28.054 85.130 107.898 1.00119.77 S ATOM 19836 SG CYS B1102 31.865 82.064 109.858 1.00122.54 S ATOM 19922 SG CYS B1113 28.054 85.130 107.898 1.00119.77 S ATOM 19885 SG CYS B1108 30.476 82.708 104.296 1.00120.39 S ATOM 31259 SG CYS C1113 136.590 57.080 71.108 1.00 48.85 S ATOM 31173 SG CYS C1102 131.933 60.711 69.603 1.00 42.66 S ATOM 31222 SG CYS C1108 130.767 55.276 72.698 1.00 53.14 S ATOM 42596 SG CYS D1113 165.955 122.538 106.625 1.00 73.28 S ATOM 42510 SG CYS D1102 161.140 125.000 108.192 1.00 68.94 S ATOM 42559 SG CYS D1108 163.205 124.318 102.894 1.00 70.77 S ATOM 45743 SG CYS E 51 58.874 150.120 56.792 1.00 53.57 S ATOM 45743 SG CYS E 51 58.874 150.120 56.792 1.00 53.57 S ATOM 45778 SG CYS E 56 58.104 149.749 51.934 1.00 48.22 S ATOM 45722 SG CYS E 48 56.197 154.189 54.940 1.00 61.73 S ATOM 46193 SG CYS E 109 53.910 149.087 54.813 1.00 51.65 S ATOM 45810 SG CYS E 60 56.778 146.988 43.514 1.00 53.20 S ATOM 46166 SG CYS E 105 53.494 147.386 45.022 1.00 60.80 S ATOM 45810 SG CYS E 60 56.778 146.988 43.514 1.00 53.20 S ATOM 46117 SG CYS E 99 52.223 145.941 41.534 1.00 63.29 S ATOM 46166 SG CYS E 105 53.494 147.386 45.022 1.00 60.80 S ATOM 49334 SG CYS F 48 137.382 50.603 58.145 1.00 61.51 S ATOM 49355 SG CYS F 51 135.027 54.115 59.686 1.00 51.90 S ATOM 49390 SG CYS F 56 135.511 54.381 55.180 1.00 49.09 S ATOM 49334 SG CYS F 48 137.382 50.603 58.145 1.00 61.51 S ATOM 49805 SG CYS F 109 140.053 54.523 58.014 1.00 53.53 S ATOM 49805 SG CYS F 109 140.053 54.523 58.014 1.00 53.53 S ATOM 49778 SG CYS F 105 139.740 56.307 48.094 1.00 67.49 S ATOM 49422 SG CYS F 60 136.523 56.484 46.732 1.00 54.80 S ATOM 49729 SG CYS F 99 141.358 57.227 44.458 1.00 72.00 S ATOM 49778 SG CYS F 105 139.740 56.307 48.094 1.00 67.49 S ATOM 52967 SG CYS G 51 170.773 132.556 108.282 1.00 91.57 S ATOM 53002 SG CYS G 56 173.444 136.478 110.591 1.00 85.64 S ATOM 52946 SG CYS G 48 176.187 133.012 106.304 1.00 95.89 S ATOM 53417 SG CYS G 109 175.287 131.171 112.069 1.00 83.15 S ATOM 53390 SG CYS G 105 178.036 139.267 116.895 1.00110.02 S ATOM 53034 SG CYS G 60 176.223 142.599 115.825 1.00 98.57 S ATOM 53341 SG CYS G 99 181.158 141.064 119.295 1.00123.37 S ATOM 53390 SG CYS G 105 178.036 139.267 116.895 1.00110.02 S Time building chain proxies: 23.26, per 1000 atoms: 0.41 Number of scatterers: 56543 At special positions: 0 Unit cell: (216.752, 205.344, 171.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 36 26.01 S 331 16.00 P 10 15.00 O 10667 8.00 N 10164 7.00 C 35335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 16.62 Conformation dependent library (CDL) restraints added in 7.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A1502 " pdb="FE1 F3S A1502 " - pdb=" SG CYS A1113 " pdb="FE3 F3S A1502 " - pdb=" SG CYS A1102 " pdb="FE4 F3S A1502 " - pdb=" SG CYS A1108 " pdb=" F3S B1502 " pdb="FE3 F3S B1502 " - pdb=" SG CYS B1102 " pdb="FE4 F3S B1502 " - pdb=" SG CYS B1108 " pdb="FE1 F3S B1502 " - pdb=" SG CYS B1113 " pdb=" F3S C1502 " pdb="FE1 F3S C1502 " - pdb=" SG CYS C1113 " pdb="FE3 F3S C1502 " - pdb=" SG CYS C1102 " pdb="FE4 F3S C1502 " - pdb=" SG CYS C1108 " pdb=" F3S D1502 " pdb="FE3 F3S D1502 " - pdb=" SG CYS D1102 " pdb="FE4 F3S D1502 " - pdb=" SG CYS D1108 " pdb="FE1 F3S D1502 " - pdb=" SG CYS D1113 " pdb=" SF4 E 501 " pdb="FE1 SF4 E 501 " - pdb=" SG CYS E 51 " pdb="FE4 SF4 E 501 " - pdb=" SG CYS E 109 " pdb="FE3 SF4 E 501 " - pdb=" SG CYS E 48 " pdb="FE2 SF4 E 501 " - pdb=" SG CYS E 56 " pdb=" SF4 E 502 " pdb="FE1 SF4 E 502 " - pdb=" SG CYS E 105 " pdb="FE2 SF4 E 502 " - pdb=" SG CYS E 60 " pdb="FE4 SF4 E 502 " - pdb=" SG CYS E 99 " pdb=" SF4 F 501 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 48 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 51 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 56 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 109 " pdb=" SF4 F 502 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 105 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 60 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 99 " pdb=" SF4 G 501 " pdb="FE4 SF4 G 501 " - pdb=" SG CYS G 109 " pdb="FE2 SF4 G 501 " - pdb=" SG CYS G 56 " pdb="FE1 SF4 G 501 " - pdb=" SG CYS G 51 " pdb="FE3 SF4 G 501 " - pdb=" SG CYS G 48 " pdb=" SF4 G 502 " pdb="FE1 SF4 G 502 " - pdb=" SG CYS G 105 " pdb="FE2 SF4 G 502 " - pdb=" SG CYS G 60 " pdb="FE4 SF4 G 502 " - pdb=" SG CYS G 99 " Number of angles added : 99 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13166 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 303 helices and 52 sheets defined 35.2% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.99 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.841A pdb=" N ALA A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 85 through 97 Processing helix chain 'A' and resid 119 through 124 removed outlier: 4.125A pdb=" N THR A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 161 Processing helix chain 'A' and resid 186 through 191 removed outlier: 4.160A pdb=" N THR A 189 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 254 through 263 removed outlier: 7.209A pdb=" N THR A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 removed outlier: 4.066A pdb=" N ALA A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 403 through 413 removed outlier: 4.855A pdb=" N LEU A 413 " --> pdb=" O HIS A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.641A pdb=" N VAL A 420 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 444 through 454 removed outlier: 3.571A pdb=" N PHE A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 463 removed outlier: 3.896A pdb=" N LEU A 463 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 495 through 498 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 581 through 597 removed outlier: 4.042A pdb=" N GLU A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 633 Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 670 through 680 Processing helix chain 'A' and resid 689 through 711 removed outlier: 4.726A pdb=" N MET A 711 " --> pdb=" O ILE A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 718 No H-bonds generated for 'chain 'A' and resid 716 through 718' Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 751 through 766 Processing helix chain 'A' and resid 792 through 804 Processing helix chain 'A' and resid 807 through 818 Processing helix chain 'A' and resid 825 through 828 No H-bonds generated for 'chain 'A' and resid 825 through 828' Processing helix chain 'A' and resid 846 through 852 removed outlier: 5.015A pdb=" N ARG A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 878 removed outlier: 3.984A pdb=" N ILE A 878 " --> pdb=" O ALA A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 920 through 922 No H-bonds generated for 'chain 'A' and resid 920 through 922' Processing helix chain 'A' and resid 951 through 957 Processing helix chain 'A' and resid 977 through 990 Processing helix chain 'A' and resid 1006 through 1015 Processing helix chain 'A' and resid 1035 through 1039 Processing helix chain 'A' and resid 1045 through 1058 Processing helix chain 'A' and resid 1062 through 1064 No H-bonds generated for 'chain 'A' and resid 1062 through 1064' Processing helix chain 'A' and resid 1076 through 1085 Processing helix chain 'A' and resid 1093 through 1100 Processing helix chain 'A' and resid 1108 through 1110 No H-bonds generated for 'chain 'A' and resid 1108 through 1110' Processing helix chain 'A' and resid 1132 through 1153 Processing helix chain 'A' and resid 1158 through 1160 No H-bonds generated for 'chain 'A' and resid 1158 through 1160' Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1183 through 1187 Processing helix chain 'A' and resid 1211 through 1216 Processing helix chain 'A' and resid 1220 through 1225 Processing helix chain 'A' and resid 1244 through 1253 Processing helix chain 'A' and resid 1317 through 1319 No H-bonds generated for 'chain 'A' and resid 1317 through 1319' Processing helix chain 'A' and resid 1401 through 1404 No H-bonds generated for 'chain 'A' and resid 1401 through 1404' Processing helix chain 'A' and resid 1418 through 1434 Processing helix chain 'A' and resid 1439 through 1445 Processing helix chain 'A' and resid 1460 through 1462 No H-bonds generated for 'chain 'A' and resid 1460 through 1462' Processing helix chain 'B' and resid 15 through 27 removed outlier: 3.930A pdb=" N ALA B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 62 Processing helix chain 'B' and resid 83 through 97 removed outlier: 3.774A pdb=" N GLU B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 162 removed outlier: 3.544A pdb=" N GLU B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 4.370A pdb=" N THR B 189 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 196 Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 240 through 250 removed outlier: 4.634A pdb=" N THR B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ARG B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 263 Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 311 through 323 Processing helix chain 'B' and resid 403 through 411 Processing helix chain 'B' and resid 420 through 422 No H-bonds generated for 'chain 'B' and resid 420 through 422' Processing helix chain 'B' and resid 427 through 431 Processing helix chain 'B' and resid 444 through 454 removed outlier: 3.629A pdb=" N PHE B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 463 Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 495 through 498 Processing helix chain 'B' and resid 538 through 540 No H-bonds generated for 'chain 'B' and resid 538 through 540' Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 581 through 598 removed outlier: 3.902A pdb=" N ARG B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 633 Processing helix chain 'B' and resid 652 through 661 removed outlier: 3.877A pdb=" N ALA B 656 " --> pdb=" O THR B 652 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 661 " --> pdb=" O VAL B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 680 Processing helix chain 'B' and resid 689 through 709 Processing helix chain 'B' and resid 716 through 718 No H-bonds generated for 'chain 'B' and resid 716 through 718' Processing helix chain 'B' and resid 732 through 737 Processing helix chain 'B' and resid 752 through 766 Processing helix chain 'B' and resid 792 through 803 Processing helix chain 'B' and resid 808 through 818 Processing helix chain 'B' and resid 825 through 828 No H-bonds generated for 'chain 'B' and resid 825 through 828' Processing helix chain 'B' and resid 846 through 852 removed outlier: 5.254A pdb=" N ARG B 852 " --> pdb=" O ALA B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 878 removed outlier: 3.660A pdb=" N ILE B 878 " --> pdb=" O ALA B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 893 No H-bonds generated for 'chain 'B' and resid 891 through 893' Processing helix chain 'B' and resid 921 through 923 No H-bonds generated for 'chain 'B' and resid 921 through 923' Processing helix chain 'B' and resid 946 through 948 No H-bonds generated for 'chain 'B' and resid 946 through 948' Processing helix chain 'B' and resid 951 through 956 Processing helix chain 'B' and resid 977 through 990 Processing helix chain 'B' and resid 1006 through 1016 removed outlier: 3.866A pdb=" N LYS B1015 " --> pdb=" O ALA B1011 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B1016 " --> pdb=" O GLY B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1039 Processing helix chain 'B' and resid 1045 through 1058 removed outlier: 3.707A pdb=" N GLN B1054 " --> pdb=" O SER B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1062 through 1064 No H-bonds generated for 'chain 'B' and resid 1062 through 1064' Processing helix chain 'B' and resid 1076 through 1085 Processing helix chain 'B' and resid 1093 through 1100 Processing helix chain 'B' and resid 1108 through 1110 No H-bonds generated for 'chain 'B' and resid 1108 through 1110' Processing helix chain 'B' and resid 1125 through 1127 No H-bonds generated for 'chain 'B' and resid 1125 through 1127' Processing helix chain 'B' and resid 1132 through 1153 Processing helix chain 'B' and resid 1158 through 1160 No H-bonds generated for 'chain 'B' and resid 1158 through 1160' Processing helix chain 'B' and resid 1165 through 1167 No H-bonds generated for 'chain 'B' and resid 1165 through 1167' Processing helix chain 'B' and resid 1183 through 1187 Processing helix chain 'B' and resid 1211 through 1218 Processing helix chain 'B' and resid 1221 through 1224 No H-bonds generated for 'chain 'B' and resid 1221 through 1224' Processing helix chain 'B' and resid 1244 through 1253 Processing helix chain 'B' and resid 1401 through 1403 No H-bonds generated for 'chain 'B' and resid 1401 through 1403' Processing helix chain 'B' and resid 1418 through 1435 Processing helix chain 'B' and resid 1439 through 1445 Processing helix chain 'B' and resid 1447 through 1453 removed outlier: 4.106A pdb=" N VAL B1451 " --> pdb=" O TRP B1447 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR B1452 " --> pdb=" O ALA B1448 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LYS B1453 " --> pdb=" O ARG B1449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1447 through 1453' Processing helix chain 'B' and resid 1460 through 1462 No H-bonds generated for 'chain 'B' and resid 1460 through 1462' Processing helix chain 'C' and resid 15 through 27 removed outlier: 3.908A pdb=" N ALA C 27 " --> pdb=" O GLU C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 52 through 62 Processing helix chain 'C' and resid 85 through 97 Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 119 through 124 removed outlier: 4.168A pdb=" N THR C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 162 removed outlier: 3.804A pdb=" N GLU C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 191 removed outlier: 4.032A pdb=" N LEU C 188 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR C 189 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 196 Processing helix chain 'C' and resid 219 through 221 No H-bonds generated for 'chain 'C' and resid 219 through 221' Processing helix chain 'C' and resid 238 through 249 removed outlier: 4.194A pdb=" N ASN C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TRP C 243 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 273 through 287 removed outlier: 4.182A pdb=" N ALA C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 311 through 323 Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'C' and resid 403 through 411 Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'C' and resid 444 through 454 removed outlier: 3.955A pdb=" N PHE C 454 " --> pdb=" O ARG C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 463 No H-bonds generated for 'chain 'C' and resid 460 through 463' Processing helix chain 'C' and resid 465 through 470 Processing helix chain 'C' and resid 486 through 488 No H-bonds generated for 'chain 'C' and resid 486 through 488' Processing helix chain 'C' and resid 495 through 497 No H-bonds generated for 'chain 'C' and resid 495 through 497' Processing helix chain 'C' and resid 517 through 519 No H-bonds generated for 'chain 'C' and resid 517 through 519' Processing helix chain 'C' and resid 537 through 540 removed outlier: 3.605A pdb=" N THR C 540 " --> pdb=" O GLU C 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 537 through 540' Processing helix chain 'C' and resid 552 through 562 Processing helix chain 'C' and resid 575 through 577 No H-bonds generated for 'chain 'C' and resid 575 through 577' Processing helix chain 'C' and resid 581 through 599 removed outlier: 4.494A pdb=" N GLU C 594 " --> pdb=" O ARG C 590 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY C 599 " --> pdb=" O ASP C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 634 Processing helix chain 'C' and resid 637 through 639 No H-bonds generated for 'chain 'C' and resid 637 through 639' Processing helix chain 'C' and resid 652 through 660 Processing helix chain 'C' and resid 669 through 681 removed outlier: 3.722A pdb=" N GLU C 673 " --> pdb=" O TYR C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 711 removed outlier: 4.575A pdb=" N MET C 711 " --> pdb=" O ILE C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 718 No H-bonds generated for 'chain 'C' and resid 716 through 718' Processing helix chain 'C' and resid 732 through 738 Processing helix chain 'C' and resid 752 through 765 Processing helix chain 'C' and resid 792 through 804 Processing helix chain 'C' and resid 807 through 818 Processing helix chain 'C' and resid 825 through 827 No H-bonds generated for 'chain 'C' and resid 825 through 827' Processing helix chain 'C' and resid 840 through 842 No H-bonds generated for 'chain 'C' and resid 840 through 842' Processing helix chain 'C' and resid 846 through 852 removed outlier: 4.317A pdb=" N ARG C 852 " --> pdb=" O ALA C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 878 removed outlier: 4.223A pdb=" N ILE C 878 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 893 No H-bonds generated for 'chain 'C' and resid 891 through 893' Processing helix chain 'C' and resid 946 through 948 No H-bonds generated for 'chain 'C' and resid 946 through 948' Processing helix chain 'C' and resid 951 through 957 Processing helix chain 'C' and resid 977 through 990 Processing helix chain 'C' and resid 1006 through 1016 removed outlier: 3.659A pdb=" N LYS C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA C1016 " --> pdb=" O GLY C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1039 Processing helix chain 'C' and resid 1045 through 1058 Processing helix chain 'C' and resid 1076 through 1085 Processing helix chain 'C' and resid 1093 through 1100 Processing helix chain 'C' and resid 1108 through 1110 No H-bonds generated for 'chain 'C' and resid 1108 through 1110' Processing helix chain 'C' and resid 1124 through 1126 No H-bonds generated for 'chain 'C' and resid 1124 through 1126' Processing helix chain 'C' and resid 1132 through 1153 Processing helix chain 'C' and resid 1158 through 1160 No H-bonds generated for 'chain 'C' and resid 1158 through 1160' Processing helix chain 'C' and resid 1165 through 1167 No H-bonds generated for 'chain 'C' and resid 1165 through 1167' Processing helix chain 'C' and resid 1183 through 1186 Processing helix chain 'C' and resid 1211 through 1216 Processing helix chain 'C' and resid 1220 through 1225 Processing helix chain 'C' and resid 1245 through 1253 Processing helix chain 'C' and resid 1401 through 1403 No H-bonds generated for 'chain 'C' and resid 1401 through 1403' Processing helix chain 'C' and resid 1418 through 1435 Processing helix chain 'C' and resid 1439 through 1445 Processing helix chain 'C' and resid 1447 through 1449 No H-bonds generated for 'chain 'C' and resid 1447 through 1449' Processing helix chain 'C' and resid 1460 through 1462 No H-bonds generated for 'chain 'C' and resid 1460 through 1462' Processing helix chain 'D' and resid 15 through 27 removed outlier: 3.736A pdb=" N ALA D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 83 through 97 removed outlier: 4.385A pdb=" N GLU D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 162 removed outlier: 3.760A pdb=" N GLU D 162 " --> pdb=" O ALA D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 191 No H-bonds generated for 'chain 'D' and resid 188 through 191' Processing helix chain 'D' and resid 193 through 196 Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 238 through 250 removed outlier: 3.801A pdb=" N ASN D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR D 249 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 263 Processing helix chain 'D' and resid 273 through 287 removed outlier: 4.513A pdb=" N ALA D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 403 through 411 Processing helix chain 'D' and resid 416 through 419 No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 427 through 431 Processing helix chain 'D' and resid 444 through 454 removed outlier: 3.775A pdb=" N PHE D 454 " --> pdb=" O ARG D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 463 No H-bonds generated for 'chain 'D' and resid 460 through 463' Processing helix chain 'D' and resid 466 through 470 Processing helix chain 'D' and resid 495 through 498 Processing helix chain 'D' and resid 517 through 519 No H-bonds generated for 'chain 'D' and resid 517 through 519' Processing helix chain 'D' and resid 552 through 562 Processing helix chain 'D' and resid 575 through 577 No H-bonds generated for 'chain 'D' and resid 575 through 577' Processing helix chain 'D' and resid 581 through 599 removed outlier: 4.107A pdb=" N GLU D 594 " --> pdb=" O ARG D 590 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY D 599 " --> pdb=" O ASP D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 633 Processing helix chain 'D' and resid 637 through 639 No H-bonds generated for 'chain 'D' and resid 637 through 639' Processing helix chain 'D' and resid 652 through 661 removed outlier: 3.699A pdb=" N VAL D 661 " --> pdb=" O VAL D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 680 removed outlier: 3.769A pdb=" N GLU D 673 " --> pdb=" O TYR D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 709 Processing helix chain 'D' and resid 716 through 719 No H-bonds generated for 'chain 'D' and resid 716 through 719' Processing helix chain 'D' and resid 732 through 738 Processing helix chain 'D' and resid 751 through 766 removed outlier: 3.674A pdb=" N GLN D 755 " --> pdb=" O LEU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 804 Processing helix chain 'D' and resid 807 through 818 Processing helix chain 'D' and resid 825 through 827 No H-bonds generated for 'chain 'D' and resid 825 through 827' Processing helix chain 'D' and resid 840 through 842 No H-bonds generated for 'chain 'D' and resid 840 through 842' Processing helix chain 'D' and resid 847 through 850 No H-bonds generated for 'chain 'D' and resid 847 through 850' Processing helix chain 'D' and resid 865 through 878 removed outlier: 4.283A pdb=" N ILE D 878 " --> pdb=" O ALA D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 891 through 894 Processing helix chain 'D' and resid 920 through 922 No H-bonds generated for 'chain 'D' and resid 920 through 922' Processing helix chain 'D' and resid 951 through 957 Processing helix chain 'D' and resid 977 through 990 Processing helix chain 'D' and resid 1006 through 1016 removed outlier: 3.562A pdb=" N LYS D1015 " --> pdb=" O ALA D1011 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D1016 " --> pdb=" O GLY D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1035 through 1039 Processing helix chain 'D' and resid 1045 through 1058 removed outlier: 3.603A pdb=" N GLN D1054 " --> pdb=" O SER D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1062 through 1064 No H-bonds generated for 'chain 'D' and resid 1062 through 1064' Processing helix chain 'D' and resid 1076 through 1085 Processing helix chain 'D' and resid 1093 through 1100 Processing helix chain 'D' and resid 1108 through 1110 No H-bonds generated for 'chain 'D' and resid 1108 through 1110' Processing helix chain 'D' and resid 1122 through 1127 removed outlier: 3.963A pdb=" N GLN D1126 " --> pdb=" O ASP D1122 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS D1127 " --> pdb=" O LYS D1123 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1122 through 1127' Processing helix chain 'D' and resid 1132 through 1153 Processing helix chain 'D' and resid 1158 through 1160 No H-bonds generated for 'chain 'D' and resid 1158 through 1160' Processing helix chain 'D' and resid 1165 through 1167 No H-bonds generated for 'chain 'D' and resid 1165 through 1167' Processing helix chain 'D' and resid 1183 through 1187 Processing helix chain 'D' and resid 1211 through 1218 removed outlier: 3.558A pdb=" N ASP D1218 " --> pdb=" O ARG D1214 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1224 Processing helix chain 'D' and resid 1245 through 1253 Processing helix chain 'D' and resid 1317 through 1319 No H-bonds generated for 'chain 'D' and resid 1317 through 1319' Processing helix chain 'D' and resid 1401 through 1404 No H-bonds generated for 'chain 'D' and resid 1401 through 1404' Processing helix chain 'D' and resid 1418 through 1434 Processing helix chain 'D' and resid 1438 through 1445 Processing helix chain 'D' and resid 1451 through 1453 No H-bonds generated for 'chain 'D' and resid 1451 through 1453' Processing helix chain 'E' and resid 8 through 10 No H-bonds generated for 'chain 'E' and resid 8 through 10' Processing helix chain 'E' and resid 23 through 25 No H-bonds generated for 'chain 'E' and resid 23 through 25' Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 66 through 75 removed outlier: 3.541A pdb=" N GLU E 75 " --> pdb=" O LYS E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 86 Processing helix chain 'E' and resid 92 through 98 Processing helix chain 'E' and resid 110 through 113 No H-bonds generated for 'chain 'E' and resid 110 through 113' Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'E' and resid 158 through 170 Processing helix chain 'E' and resid 185 through 187 No H-bonds generated for 'chain 'E' and resid 185 through 187' Processing helix chain 'E' and resid 198 through 211 removed outlier: 3.717A pdb=" N ALA E 211 " --> pdb=" O LEU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 262 through 274 Processing helix chain 'E' and resid 279 through 282 No H-bonds generated for 'chain 'E' and resid 279 through 282' Processing helix chain 'E' and resid 299 through 311 Processing helix chain 'E' and resid 325 through 327 No H-bonds generated for 'chain 'E' and resid 325 through 327' Processing helix chain 'E' and resid 332 through 341 Processing helix chain 'E' and resid 407 through 410 No H-bonds generated for 'chain 'E' and resid 407 through 410' Processing helix chain 'E' and resid 443 through 446 No H-bonds generated for 'chain 'E' and resid 443 through 446' Processing helix chain 'E' and resid 451 through 474 Processing helix chain 'F' and resid 8 through 10 No H-bonds generated for 'chain 'F' and resid 8 through 10' Processing helix chain 'F' and resid 23 through 25 No H-bonds generated for 'chain 'F' and resid 23 through 25' Processing helix chain 'F' and resid 38 through 46 removed outlier: 3.733A pdb=" N ASN F 46 " --> pdb=" O ASN F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 58 No H-bonds generated for 'chain 'F' and resid 55 through 58' Processing helix chain 'F' and resid 66 through 75 Processing helix chain 'F' and resid 78 through 88 removed outlier: 4.480A pdb=" N THR F 88 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 98 Processing helix chain 'F' and resid 110 through 113 No H-bonds generated for 'chain 'F' and resid 110 through 113' Processing helix chain 'F' and resid 121 through 133 removed outlier: 3.592A pdb=" N ALA F 132 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP F 133 " --> pdb=" O ASN F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 170 Processing helix chain 'F' and resid 185 through 187 No H-bonds generated for 'chain 'F' and resid 185 through 187' Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 227 through 233 Processing helix chain 'F' and resid 262 through 274 Processing helix chain 'F' and resid 279 through 282 No H-bonds generated for 'chain 'F' and resid 279 through 282' Processing helix chain 'F' and resid 300 through 311 Processing helix chain 'F' and resid 325 through 327 No H-bonds generated for 'chain 'F' and resid 325 through 327' Processing helix chain 'F' and resid 333 through 341 Processing helix chain 'F' and resid 407 through 411 removed outlier: 3.698A pdb=" N PHE F 411 " --> pdb=" O LEU F 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 407 through 411' Processing helix chain 'F' and resid 451 through 474 Processing helix chain 'G' and resid 23 through 25 No H-bonds generated for 'chain 'G' and resid 23 through 25' Processing helix chain 'G' and resid 38 through 44 Processing helix chain 'G' and resid 66 through 75 Processing helix chain 'G' and resid 78 through 88 removed outlier: 4.550A pdb=" N THR G 88 " --> pdb=" O VAL G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 98 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 121 through 133 removed outlier: 3.964A pdb=" N ALA G 132 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TRP G 133 " --> pdb=" O ASN G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 170 Processing helix chain 'G' and resid 185 through 189 removed outlier: 3.567A pdb=" N VAL G 188 " --> pdb=" O GLY G 185 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR G 189 " --> pdb=" O LEU G 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 185 through 189' Processing helix chain 'G' and resid 198 through 211 removed outlier: 3.535A pdb=" N ALA G 211 " --> pdb=" O LEU G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 224 No H-bonds generated for 'chain 'G' and resid 221 through 224' Processing helix chain 'G' and resid 227 through 233 Processing helix chain 'G' and resid 262 through 274 Processing helix chain 'G' and resid 279 through 282 No H-bonds generated for 'chain 'G' and resid 279 through 282' Processing helix chain 'G' and resid 300 through 311 Processing helix chain 'G' and resid 325 through 327 No H-bonds generated for 'chain 'G' and resid 325 through 327' Processing helix chain 'G' and resid 333 through 341 Processing helix chain 'G' and resid 407 through 410 No H-bonds generated for 'chain 'G' and resid 407 through 410' Processing helix chain 'G' and resid 443 through 446 No H-bonds generated for 'chain 'G' and resid 443 through 446' Processing helix chain 'G' and resid 451 through 474 Processing sheet with id= A, first strand: chain 'A' and resid 379 through 384 removed outlier: 6.942A pdb=" N ILE A 357 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS A 382 " --> pdb=" O TYR A 355 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR A 355 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE A 204 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 49 " --> pdb=" O PHE A 204 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 168 through 173 removed outlier: 7.083A pdb=" N GLN A 75 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU A 172 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL A 73 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY A 106 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY A 134 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE A 104 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 332 through 335 Processing sheet with id= D, first strand: chain 'A' and resid 499 through 501 Processing sheet with id= E, first strand: chain 'A' and resid 524 through 526 Processing sheet with id= F, first strand: chain 'A' and resid 566 through 569 removed outlier: 6.656A pdb=" N HIS A 603 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE A 569 " --> pdb=" O HIS A 603 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE A 605 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASN A 643 " --> pdb=" O LEU A 606 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 572 through 574 Processing sheet with id= H, first strand: chain 'A' and resid 829 through 831 Processing sheet with id= I, first strand: chain 'A' and resid 998 through 1001 removed outlier: 3.582A pdb=" N SER A1024 " --> pdb=" O LEU A1000 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG A1066 " --> pdb=" O ILE A1021 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE A1023 " --> pdb=" O ARG A1066 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ARG A1068 " --> pdb=" O ILE A1023 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLU A1089 " --> pdb=" O THR A1069 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1229 through 1231 removed outlier: 3.526A pdb=" N THR A1265 " --> pdb=" O MET A1229 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR A1304 " --> pdb=" O LEU A1286 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N VAL A1288 " --> pdb=" O THR A1304 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL A1306 " --> pdb=" O VAL A1288 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS A1335 " --> pdb=" O ILE A1305 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL A1307 " --> pdb=" O LYS A1335 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE A1337 " --> pdb=" O VAL A1307 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET A1391 " --> pdb=" O ALA A1373 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE A1375 " --> pdb=" O MET A1391 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR A1393 " --> pdb=" O ILE A1375 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 379 through 383 removed outlier: 6.593A pdb=" N ILE B 357 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS B 382 " --> pdb=" O TYR B 355 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR B 355 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU B 362 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE B 204 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA B 49 " --> pdb=" O PHE B 204 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 168 through 173 removed outlier: 6.910A pdb=" N GLN B 75 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU B 172 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL B 73 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 333 through 336 Processing sheet with id= N, first strand: chain 'B' and resid 499 through 501 Processing sheet with id= O, first strand: chain 'B' and resid 524 through 526 Processing sheet with id= P, first strand: chain 'B' and resid 566 through 570 removed outlier: 6.959A pdb=" N HIS B 603 " --> pdb=" O ALA B 567 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ILE B 569 " --> pdb=" O HIS B 603 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE B 605 " --> pdb=" O ILE B 569 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER B 641 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU B 606 " --> pdb=" O SER B 641 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASN B 643 " --> pdb=" O LEU B 606 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'B' and resid 572 through 574 Processing sheet with id= R, first strand: chain 'B' and resid 829 through 831 Processing sheet with id= S, first strand: chain 'B' and resid 907 through 910 removed outlier: 6.817A pdb=" N GLU B 927 " --> pdb=" O LYS B 908 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL B 910 " --> pdb=" O GLU B 927 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU B 929 " --> pdb=" O VAL B 910 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS B 995 " --> pdb=" O LEU B 928 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE B 930 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR B 997 " --> pdb=" O ILE B 930 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE B1020 " --> pdb=" O VAL B 996 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG B1066 " --> pdb=" O ILE B1021 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE B1023 " --> pdb=" O ARG B1066 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG B1068 " --> pdb=" O ILE B1023 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU B1089 " --> pdb=" O THR B1069 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 1229 through 1234 removed outlier: 6.640A pdb=" N THR B1304 " --> pdb=" O LEU B1286 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL B1288 " --> pdb=" O THR B1304 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B1306 " --> pdb=" O VAL B1288 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS B1335 " --> pdb=" O ILE B1305 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N VAL B1307 " --> pdb=" O LYS B1335 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE B1337 " --> pdb=" O VAL B1307 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET B1391 " --> pdb=" O ALA B1373 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE B1375 " --> pdb=" O MET B1391 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N TYR B1393 " --> pdb=" O ILE B1375 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 379 through 384 removed outlier: 6.867A pdb=" N ILE C 357 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LYS C 382 " --> pdb=" O TYR C 355 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR C 355 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N PHE C 204 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA C 49 " --> pdb=" O PHE C 204 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 168 through 173 removed outlier: 6.868A pdb=" N GLN C 75 " --> pdb=" O CYS C 170 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU C 172 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL C 73 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY C 134 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE C 104 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 332 through 335 Processing sheet with id= X, first strand: chain 'C' and resid 499 through 501 Processing sheet with id= Y, first strand: chain 'C' and resid 524 through 526 Processing sheet with id= Z, first strand: chain 'C' and resid 566 through 570 removed outlier: 6.903A pdb=" N HIS C 603 " --> pdb=" O ALA C 567 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE C 569 " --> pdb=" O HIS C 603 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE C 605 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'C' and resid 572 through 574 Processing sheet with id= AB, first strand: chain 'C' and resid 829 through 831 Processing sheet with id= AC, first strand: chain 'C' and resid 997 through 1001 removed outlier: 6.411A pdb=" N ILE C1020 " --> pdb=" O VAL C 998 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU C1000 " --> pdb=" O ILE C1020 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU C1022 " --> pdb=" O LEU C1000 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG C1066 " --> pdb=" O ILE C1021 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE C1023 " --> pdb=" O ARG C1066 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG C1068 " --> pdb=" O ILE C1023 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU C1089 " --> pdb=" O THR C1069 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'C' and resid 1229 through 1234 removed outlier: 3.757A pdb=" N THR C1265 " --> pdb=" O MET C1229 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR C1304 " --> pdb=" O LEU C1286 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL C1288 " --> pdb=" O THR C1304 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL C1306 " --> pdb=" O VAL C1288 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS C1335 " --> pdb=" O ILE C1305 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N VAL C1307 " --> pdb=" O LYS C1335 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE C1337 " --> pdb=" O VAL C1307 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N MET C1391 " --> pdb=" O ALA C1373 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE C1375 " --> pdb=" O MET C1391 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N TYR C1393 " --> pdb=" O ILE C1375 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 379 through 384 removed outlier: 6.871A pdb=" N ILE D 357 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS D 382 " --> pdb=" O TYR D 355 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TYR D 355 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE D 204 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA D 49 " --> pdb=" O PHE D 204 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 168 through 173 removed outlier: 7.171A pdb=" N GLN D 75 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU D 172 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL D 73 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY D 106 " --> pdb=" O ILE D 132 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY D 134 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE D 104 " --> pdb=" O GLY D 134 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 332 through 335 Processing sheet with id= AH, first strand: chain 'D' and resid 499 through 501 Processing sheet with id= AI, first strand: chain 'D' and resid 524 through 526 Processing sheet with id= AJ, first strand: chain 'D' and resid 566 through 570 removed outlier: 6.792A pdb=" N HIS D 603 " --> pdb=" O ALA D 567 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ILE D 569 " --> pdb=" O HIS D 603 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE D 605 " --> pdb=" O ILE D 569 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR D 665 " --> pdb=" O VAL D 644 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N THR D 646 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN D 667 " --> pdb=" O THR D 646 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'D' and resid 572 through 574 Processing sheet with id= AL, first strand: chain 'D' and resid 829 through 831 Processing sheet with id= AM, first strand: chain 'D' and resid 927 through 930 removed outlier: 6.607A pdb=" N LYS D 995 " --> pdb=" O LEU D 928 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ILE D 930 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR D 997 " --> pdb=" O ILE D 930 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE D1020 " --> pdb=" O VAL D 998 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU D1000 " --> pdb=" O ILE D1020 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU D1022 " --> pdb=" O LEU D1000 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG D1066 " --> pdb=" O ILE D1021 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE D1023 " --> pdb=" O ARG D1066 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG D1068 " --> pdb=" O ILE D1023 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'D' and resid 1229 through 1234 removed outlier: 3.752A pdb=" N THR D1265 " --> pdb=" O MET D1229 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR D1304 " --> pdb=" O LEU D1286 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL D1288 " --> pdb=" O THR D1304 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D1306 " --> pdb=" O VAL D1288 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS D1335 " --> pdb=" O ILE D1305 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL D1307 " --> pdb=" O LYS D1335 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE D1337 " --> pdb=" O VAL D1307 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR D1354 " --> pdb=" O LEU D1336 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET D1391 " --> pdb=" O ALA D1373 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ILE D1375 " --> pdb=" O MET D1391 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR D1393 " --> pdb=" O ILE D1375 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'E' and resid 151 through 154 removed outlier: 5.896A pdb=" N ALA E 236 " --> pdb=" O GLY E 152 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE E 154 " --> pdb=" O ALA E 236 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU E 238 " --> pdb=" O ILE E 154 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.805A pdb=" N VAL E 396 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N SER E 316 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL E 295 " --> pdb=" O SER E 316 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS E 318 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLU E 344 " --> pdb=" O CYS E 319 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'E' and resid 389 through 392 removed outlier: 6.269A pdb=" N VAL E 366 " --> pdb=" O PRO E 351 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'E' and resid 368 through 370 Processing sheet with id= AS, first strand: chain 'F' and resid 236 through 239 removed outlier: 7.683A pdb=" N ILE F 214 " --> pdb=" O VAL F 176 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'F' and resid 395 through 398 removed outlier: 3.917A pdb=" N LEU F 320 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU F 344 " --> pdb=" O CYS F 319 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'F' and resid 389 through 392 removed outlier: 5.820A pdb=" N VAL F 366 " --> pdb=" O PRO F 351 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'F' and resid 368 through 370 Processing sheet with id= AW, first strand: chain 'G' and resid 173 through 177 Processing sheet with id= AX, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.406A pdb=" N VAL G 396 " --> pdb=" O VAL G 260 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER G 316 " --> pdb=" O VAL G 293 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL G 295 " --> pdb=" O SER G 316 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS G 318 " --> pdb=" O VAL G 295 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'G' and resid 389 through 392 removed outlier: 5.729A pdb=" N VAL G 366 " --> pdb=" O PRO G 351 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'G' and resid 368 through 370 1782 hydrogen bonds defined for protein. 5016 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: 21.54 Time building geometry restraints manager: 18.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.77: 57026 1.77 - 2.32: 596 2.32 - 2.87: 0 2.87 - 3.42: 0 3.42 - 3.97: 12 Bond restraints: 57634 Sorted by residual: bond pdb=" S4 F3S A1502 " pdb="FE1 F3S A1502 " ideal model delta sigma weight residual 2.233 3.956 -1.723 2.00e-02 2.50e+03 7.42e+03 bond pdb=" S4 F3S D1502 " pdb="FE1 F3S D1502 " ideal model delta sigma weight residual 2.233 3.954 -1.721 2.00e-02 2.50e+03 7.40e+03 bond pdb=" S4 F3S B1502 " pdb="FE1 F3S B1502 " ideal model delta sigma weight residual 2.233 3.939 -1.706 2.00e-02 2.50e+03 7.27e+03 bond pdb=" S4 F3S C1502 " pdb="FE1 F3S C1502 " ideal model delta sigma weight residual 2.233 3.938 -1.705 2.00e-02 2.50e+03 7.27e+03 bond pdb=" S2 F3S B1502 " pdb="FE3 F3S B1502 " ideal model delta sigma weight residual 2.300 3.967 -1.667 2.00e-02 2.50e+03 6.95e+03 ... (remaining 57629 not shown) Histogram of bond angle deviations from ideal: 40.97 - 59.59: 16 59.59 - 78.20: 104 78.20 - 96.82: 0 96.82 - 115.44: 37440 115.44 - 134.06: 40521 Bond angle restraints: 78081 Sorted by residual: angle pdb=" S1 F3S D1502 " pdb="FE4 F3S D1502 " pdb=" S3 F3S D1502 " ideal model delta sigma weight residual 114.75 64.31 50.44 3.00e+00 1.11e-01 2.83e+02 angle pdb=" S3 F3S A1502 " pdb="FE1 F3S A1502 " pdb=" S4 F3S A1502 " ideal model delta sigma weight residual 112.59 62.99 49.60 3.00e+00 1.11e-01 2.73e+02 angle pdb=" S1 F3S A1502 " pdb="FE4 F3S A1502 " pdb=" S3 F3S A1502 " ideal model delta sigma weight residual 114.75 65.21 49.54 3.00e+00 1.11e-01 2.73e+02 angle pdb=" S1 F3S B1502 " pdb="FE4 F3S B1502 " pdb=" S3 F3S B1502 " ideal model delta sigma weight residual 114.75 65.45 49.30 3.00e+00 1.11e-01 2.70e+02 angle pdb=" S1 F3S C1502 " pdb="FE4 F3S C1502 " pdb=" S3 F3S C1502 " ideal model delta sigma weight residual 114.75 65.53 49.22 3.00e+00 1.11e-01 2.69e+02 ... (remaining 78076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.62: 33998 32.62 - 65.24: 591 65.24 - 97.86: 59 97.86 - 130.48: 1 130.48 - 163.10: 2 Dihedral angle restraints: 34651 sinusoidal: 14013 harmonic: 20638 Sorted by residual: dihedral pdb=" O5' FAD E 503 " pdb=" O3P FAD E 503 " pdb=" P FAD E 503 " pdb=" PA FAD E 503 " ideal model delta sinusoidal sigma weight residual -61.77 101.33 -163.10 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" CA PHE G 36 " pdb=" C PHE G 36 " pdb=" N SER G 37 " pdb=" CA SER G 37 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" O5' FAD G 503 " pdb=" O3P FAD G 503 " pdb=" P FAD G 503 " pdb=" PA FAD G 503 " ideal model delta sinusoidal sigma weight residual -61.77 77.68 -139.45 1 3.00e+01 1.11e-03 1.88e+01 ... (remaining 34648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.722: 8689 0.722 - 1.444: 0 1.444 - 2.167: 0 2.167 - 2.889: 0 2.889 - 3.611: 4 Chirality restraints: 8693 Sorted by residual: chirality pdb=" S2 F3S B1502 " pdb="FE1 F3S B1502 " pdb="FE3 F3S B1502 " pdb="FE4 F3S B1502 " both_signs ideal model delta sigma weight residual False 10.77 7.16 3.61 2.00e-01 2.50e+01 3.26e+02 chirality pdb=" S2 F3S C1502 " pdb="FE1 F3S C1502 " pdb="FE3 F3S C1502 " pdb="FE4 F3S C1502 " both_signs ideal model delta sigma weight residual False 10.77 7.49 3.28 2.00e-01 2.50e+01 2.69e+02 chirality pdb=" S2 F3S D1502 " pdb="FE1 F3S D1502 " pdb="FE3 F3S D1502 " pdb="FE4 F3S D1502 " both_signs ideal model delta sigma weight residual False 10.77 7.67 3.10 2.00e-01 2.50e+01 2.40e+02 ... (remaining 8690 not shown) Planarity restraints: 10217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B1184 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO B1185 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B1185 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B1185 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 191 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO E 192 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 192 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 192 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 968 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO D 969 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 969 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 969 " 0.022 5.00e-02 4.00e+02 ... (remaining 10214 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.91: 3 1.91 - 2.66: 972 2.66 - 3.41: 77922 3.41 - 4.15: 125345 4.15 - 4.90: 228977 Nonbonded interactions: 433219 Sorted by model distance: nonbonded pdb=" SG CYS A1113 " pdb=" S1 F3S A1502 " model vdw 1.163 3.760 nonbonded pdb=" SG CYS A1102 " pdb=" S3 F3S A1502 " model vdw 1.244 3.760 nonbonded pdb=" SG CYS D1102 " pdb=" S3 F3S D1502 " model vdw 1.547 3.760 nonbonded pdb=" OE1 GLU G 125 " pdb="FE3 SF4 G 502 " model vdw 2.119 3.000 nonbonded pdb=" OG SER D 864 " pdb=" OE1 GLU D 866 " model vdw 2.168 2.440 ... (remaining 433214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.520 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: 0.030 Extract box with map and model: 8.580 Check model and map are aligned: 0.640 Set scattering table: 0.410 Process input model: 128.040 Find NCS groups from input model: 2.840 Set up NCS constraints: 0.320 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: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 : 0.024 1.723 57634 Z= 1.643 Angle : 0.981 50.437 78081 Z= 0.412 Chirality : 0.081 3.611 8693 Planarity : 0.003 0.041 10217 Dihedral : 13.048 163.099 21485 Min Nonbonded Distance : 1.163 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.02 % Allowed : 6.13 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -3.19 (0.08), residues: 7290 helix: -0.97 (0.09), residues: 2451 sheet: -2.33 (0.15), residues: 910 loop : -2.92 (0.08), residues: 3929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 69 HIS 0.005 0.001 HIS A 796 PHE 0.019 0.001 PHE G 36 TYR 0.020 0.001 TYR D1367 ARG 0.006 0.000 ARG A1186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 779 time to evaluate : 5.370 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: A 233 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7586 (mm-30) REVERT: A 371 MET cc_start: 0.7923 (mtm) cc_final: 0.7718 (mtm) REVERT: A 458 MET cc_start: 0.8278 (ppp) cc_final: 0.8019 (ppp) REVERT: A 693 MET cc_start: 0.8692 (mmm) cc_final: 0.8457 (mmm) REVERT: A 1368 MET cc_start: 0.8876 (ttt) cc_final: 0.8560 (ttm) REVERT: A 1387 MET cc_start: 0.8680 (ttt) cc_final: 0.7629 (ttt) REVERT: B 86 GLN cc_start: 0.8051 (mt0) cc_final: 0.7754 (mt0) REVERT: B 251 MET cc_start: 0.8314 (ptt) cc_final: 0.8109 (ptm) REVERT: B 461 MET cc_start: 0.8100 (mmt) cc_final: 0.7723 (mmt) REVERT: B 562 MET cc_start: 0.8718 (mtm) cc_final: 0.8457 (mtm) REVERT: B 895 ARG cc_start: 0.4994 (mmt90) cc_final: 0.4301 (ptp90) REVERT: B 1017 ASN cc_start: 0.8585 (m-40) cc_final: 0.8029 (m-40) REVERT: B 1137 ASN cc_start: 0.6737 (m-40) cc_final: 0.6403 (p0) REVERT: C 235 ASN cc_start: 0.8205 (m-40) cc_final: 0.7917 (m-40) REVERT: C 244 MET cc_start: 0.8663 (tpp) cc_final: 0.8388 (tpp) REVERT: C 350 LEU cc_start: 0.9019 (mt) cc_final: 0.8684 (mp) REVERT: C 458 MET cc_start: 0.8497 (ppp) cc_final: 0.8253 (tmm) REVERT: C 708 MET cc_start: 0.8863 (ttp) cc_final: 0.8651 (ttp) REVERT: C 953 ILE cc_start: 0.8509 (tp) cc_final: 0.7882 (tp) REVERT: C 1249 MET cc_start: 0.8313 (mmm) cc_final: 0.8041 (tpp) REVERT: C 1368 MET cc_start: 0.8566 (ttt) cc_final: 0.8028 (ttp) REVERT: C 1387 MET cc_start: 0.9019 (ttt) cc_final: 0.8784 (ttm) REVERT: D 416 TRP cc_start: 0.7065 (m100) cc_final: 0.6854 (m100) REVERT: D 427 ASP cc_start: 0.8174 (p0) cc_final: 0.7876 (p0) REVERT: D 448 ARG cc_start: 0.8213 (mtt-85) cc_final: 0.7935 (mtp85) REVERT: D 591 GLN cc_start: 0.8008 (tt0) cc_final: 0.7742 (tm-30) REVERT: D 767 ASN cc_start: 0.8033 (t0) cc_final: 0.7830 (t0) REVERT: D 929 GLU cc_start: 0.7724 (tt0) cc_final: 0.7523 (tt0) REVERT: D 1009 ILE cc_start: 0.9124 (mp) cc_final: 0.8789 (mt) REVERT: D 1100 MET cc_start: 0.8748 (mmm) cc_final: 0.8459 (mmp) REVERT: E 183 MET cc_start: 0.7570 (mtp) cc_final: 0.7200 (mtt) REVERT: E 270 ASN cc_start: 0.8102 (t0) cc_final: 0.7568 (t0) REVERT: F 6 MET cc_start: 0.6930 (ptp) cc_final: 0.6438 (ptp) REVERT: F 27 GLN cc_start: 0.7455 (mp10) cc_final: 0.7248 (mt0) REVERT: G 149 LEU cc_start: 0.6615 (tp) cc_final: 0.6359 (tp) REVERT: G 435 MET cc_start: 0.6818 (ptm) cc_final: 0.6185 (ptm) outliers start: 1 outliers final: 0 residues processed: 780 average time/residue: 0.5918 time to fit residues: 751.4424 Evaluate side-chains 484 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 4.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 615 optimal weight: 20.0000 chunk 552 optimal weight: 7.9990 chunk 306 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 372 optimal weight: 4.9990 chunk 295 optimal weight: 0.2980 chunk 571 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 347 optimal weight: 4.9990 chunk 425 optimal weight: 10.0000 chunk 662 optimal weight: 0.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 165 ASN A 235 ASN A 923 ASN A1054 GLN A1205 ASN ** A1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1282 GLN A1293 ASN ** A1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1341 GLN A1419 HIS A1471 HIS B 30 HIS B 52 GLN B 58 HIS B 75 GLN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 187 GLN B 235 ASN B 653 HIS B 796 HIS B 800 GLN B 924 GLN ** B 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1126 GLN ** B1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1341 GLN ** B1363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 135 ASN C 321 ASN C 409 HIS C 643 ASN ** C 724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 HIS C 767 ASN C 924 GLN ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1107 GLN C1234 ASN C1325 ASN C1419 HIS C1431 HIS ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 422 ASN D 539 GLN D 635 ASN D 643 ASN D 653 HIS D 943 GLN D 971 HIS ** D 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1120 GLN D1137 ASN D1177 HIS ** D1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1325 ASN D1413 GLN D1419 HIS D1431 HIS E 57 GLN E 129 ASN E 312 GLN E 379 GLN E 392 GLN F 11 HIS F 50 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 GLN F 434 ASN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 258 ASN G 379 GLN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.189 57634 Z= 0.259 Angle : 0.871 75.962 78081 Z= 0.353 Chirality : 0.046 1.391 8693 Planarity : 0.004 0.079 10217 Dihedral : 5.719 161.326 8145 Min Nonbonded Distance : 1.521 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.07 % Allowed : 4.27 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -2.36 (0.09), residues: 7290 helix: -0.13 (0.10), residues: 2463 sheet: -1.90 (0.16), residues: 866 loop : -2.54 (0.09), residues: 3961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 69 HIS 0.006 0.001 HIS C1109 PHE 0.017 0.001 PHE G 36 TYR 0.013 0.001 TYR D1367 ARG 0.010 0.000 ARG C1186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 607 time to evaluate : 4.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8142 (mmm) cc_final: 0.7779 (tpp) REVERT: A 964 MET cc_start: 0.8007 (ttp) cc_final: 0.7261 (pmm) REVERT: A 1047 MET cc_start: 0.7700 (mtt) cc_final: 0.7482 (mtt) REVERT: A 1368 MET cc_start: 0.8836 (ttt) cc_final: 0.8525 (ttm) REVERT: A 1387 MET cc_start: 0.8715 (ttt) cc_final: 0.7668 (ttt) REVERT: A 1462 MET cc_start: 0.8098 (mmm) cc_final: 0.7716 (mmp) REVERT: B 458 MET cc_start: 0.6937 (tmm) cc_final: 0.6730 (tmm) REVERT: B 461 MET cc_start: 0.8099 (mmt) cc_final: 0.7833 (mmt) REVERT: B 562 MET cc_start: 0.8723 (mtm) cc_final: 0.8502 (mtm) REVERT: B 895 ARG cc_start: 0.5077 (mmt90) cc_final: 0.4328 (ptp90) REVERT: B 1017 ASN cc_start: 0.8555 (m-40) cc_final: 0.8045 (m-40) REVERT: B 1047 MET cc_start: 0.8468 (ptp) cc_final: 0.7743 (mtm) REVERT: B 1104 MET cc_start: 0.7338 (mmm) cc_final: 0.6754 (mmm) REVERT: B 1137 ASN cc_start: 0.6844 (m-40) cc_final: 0.6556 (p0) REVERT: B 1387 MET cc_start: 0.8260 (ttt) cc_final: 0.7935 (ttm) REVERT: C 244 MET cc_start: 0.8671 (tpp) cc_final: 0.8352 (tpp) REVERT: C 296 MET cc_start: 0.8240 (mmm) cc_final: 0.7970 (mmt) REVERT: C 350 LEU cc_start: 0.8974 (mt) cc_final: 0.8661 (mp) REVERT: C 520 MET cc_start: 0.8280 (ptp) cc_final: 0.7921 (ptm) REVERT: C 978 GLU cc_start: 0.8550 (pm20) cc_final: 0.8340 (mp0) REVERT: C 1249 MET cc_start: 0.8331 (mmm) cc_final: 0.8043 (tpp) REVERT: C 1419 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7784 (t-170) REVERT: D 416 TRP cc_start: 0.7039 (m100) cc_final: 0.6794 (m100) REVERT: D 448 ARG cc_start: 0.8264 (mtt-85) cc_final: 0.7976 (mtp85) REVERT: D 591 GLN cc_start: 0.8063 (tt0) cc_final: 0.7745 (tm-30) REVERT: D 767 ASN cc_start: 0.7991 (t0) cc_final: 0.7741 (t0) REVERT: D 929 GLU cc_start: 0.7758 (tt0) cc_final: 0.7544 (tt0) REVERT: D 980 LEU cc_start: 0.9200 (tp) cc_final: 0.8969 (tp) REVERT: D 1100 MET cc_start: 0.8634 (mmm) cc_final: 0.8375 (mmp) REVERT: E 183 MET cc_start: 0.7535 (mtp) cc_final: 0.7225 (mtm) REVERT: E 303 MET cc_start: 0.8105 (mmp) cc_final: 0.7857 (mmp) REVERT: E 392 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8544 (tm-30) REVERT: F 6 MET cc_start: 0.7042 (ptp) cc_final: 0.6505 (ptp) REVERT: G 303 MET cc_start: 0.5990 (tpp) cc_final: 0.5789 (tpp) REVERT: G 328 MET cc_start: 0.5015 (ptm) cc_final: 0.4596 (ptm) REVERT: G 332 GLN cc_start: 0.7251 (pp30) cc_final: 0.6131 (mp10) REVERT: G 435 MET cc_start: 0.6274 (ptm) cc_final: 0.5788 (ptm) outliers start: 4 outliers final: 1 residues processed: 611 average time/residue: 0.5310 time to fit residues: 550.4478 Evaluate side-chains 454 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 451 time to evaluate : 4.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 367 optimal weight: 8.9990 chunk 205 optimal weight: 8.9990 chunk 550 optimal weight: 0.8980 chunk 450 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 663 optimal weight: 0.9990 chunk 716 optimal weight: 8.9990 chunk 590 optimal weight: 20.0000 chunk 657 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 chunk 532 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN A1293 ASN A1325 ASN B 64 HIS B 75 GLN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 GLN B 818 ASN ** B 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1205 ASN B1363 ASN ** B1471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 ASN C 501 GLN ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 767 ASN C 923 ASN C 971 HIS ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1436 GLN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 HIS ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 HIS G 50 GLN G 258 ASN G 379 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 57634 Z= 0.339 Angle : 0.821 90.954 78081 Z= 0.357 Chirality : 0.055 2.211 8693 Planarity : 0.004 0.055 10217 Dihedral : 5.778 160.978 8145 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.05 % Allowed : 5.02 % Favored : 94.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -2.13 (0.09), residues: 7290 helix: 0.02 (0.10), residues: 2491 sheet: -1.75 (0.17), residues: 870 loop : -2.37 (0.09), residues: 3929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 69 HIS 0.012 0.001 HIS A 603 PHE 0.017 0.002 PHE G 36 TYR 0.016 0.001 TYR D1367 ARG 0.005 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 573 time to evaluate : 4.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8232 (mmm) cc_final: 0.7850 (tpt) REVERT: A 296 MET cc_start: 0.8755 (mmt) cc_final: 0.8488 (mmm) REVERT: A 505 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8610 (mp-120) REVERT: A 1047 MET cc_start: 0.7793 (mtt) cc_final: 0.7575 (mtt) REVERT: A 1289 MET cc_start: 0.8401 (mmt) cc_final: 0.8096 (mmt) REVERT: A 1366 GLU cc_start: 0.8348 (tt0) cc_final: 0.8046 (tt0) REVERT: A 1368 MET cc_start: 0.8831 (ttt) cc_final: 0.8629 (ttm) REVERT: A 1387 MET cc_start: 0.8704 (ttt) cc_final: 0.7955 (ttt) REVERT: A 1462 MET cc_start: 0.8192 (mmm) cc_final: 0.7777 (mmp) REVERT: B 335 MET cc_start: 0.8111 (pmm) cc_final: 0.7821 (pmm) REVERT: B 442 MET cc_start: 0.6586 (ptt) cc_final: 0.6310 (ptt) REVERT: B 461 MET cc_start: 0.8131 (mmt) cc_final: 0.7850 (mmt) REVERT: B 611 MET cc_start: 0.8195 (tpp) cc_final: 0.7787 (tpt) REVERT: B 687 MET cc_start: 0.6899 (ppp) cc_final: 0.6521 (ppp) REVERT: B 858 MET cc_start: 0.6794 (mmt) cc_final: 0.6357 (mmt) REVERT: B 895 ARG cc_start: 0.5119 (mmt90) cc_final: 0.4332 (ptp90) REVERT: B 1017 ASN cc_start: 0.8840 (m-40) cc_final: 0.8528 (m-40) REVERT: B 1137 ASN cc_start: 0.7201 (m-40) cc_final: 0.6685 (p0) REVERT: B 1295 TYR cc_start: 0.9045 (m-80) cc_final: 0.8838 (m-80) REVERT: B 1387 MET cc_start: 0.8297 (ttt) cc_final: 0.8086 (ttm) REVERT: C 83 LEU cc_start: 0.8921 (mt) cc_final: 0.8566 (tt) REVERT: C 207 TYR cc_start: 0.9191 (p90) cc_final: 0.8984 (p90) REVERT: C 244 MET cc_start: 0.8702 (tpp) cc_final: 0.8413 (tpp) REVERT: C 520 MET cc_start: 0.8345 (ptp) cc_final: 0.8081 (ptm) REVERT: C 542 LEU cc_start: 0.8428 (pt) cc_final: 0.8157 (pt) REVERT: C 1249 MET cc_start: 0.8363 (mmm) cc_final: 0.8125 (tpp) REVERT: C 1366 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7857 (tm-30) REVERT: C 1368 MET cc_start: 0.8555 (ttt) cc_final: 0.8141 (ttp) REVERT: D 448 ARG cc_start: 0.8243 (mtt-85) cc_final: 0.8012 (mtp85) REVERT: D 454 PHE cc_start: 0.8594 (m-10) cc_final: 0.8232 (m-10) REVERT: D 479 MET cc_start: 0.8376 (tpp) cc_final: 0.8048 (tpp) REVERT: D 591 GLN cc_start: 0.8201 (tt0) cc_final: 0.7845 (tm-30) REVERT: D 651 ASP cc_start: 0.8177 (t0) cc_final: 0.7840 (t0) REVERT: D 767 ASN cc_start: 0.8085 (t0) cc_final: 0.7785 (t0) REVERT: D 929 GLU cc_start: 0.7656 (tt0) cc_final: 0.7328 (tt0) REVERT: D 980 LEU cc_start: 0.9242 (tp) cc_final: 0.9034 (tp) REVERT: D 1100 MET cc_start: 0.8719 (mmm) cc_final: 0.8505 (mmp) REVERT: E 183 MET cc_start: 0.7698 (mtp) cc_final: 0.7449 (mtm) REVERT: F 6 MET cc_start: 0.7225 (ptp) cc_final: 0.6662 (ptp) REVERT: G 332 GLN cc_start: 0.7082 (pp30) cc_final: 0.6015 (mp10) REVERT: G 435 MET cc_start: 0.6311 (ptm) cc_final: 0.5817 (ptm) outliers start: 3 outliers final: 0 residues processed: 576 average time/residue: 0.5355 time to fit residues: 527.1387 Evaluate side-chains 425 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 424 time to evaluate : 5.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 655 optimal weight: 8.9990 chunk 498 optimal weight: 5.9990 chunk 344 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 316 optimal weight: 0.9980 chunk 445 optimal weight: 9.9990 chunk 665 optimal weight: 2.9990 chunk 704 optimal weight: 7.9990 chunk 347 optimal weight: 0.3980 chunk 630 optimal weight: 9.9990 chunk 189 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 GLN A1260 GLN A1293 ASN B 75 GLN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 HIS C 501 GLN C 724 ASN C 767 ASN C 818 ASN C 982 GLN C1054 GLN D 724 ASN D 755 GLN E 57 GLN E 89 ASN E 108 ASN ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 ASN G 379 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 57634 Z= 0.171 Angle : 0.755 83.857 78081 Z= 0.315 Chirality : 0.050 1.543 8693 Planarity : 0.003 0.043 10217 Dihedral : 5.408 161.033 8145 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.02 % Allowed : 2.47 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -1.69 (0.10), residues: 7290 helix: 0.40 (0.11), residues: 2495 sheet: -1.46 (0.17), residues: 866 loop : -2.13 (0.09), residues: 3929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 69 HIS 0.005 0.001 HIS A1109 PHE 0.016 0.001 PHE G 36 TYR 0.015 0.001 TYR C1393 ARG 0.006 0.000 ARG B1106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 621 time to evaluate : 4.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.8316 (mp10) cc_final: 0.8052 (tm-30) REVERT: A 875 MET cc_start: 0.8539 (mmm) cc_final: 0.8249 (mmm) REVERT: A 964 MET cc_start: 0.7794 (ttp) cc_final: 0.7282 (pmm) REVERT: A 1366 GLU cc_start: 0.8137 (tt0) cc_final: 0.7829 (tt0) REVERT: A 1368 MET cc_start: 0.8797 (ttt) cc_final: 0.8457 (ttm) REVERT: A 1387 MET cc_start: 0.8584 (ttt) cc_final: 0.7499 (ttt) REVERT: A 1462 MET cc_start: 0.8143 (mmm) cc_final: 0.7733 (mmp) REVERT: B 112 ILE cc_start: 0.9179 (pt) cc_final: 0.8894 (mt) REVERT: B 296 MET cc_start: 0.7968 (tpp) cc_final: 0.7652 (tpp) REVERT: B 458 MET cc_start: 0.7004 (tmm) cc_final: 0.6543 (tmm) REVERT: B 461 MET cc_start: 0.7880 (mmt) cc_final: 0.7462 (mmm) REVERT: B 520 MET cc_start: 0.8251 (mmt) cc_final: 0.7855 (mmp) REVERT: B 562 MET cc_start: 0.8711 (mtm) cc_final: 0.8491 (mtm) REVERT: B 611 MET cc_start: 0.7884 (tpp) cc_final: 0.7660 (tpt) REVERT: B 725 PHE cc_start: 0.8127 (m-80) cc_final: 0.7926 (m-80) REVERT: B 858 MET cc_start: 0.6791 (mmt) cc_final: 0.6411 (mmt) REVERT: B 895 ARG cc_start: 0.5090 (mmt90) cc_final: 0.4347 (ptp90) REVERT: B 964 MET cc_start: 0.8027 (ppp) cc_final: 0.7606 (ppp) REVERT: B 1017 ASN cc_start: 0.8724 (m-40) cc_final: 0.8245 (m-40) REVERT: B 1047 MET cc_start: 0.8247 (ptp) cc_final: 0.7755 (mtm) REVERT: B 1084 MET cc_start: 0.8712 (tpp) cc_final: 0.8332 (tpt) REVERT: B 1137 ASN cc_start: 0.6764 (m-40) cc_final: 0.6285 (p0) REVERT: B 1387 MET cc_start: 0.8210 (ttt) cc_final: 0.7992 (ttm) REVERT: C 244 MET cc_start: 0.8585 (tpp) cc_final: 0.8318 (tpp) REVERT: C 260 MET cc_start: 0.8158 (tpp) cc_final: 0.7627 (tpp) REVERT: C 345 MET cc_start: 0.8579 (tpp) cc_final: 0.8168 (tpp) REVERT: C 520 MET cc_start: 0.8303 (ptp) cc_final: 0.7989 (ptm) REVERT: C 562 MET cc_start: 0.7815 (mtm) cc_final: 0.7590 (mtm) REVERT: C 953 ILE cc_start: 0.8961 (pt) cc_final: 0.8756 (mt) REVERT: C 982 GLN cc_start: 0.8554 (tp-100) cc_final: 0.7086 (tm-30) REVERT: C 1249 MET cc_start: 0.8251 (mmm) cc_final: 0.8047 (tpp) REVERT: C 1366 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7825 (tm-30) REVERT: C 1368 MET cc_start: 0.8480 (ttt) cc_final: 0.8059 (ttt) REVERT: D 448 ARG cc_start: 0.8335 (mtt-85) cc_final: 0.8068 (mtp85) REVERT: D 454 PHE cc_start: 0.8596 (m-10) cc_final: 0.8247 (m-10) REVERT: D 591 GLN cc_start: 0.8045 (tt0) cc_final: 0.7751 (tm-30) REVERT: D 651 ASP cc_start: 0.8119 (t0) cc_final: 0.7836 (t0) REVERT: D 767 ASN cc_start: 0.8172 (t0) cc_final: 0.7807 (t0) REVERT: D 927 GLU cc_start: 0.8156 (tp30) cc_final: 0.7836 (tp30) REVERT: D 929 GLU cc_start: 0.7532 (tt0) cc_final: 0.7226 (tt0) REVERT: D 980 LEU cc_start: 0.9301 (tp) cc_final: 0.9094 (tp) REVERT: D 1100 MET cc_start: 0.8674 (mmm) cc_final: 0.8416 (mmp) REVERT: E 183 MET cc_start: 0.7731 (mtp) cc_final: 0.7472 (mtt) REVERT: F 6 MET cc_start: 0.7164 (ptp) cc_final: 0.6731 (ptp) REVERT: G 332 GLN cc_start: 0.7131 (pp30) cc_final: 0.6073 (mp10) REVERT: G 435 MET cc_start: 0.6274 (ptm) cc_final: 0.5866 (ptm) outliers start: 1 outliers final: 1 residues processed: 622 average time/residue: 0.5246 time to fit residues: 559.1303 Evaluate side-chains 457 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 456 time to evaluate : 4.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 586 optimal weight: 10.0000 chunk 400 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 524 optimal weight: 9.9990 chunk 290 optimal weight: 5.9990 chunk 601 optimal weight: 9.9990 chunk 487 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 359 optimal weight: 10.0000 chunk 632 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A1293 ASN B 75 GLN B 409 HIS ** B 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 ASN B 824 GLN ** B 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1282 GLN ** B1471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 GLN C 667 ASN C 971 HIS ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1205 ASN D 30 HIS D 724 ASN ** D 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 GLN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 GLN G 379 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 57634 Z= 0.485 Angle : 0.907 82.863 78081 Z= 0.409 Chirality : 0.056 1.581 8693 Planarity : 0.005 0.059 10217 Dihedral : 5.993 160.694 8145 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.02 % Allowed : 3.82 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -2.02 (0.09), residues: 7290 helix: -0.03 (0.10), residues: 2527 sheet: -1.66 (0.17), residues: 900 loop : -2.23 (0.09), residues: 3863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 69 HIS 0.009 0.002 HIS B 47 PHE 0.025 0.002 PHE D 781 TYR 0.020 0.002 TYR A 207 ARG 0.012 0.001 ARG D 289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 547 time to evaluate : 5.282 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: A 296 MET cc_start: 0.8688 (mmm) cc_final: 0.8468 (mmm) REVERT: A 463 LEU cc_start: 0.8441 (tp) cc_final: 0.8241 (tp) REVERT: A 986 ASP cc_start: 0.8726 (m-30) cc_final: 0.8459 (m-30) REVERT: A 1289 MET cc_start: 0.8459 (mmt) cc_final: 0.8209 (mmt) REVERT: A 1366 GLU cc_start: 0.8412 (tt0) cc_final: 0.8086 (tt0) REVERT: A 1387 MET cc_start: 0.8650 (ttt) cc_final: 0.7953 (ttt) REVERT: A 1462 MET cc_start: 0.8277 (mmm) cc_final: 0.7843 (mmp) REVERT: B 112 ILE cc_start: 0.9209 (pt) cc_final: 0.8936 (mt) REVERT: B 458 MET cc_start: 0.6930 (tmm) cc_final: 0.6324 (tmm) REVERT: B 461 MET cc_start: 0.8151 (mmt) cc_final: 0.7918 (mmt) REVERT: B 562 MET cc_start: 0.8829 (mtm) cc_final: 0.8551 (mtm) REVERT: B 687 MET cc_start: 0.6588 (ppp) cc_final: 0.6284 (ppp) REVERT: B 895 ARG cc_start: 0.5201 (mmt90) cc_final: 0.4369 (ptp90) REVERT: B 1017 ASN cc_start: 0.8729 (m-40) cc_final: 0.8384 (m-40) REVERT: B 1137 ASN cc_start: 0.7401 (m-40) cc_final: 0.6672 (p0) REVERT: B 1289 MET cc_start: 0.8432 (mmm) cc_final: 0.7702 (mtm) REVERT: B 1295 TYR cc_start: 0.9087 (m-80) cc_final: 0.8830 (m-80) REVERT: B 1387 MET cc_start: 0.8438 (ttt) cc_final: 0.8230 (ttm) REVERT: C 83 LEU cc_start: 0.8863 (mt) cc_final: 0.8646 (tt) REVERT: C 244 MET cc_start: 0.8770 (tpp) cc_final: 0.8434 (tpp) REVERT: C 345 MET cc_start: 0.8573 (tpp) cc_final: 0.7797 (ttt) REVERT: C 442 MET cc_start: 0.7338 (mtm) cc_final: 0.7055 (mtp) REVERT: C 542 LEU cc_start: 0.8472 (pt) cc_final: 0.8178 (pt) REVERT: C 986 ASP cc_start: 0.8766 (m-30) cc_final: 0.8482 (m-30) REVERT: C 1249 MET cc_start: 0.8448 (mmm) cc_final: 0.8133 (tpp) REVERT: C 1366 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7886 (tm-30) REVERT: D 448 ARG cc_start: 0.8278 (mtt-85) cc_final: 0.8021 (mtp85) REVERT: D 591 GLN cc_start: 0.8306 (tt0) cc_final: 0.7898 (tm-30) REVERT: D 767 ASN cc_start: 0.8076 (t0) cc_final: 0.7760 (t0) REVERT: D 875 MET cc_start: 0.7890 (mmm) cc_final: 0.7587 (mmp) REVERT: D 929 GLU cc_start: 0.7597 (tt0) cc_final: 0.7273 (tt0) REVERT: D 980 LEU cc_start: 0.9293 (tp) cc_final: 0.9090 (tp) REVERT: D 1100 MET cc_start: 0.8716 (mmm) cc_final: 0.8471 (mmp) REVERT: E 303 MET cc_start: 0.8336 (mmm) cc_final: 0.8107 (mmp) REVERT: F 304 ASP cc_start: 0.7607 (m-30) cc_final: 0.7174 (m-30) REVERT: G 332 GLN cc_start: 0.7147 (pp30) cc_final: 0.6069 (mp10) REVERT: G 435 MET cc_start: 0.6082 (ptm) cc_final: 0.5669 (ptm) outliers start: 1 outliers final: 1 residues processed: 548 average time/residue: 0.5594 time to fit residues: 530.3763 Evaluate side-chains 406 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 405 time to evaluate : 4.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 237 optimal weight: 7.9990 chunk 634 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 413 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 705 optimal weight: 30.0000 chunk 585 optimal weight: 10.0000 chunk 326 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 233 optimal weight: 9.9990 chunk 370 optimal weight: 0.4980 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 GLN C 767 ASN ** C 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 971 HIS ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 ASN D 724 ASN D 943 GLN ** D 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 GLN F 4 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 337 HIS G 379 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 57634 Z= 0.322 Angle : 0.829 82.830 78081 Z= 0.362 Chirality : 0.053 1.560 8693 Planarity : 0.004 0.119 10217 Dihedral : 5.822 161.402 8145 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.03 % Allowed : 2.45 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -1.86 (0.09), residues: 7290 helix: 0.10 (0.10), residues: 2539 sheet: -1.57 (0.17), residues: 896 loop : -2.14 (0.09), residues: 3855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 347 HIS 0.009 0.001 HIS D 868 PHE 0.016 0.001 PHE G 36 TYR 0.019 0.002 TYR C1367 ARG 0.010 0.000 ARG B 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 577 time to evaluate : 5.025 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: A 986 ASP cc_start: 0.8659 (m-30) cc_final: 0.8420 (m-30) REVERT: A 1366 GLU cc_start: 0.8269 (tt0) cc_final: 0.8054 (tt0) REVERT: A 1462 MET cc_start: 0.8114 (mmm) cc_final: 0.7645 (mmp) REVERT: B 458 MET cc_start: 0.7009 (tmm) cc_final: 0.6340 (tmm) REVERT: B 461 MET cc_start: 0.8067 (mmt) cc_final: 0.7503 (mmm) REVERT: B 520 MET cc_start: 0.8177 (mmt) cc_final: 0.7953 (mmp) REVERT: B 562 MET cc_start: 0.8784 (mtm) cc_final: 0.8505 (mtm) REVERT: B 858 MET cc_start: 0.6769 (mmt) cc_final: 0.6376 (mmt) REVERT: B 895 ARG cc_start: 0.5221 (mmt90) cc_final: 0.4395 (ptp90) REVERT: B 1017 ASN cc_start: 0.8651 (m-40) cc_final: 0.8286 (m110) REVERT: B 1047 MET cc_start: 0.8251 (ptp) cc_final: 0.7769 (mtm) REVERT: B 1084 MET cc_start: 0.8786 (tpp) cc_final: 0.8477 (tpt) REVERT: B 1137 ASN cc_start: 0.7294 (m-40) cc_final: 0.6811 (p0) REVERT: B 1289 MET cc_start: 0.8266 (mmm) cc_final: 0.7452 (mtm) REVERT: B 1295 TYR cc_start: 0.9040 (m-80) cc_final: 0.8780 (m-80) REVERT: B 1387 MET cc_start: 0.8442 (ttt) cc_final: 0.8209 (ttm) REVERT: C 203 ASP cc_start: 0.8521 (m-30) cc_final: 0.8231 (m-30) REVERT: C 244 MET cc_start: 0.8679 (tpp) cc_final: 0.8413 (tpp) REVERT: C 260 MET cc_start: 0.8275 (tpp) cc_final: 0.7733 (tpp) REVERT: C 345 MET cc_start: 0.8456 (tpp) cc_final: 0.7499 (ttt) REVERT: C 542 LEU cc_start: 0.8753 (pt) cc_final: 0.8463 (pt) REVERT: C 986 ASP cc_start: 0.8725 (m-30) cc_final: 0.8382 (m-30) REVERT: C 1249 MET cc_start: 0.8338 (mmm) cc_final: 0.8024 (tpp) REVERT: C 1300 LEU cc_start: 0.8681 (tp) cc_final: 0.8391 (tp) REVERT: C 1366 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8024 (tm-30) REVERT: C 1368 MET cc_start: 0.8736 (ttt) cc_final: 0.8255 (ttp) REVERT: D 442 MET cc_start: 0.3509 (ptp) cc_final: 0.3098 (ptp) REVERT: D 448 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.8041 (mtp85) REVERT: D 591 GLN cc_start: 0.8252 (tt0) cc_final: 0.7871 (tm-30) REVERT: D 767 ASN cc_start: 0.8161 (t0) cc_final: 0.7769 (t0) REVERT: D 929 GLU cc_start: 0.7522 (tt0) cc_final: 0.7191 (tt0) REVERT: D 1100 MET cc_start: 0.8695 (mmm) cc_final: 0.8415 (mmp) REVERT: E 125 GLU cc_start: 0.8443 (tt0) cc_final: 0.7837 (tm-30) REVERT: E 303 MET cc_start: 0.8351 (mmm) cc_final: 0.8021 (mmp) REVERT: F 304 ASP cc_start: 0.7427 (m-30) cc_final: 0.7095 (m-30) REVERT: G 332 GLN cc_start: 0.7093 (pp30) cc_final: 0.5906 (mp10) REVERT: G 435 MET cc_start: 0.6252 (ptm) cc_final: 0.5948 (ptm) outliers start: 2 outliers final: 1 residues processed: 579 average time/residue: 0.5271 time to fit residues: 523.2184 Evaluate side-chains 428 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 427 time to evaluate : 4.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 680 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 401 optimal weight: 4.9990 chunk 515 optimal weight: 7.9990 chunk 399 optimal weight: 0.8980 chunk 593 optimal weight: 0.1980 chunk 393 optimal weight: 9.9990 chunk 702 optimal weight: 10.0000 chunk 439 optimal weight: 3.9990 chunk 428 optimal weight: 6.9990 chunk 324 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 991 ASN A1054 GLN A1274 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 HIS B 971 HIS ** B 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 GLN C 544 GLN ** C 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 989 GLN ** C1382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 ASN D 724 ASN ** D 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 337 HIS G 379 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 57634 Z= 0.203 Angle : 0.781 82.847 78081 Z= 0.331 Chirality : 0.051 1.545 8693 Planarity : 0.004 0.093 10217 Dihedral : 5.518 161.676 8145 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.02 % Allowed : 1.55 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -1.54 (0.10), residues: 7290 helix: 0.41 (0.11), residues: 2535 sheet: -1.33 (0.17), residues: 868 loop : -2.00 (0.09), residues: 3887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 69 HIS 0.005 0.001 HIS A 603 PHE 0.016 0.001 PHE G 36 TYR 0.013 0.001 TYR C1367 ARG 0.013 0.000 ARG A1186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 591 time to evaluate : 5.089 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: A 251 MET cc_start: 0.8658 (ptm) cc_final: 0.8429 (ptm) REVERT: A 440 SER cc_start: 0.4656 (p) cc_final: 0.4388 (m) REVERT: A 479 MET cc_start: 0.8138 (tpp) cc_final: 0.7898 (mmt) REVERT: A 860 MET cc_start: 0.8675 (tpp) cc_final: 0.8462 (tpp) REVERT: A 1289 MET cc_start: 0.8393 (mmt) cc_final: 0.8114 (mmt) REVERT: A 1366 GLU cc_start: 0.8242 (tt0) cc_final: 0.7845 (tt0) REVERT: A 1368 MET cc_start: 0.8739 (ttp) cc_final: 0.8399 (ptp) REVERT: A 1462 MET cc_start: 0.8025 (mmm) cc_final: 0.7598 (mmp) REVERT: B 112 ILE cc_start: 0.9212 (pt) cc_final: 0.8913 (mt) REVERT: B 345 MET cc_start: 0.8991 (mmm) cc_final: 0.8778 (mmm) REVERT: B 458 MET cc_start: 0.7049 (tmm) cc_final: 0.6328 (tmm) REVERT: B 461 MET cc_start: 0.7878 (mmt) cc_final: 0.7536 (mmm) REVERT: B 520 MET cc_start: 0.8260 (mmt) cc_final: 0.7986 (mmp) REVERT: B 562 MET cc_start: 0.8776 (mtm) cc_final: 0.8477 (mtm) REVERT: B 895 ARG cc_start: 0.5195 (mmt90) cc_final: 0.4401 (ptp90) REVERT: B 1017 ASN cc_start: 0.8560 (m-40) cc_final: 0.8078 (m-40) REVERT: B 1047 MET cc_start: 0.8138 (ptp) cc_final: 0.7565 (mtm) REVERT: B 1104 MET cc_start: 0.7065 (mmm) cc_final: 0.6744 (mmm) REVERT: B 1137 ASN cc_start: 0.7188 (m-40) cc_final: 0.6673 (p0) REVERT: B 1256 MET cc_start: 0.7913 (ttm) cc_final: 0.7683 (ttm) REVERT: B 1387 MET cc_start: 0.8397 (ttt) cc_final: 0.8132 (ttm) REVERT: C 203 ASP cc_start: 0.8432 (m-30) cc_final: 0.8155 (m-30) REVERT: C 244 MET cc_start: 0.8570 (tpp) cc_final: 0.8155 (tpp) REVERT: C 260 MET cc_start: 0.8209 (tpp) cc_final: 0.7640 (tpp) REVERT: C 345 MET cc_start: 0.8341 (tpp) cc_final: 0.7403 (ttt) REVERT: C 442 MET cc_start: 0.7428 (mtm) cc_final: 0.7073 (mtm) REVERT: C 542 LEU cc_start: 0.8656 (pt) cc_final: 0.8334 (pt) REVERT: C 860 MET cc_start: 0.8834 (mmm) cc_final: 0.8302 (tpp) REVERT: C 1249 MET cc_start: 0.8276 (mmm) cc_final: 0.8043 (tpp) REVERT: C 1256 MET cc_start: 0.8456 (mmm) cc_final: 0.8128 (mmm) REVERT: C 1300 LEU cc_start: 0.8651 (tp) cc_final: 0.8427 (tp) REVERT: C 1366 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7794 (tm-30) REVERT: C 1368 MET cc_start: 0.8666 (ttt) cc_final: 0.8056 (ttm) REVERT: D 442 MET cc_start: 0.3340 (ptp) cc_final: 0.2957 (ptp) REVERT: D 448 ARG cc_start: 0.8367 (mtt-85) cc_final: 0.8146 (mtp85) REVERT: D 591 GLN cc_start: 0.8164 (tt0) cc_final: 0.7836 (tm-30) REVERT: D 767 ASN cc_start: 0.8168 (t0) cc_final: 0.7780 (t0) REVERT: D 860 MET cc_start: 0.8700 (mmp) cc_final: 0.8385 (mmp) REVERT: D 929 GLU cc_start: 0.7500 (tt0) cc_final: 0.7151 (tt0) REVERT: D 980 LEU cc_start: 0.9247 (tp) cc_final: 0.8949 (tp) REVERT: D 1100 MET cc_start: 0.8719 (mmm) cc_final: 0.8367 (mmp) REVERT: E 303 MET cc_start: 0.8298 (mmm) cc_final: 0.7954 (mmp) REVERT: F 304 ASP cc_start: 0.7358 (m-30) cc_final: 0.6999 (m-30) REVERT: G 332 GLN cc_start: 0.7441 (pp30) cc_final: 0.5986 (mp10) outliers start: 1 outliers final: 0 residues processed: 592 average time/residue: 0.5225 time to fit residues: 535.5370 Evaluate side-chains 451 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 451 time to evaluate : 4.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 434 optimal weight: 4.9990 chunk 280 optimal weight: 9.9990 chunk 419 optimal weight: 7.9990 chunk 211 optimal weight: 0.0770 chunk 138 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 446 optimal weight: 7.9990 chunk 478 optimal weight: 0.9990 chunk 347 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 552 optimal weight: 4.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 991 ASN B 75 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 HIS B 982 GLN ** B 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1325 ASN C 544 GLN C 767 ASN C 796 HIS C 971 HIS ** D 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 724 ASN ** D 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 434 ASN F 4 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 379 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 57634 Z= 0.243 Angle : 0.794 82.809 78081 Z= 0.338 Chirality : 0.051 1.549 8693 Planarity : 0.004 0.059 10217 Dihedral : 5.494 160.546 8145 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.03 % Allowed : 1.05 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -1.48 (0.10), residues: 7290 helix: 0.45 (0.11), residues: 2538 sheet: -1.26 (0.17), residues: 868 loop : -1.96 (0.09), residues: 3884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 69 HIS 0.006 0.001 HIS D 653 PHE 0.029 0.001 PHE C1439 TYR 0.012 0.001 TYR A 207 ARG 0.013 0.000 ARG A1186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 559 time to evaluate : 5.002 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: A 251 MET cc_start: 0.8677 (ptm) cc_final: 0.8466 (ptm) REVERT: A 440 SER cc_start: 0.4708 (p) cc_final: 0.4469 (m) REVERT: A 860 MET cc_start: 0.8658 (tpp) cc_final: 0.8449 (tpp) REVERT: A 1289 MET cc_start: 0.8403 (mmt) cc_final: 0.7946 (mmt) REVERT: A 1366 GLU cc_start: 0.8268 (tt0) cc_final: 0.7888 (tt0) REVERT: A 1462 MET cc_start: 0.8039 (mmm) cc_final: 0.7604 (mmp) REVERT: B 112 ILE cc_start: 0.9240 (pt) cc_final: 0.8926 (mt) REVERT: B 458 MET cc_start: 0.7043 (tmm) cc_final: 0.6342 (tmm) REVERT: B 461 MET cc_start: 0.8046 (mmt) cc_final: 0.7092 (tpt) REVERT: B 520 MET cc_start: 0.8226 (mmt) cc_final: 0.7930 (mmp) REVERT: B 562 MET cc_start: 0.8761 (mtm) cc_final: 0.8476 (mtm) REVERT: B 895 ARG cc_start: 0.5202 (mmt90) cc_final: 0.4402 (ptp90) REVERT: B 952 MET cc_start: 0.7831 (ppp) cc_final: 0.7545 (ppp) REVERT: B 1017 ASN cc_start: 0.8552 (m-40) cc_final: 0.8053 (m-40) REVERT: B 1084 MET cc_start: 0.8684 (tpp) cc_final: 0.8465 (tpt) REVERT: B 1137 ASN cc_start: 0.7130 (m-40) cc_final: 0.6573 (p0) REVERT: B 1256 MET cc_start: 0.7904 (ttm) cc_final: 0.7675 (ttm) REVERT: B 1387 MET cc_start: 0.8496 (ttt) cc_final: 0.8243 (ttm) REVERT: C 203 ASP cc_start: 0.8454 (m-30) cc_final: 0.8173 (m-30) REVERT: C 207 TYR cc_start: 0.9188 (p90) cc_final: 0.8980 (p90) REVERT: C 244 MET cc_start: 0.8590 (tpp) cc_final: 0.8168 (tpp) REVERT: C 260 MET cc_start: 0.8254 (tpp) cc_final: 0.7663 (tpp) REVERT: C 345 MET cc_start: 0.8441 (tpp) cc_final: 0.7637 (ttt) REVERT: C 860 MET cc_start: 0.8804 (mmm) cc_final: 0.8295 (tpp) REVERT: C 1249 MET cc_start: 0.8323 (mmm) cc_final: 0.8002 (tpp) REVERT: C 1300 LEU cc_start: 0.8776 (tp) cc_final: 0.8535 (tp) REVERT: C 1366 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7653 (tm-30) REVERT: C 1368 MET cc_start: 0.8627 (ttt) cc_final: 0.7990 (ttm) REVERT: D 227 MET cc_start: 0.8517 (ppp) cc_final: 0.7775 (ppp) REVERT: D 442 MET cc_start: 0.3366 (ptp) cc_final: 0.2978 (ptp) REVERT: D 448 ARG cc_start: 0.8376 (mtt-85) cc_final: 0.8143 (mtp85) REVERT: D 591 GLN cc_start: 0.8187 (tt0) cc_final: 0.7841 (tm-30) REVERT: D 767 ASN cc_start: 0.8118 (t0) cc_final: 0.7752 (t0) REVERT: D 929 GLU cc_start: 0.7549 (tt0) cc_final: 0.7224 (tt0) REVERT: D 980 LEU cc_start: 0.9310 (tp) cc_final: 0.8968 (tp) REVERT: D 1100 MET cc_start: 0.8684 (mmm) cc_final: 0.8356 (mmp) REVERT: F 304 ASP cc_start: 0.7376 (m-30) cc_final: 0.7044 (m-30) REVERT: G 332 GLN cc_start: 0.7547 (pp30) cc_final: 0.6109 (mp10) outliers start: 2 outliers final: 0 residues processed: 561 average time/residue: 0.5149 time to fit residues: 501.2779 Evaluate side-chains 439 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 4.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 639 optimal weight: 5.9990 chunk 673 optimal weight: 10.0000 chunk 614 optimal weight: 9.9990 chunk 654 optimal weight: 8.9990 chunk 672 optimal weight: 9.9990 chunk 394 optimal weight: 6.9990 chunk 285 optimal weight: 0.0060 chunk 514 optimal weight: 10.0000 chunk 200 optimal weight: 0.0870 chunk 591 optimal weight: 1.9990 chunk 619 optimal weight: 20.0000 overall best weight: 3.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 991 ASN A1293 ASN B 75 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 HIS B1120 GLN C 544 GLN C 672 GLN C 767 ASN ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 989 GLN D 724 ASN ** D 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 GLN F 65 ASN F 113 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 379 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 57634 Z= 0.225 Angle : 0.790 82.796 78081 Z= 0.335 Chirality : 0.051 1.543 8693 Planarity : 0.004 0.056 10217 Dihedral : 5.445 160.407 8145 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.03 % Allowed : 0.57 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -1.39 (0.10), residues: 7290 helix: 0.51 (0.11), residues: 2528 sheet: -1.21 (0.17), residues: 872 loop : -1.89 (0.09), residues: 3890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 347 HIS 0.005 0.001 HIS A1109 PHE 0.028 0.001 PHE C1439 TYR 0.032 0.001 TYR C 985 ARG 0.012 0.000 ARG A1186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 560 time to evaluate : 4.984 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: A 251 MET cc_start: 0.8691 (ptm) cc_final: 0.8408 (ptm) REVERT: A 431 LYS cc_start: 0.8710 (ptpp) cc_final: 0.8482 (ptpp) REVERT: A 860 MET cc_start: 0.8667 (tpp) cc_final: 0.8465 (tpp) REVERT: A 1047 MET cc_start: 0.7625 (mtt) cc_final: 0.7419 (mtt) REVERT: A 1289 MET cc_start: 0.8384 (mmt) cc_final: 0.7940 (mmt) REVERT: A 1344 GLU cc_start: 0.8121 (mp0) cc_final: 0.7860 (mp0) REVERT: A 1366 GLU cc_start: 0.8299 (tt0) cc_final: 0.7914 (tt0) REVERT: A 1462 MET cc_start: 0.7994 (mmm) cc_final: 0.7501 (mmp) REVERT: B 112 ILE cc_start: 0.9224 (pt) cc_final: 0.8908 (mt) REVERT: B 458 MET cc_start: 0.7060 (tmm) cc_final: 0.6355 (tmm) REVERT: B 461 MET cc_start: 0.8023 (mmt) cc_final: 0.7012 (tpt) REVERT: B 520 MET cc_start: 0.8157 (mmt) cc_final: 0.7903 (mmp) REVERT: B 562 MET cc_start: 0.8750 (mtm) cc_final: 0.8447 (mtm) REVERT: B 895 ARG cc_start: 0.5211 (mmt90) cc_final: 0.4411 (ptp90) REVERT: B 952 MET cc_start: 0.7852 (ppp) cc_final: 0.7579 (ppp) REVERT: B 1017 ASN cc_start: 0.8572 (m-40) cc_final: 0.8118 (m-40) REVERT: B 1047 MET cc_start: 0.7856 (ptp) cc_final: 0.7162 (mtm) REVERT: B 1084 MET cc_start: 0.8670 (tpp) cc_final: 0.8436 (tpt) REVERT: B 1137 ASN cc_start: 0.7113 (m-40) cc_final: 0.6568 (p0) REVERT: B 1186 ARG cc_start: 0.7379 (ttp80) cc_final: 0.7128 (ptp90) REVERT: B 1256 MET cc_start: 0.7892 (ttm) cc_final: 0.7655 (ttm) REVERT: B 1387 MET cc_start: 0.8486 (ttt) cc_final: 0.8230 (ttm) REVERT: C 203 ASP cc_start: 0.8424 (m-30) cc_final: 0.8148 (m-30) REVERT: C 207 TYR cc_start: 0.9230 (p90) cc_final: 0.8990 (p90) REVERT: C 244 MET cc_start: 0.8533 (tpp) cc_final: 0.8133 (tpp) REVERT: C 260 MET cc_start: 0.8286 (tpp) cc_final: 0.7709 (tpp) REVERT: C 345 MET cc_start: 0.8480 (tpp) cc_final: 0.7708 (ttt) REVERT: C 520 MET cc_start: 0.8846 (pmm) cc_final: 0.8408 (pmm) REVERT: C 542 LEU cc_start: 0.8535 (pt) cc_final: 0.8320 (pt) REVERT: C 860 MET cc_start: 0.8824 (mmm) cc_final: 0.8341 (tpp) REVERT: C 1249 MET cc_start: 0.8331 (mmm) cc_final: 0.8010 (tpp) REVERT: C 1300 LEU cc_start: 0.8743 (tp) cc_final: 0.8538 (tp) REVERT: C 1368 MET cc_start: 0.8610 (ttt) cc_final: 0.8015 (ttm) REVERT: D 227 MET cc_start: 0.8457 (ppp) cc_final: 0.7667 (ppp) REVERT: D 442 MET cc_start: 0.3313 (ptp) cc_final: 0.2942 (ptp) REVERT: D 448 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.8143 (mtp85) REVERT: D 591 GLN cc_start: 0.8157 (tt0) cc_final: 0.7838 (tm-30) REVERT: D 651 ASP cc_start: 0.8363 (t0) cc_final: 0.7991 (t0) REVERT: D 767 ASN cc_start: 0.8123 (t0) cc_final: 0.7754 (t0) REVERT: D 929 GLU cc_start: 0.7472 (tt0) cc_final: 0.7154 (tt0) REVERT: D 980 LEU cc_start: 0.9271 (tp) cc_final: 0.8970 (tp) REVERT: D 1100 MET cc_start: 0.8747 (mmm) cc_final: 0.8406 (mmp) REVERT: F 304 ASP cc_start: 0.7338 (m-30) cc_final: 0.6983 (m-30) REVERT: G 332 GLN cc_start: 0.7676 (pp30) cc_final: 0.6284 (mp10) outliers start: 2 outliers final: 1 residues processed: 562 average time/residue: 0.5277 time to fit residues: 516.0666 Evaluate side-chains 444 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 443 time to evaluate : 5.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 652 optimal weight: 5.9990 chunk 429 optimal weight: 9.9990 chunk 692 optimal weight: 2.9990 chunk 422 optimal weight: 0.5980 chunk 328 optimal weight: 2.9990 chunk 481 optimal weight: 5.9990 chunk 726 optimal weight: 0.0470 chunk 668 optimal weight: 8.9990 chunk 578 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 446 optimal weight: 1.9990 overall best weight: 1.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 ASN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 HIS B1120 GLN C 544 GLN C 971 HIS C 989 GLN D 724 ASN ** D 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 ASN F 4 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 379 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 57634 Z= 0.176 Angle : 0.770 82.827 78081 Z= 0.322 Chirality : 0.050 1.537 8693 Planarity : 0.003 0.061 10217 Dihedral : 5.294 160.388 8145 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.02 % Allowed : 0.25 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -1.25 (0.10), residues: 7290 helix: 0.62 (0.11), residues: 2531 sheet: -1.00 (0.18), residues: 826 loop : -1.83 (0.09), residues: 3933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 347 HIS 0.006 0.001 HIS C 796 PHE 0.026 0.001 PHE C1439 TYR 0.012 0.001 TYR C1367 ARG 0.011 0.000 ARG A1186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 583 time to evaluate : 5.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.8502 (ptm) cc_final: 0.8216 (ptm) REVERT: A 860 MET cc_start: 0.8698 (tpp) cc_final: 0.8452 (tpp) REVERT: A 1047 MET cc_start: 0.7583 (mtt) cc_final: 0.7354 (mtt) REVERT: A 1289 MET cc_start: 0.8321 (mmt) cc_final: 0.8012 (mmt) REVERT: A 1366 GLU cc_start: 0.8204 (tt0) cc_final: 0.7818 (tt0) REVERT: A 1462 MET cc_start: 0.7924 (mmm) cc_final: 0.7438 (mmp) REVERT: B 112 ILE cc_start: 0.9202 (pt) cc_final: 0.8915 (mt) REVERT: B 182 MET cc_start: 0.6624 (tpt) cc_final: 0.6352 (tpp) REVERT: B 458 MET cc_start: 0.7082 (tmm) cc_final: 0.6355 (tmm) REVERT: B 461 MET cc_start: 0.7953 (mmt) cc_final: 0.6880 (tpt) REVERT: B 520 MET cc_start: 0.8255 (mmt) cc_final: 0.7976 (mmp) REVERT: B 550 LEU cc_start: 0.8930 (mt) cc_final: 0.8679 (mt) REVERT: B 562 MET cc_start: 0.8718 (mtm) cc_final: 0.8406 (mtm) REVERT: B 895 ARG cc_start: 0.5189 (mmt90) cc_final: 0.4420 (ptp90) REVERT: B 952 MET cc_start: 0.7790 (ppp) cc_final: 0.7510 (ppp) REVERT: B 1017 ASN cc_start: 0.8427 (m-40) cc_final: 0.7982 (m-40) REVERT: B 1047 MET cc_start: 0.7698 (ptp) cc_final: 0.7238 (mtm) REVERT: B 1104 MET cc_start: 0.7035 (mmm) cc_final: 0.6616 (tpt) REVERT: B 1137 ASN cc_start: 0.7046 (m-40) cc_final: 0.6510 (p0) REVERT: B 1256 MET cc_start: 0.7856 (ttm) cc_final: 0.7615 (ttm) REVERT: B 1295 TYR cc_start: 0.8910 (m-80) cc_final: 0.8273 (m-80) REVERT: B 1387 MET cc_start: 0.8415 (ttt) cc_final: 0.8155 (ttm) REVERT: C 87 GLU cc_start: 0.7613 (pm20) cc_final: 0.7322 (pm20) REVERT: C 207 TYR cc_start: 0.9222 (p90) cc_final: 0.8910 (p90) REVERT: C 244 MET cc_start: 0.8511 (tpp) cc_final: 0.8159 (tpp) REVERT: C 260 MET cc_start: 0.8277 (tpp) cc_final: 0.7704 (tpp) REVERT: C 345 MET cc_start: 0.8324 (tpp) cc_final: 0.7557 (ttt) REVERT: C 408 ASP cc_start: 0.8805 (p0) cc_final: 0.8414 (m-30) REVERT: C 860 MET cc_start: 0.8777 (mmm) cc_final: 0.8275 (tpp) REVERT: C 1249 MET cc_start: 0.8296 (mmm) cc_final: 0.8052 (tpp) REVERT: C 1368 MET cc_start: 0.8623 (ttt) cc_final: 0.8033 (ttm) REVERT: D 227 MET cc_start: 0.8454 (ppp) cc_final: 0.8090 (ppp) REVERT: D 442 MET cc_start: 0.3228 (ptp) cc_final: 0.2889 (ptp) REVERT: D 448 ARG cc_start: 0.8358 (mtt-85) cc_final: 0.8138 (mtp85) REVERT: D 591 GLN cc_start: 0.8051 (tt0) cc_final: 0.7766 (tm-30) REVERT: D 651 ASP cc_start: 0.8315 (t0) cc_final: 0.7967 (t0) REVERT: D 742 MET cc_start: 0.7843 (mmm) cc_final: 0.7596 (mtp) REVERT: D 767 ASN cc_start: 0.8105 (t0) cc_final: 0.7751 (t0) REVERT: D 929 GLU cc_start: 0.7428 (tt0) cc_final: 0.7093 (tt0) REVERT: D 980 LEU cc_start: 0.9279 (tp) cc_final: 0.8932 (tp) REVERT: D 1100 MET cc_start: 0.8720 (mmm) cc_final: 0.8364 (mmp) REVERT: F 304 ASP cc_start: 0.7294 (m-30) cc_final: 0.6943 (m-30) REVERT: G 332 GLN cc_start: 0.7650 (pp30) cc_final: 0.6208 (mp10) outliers start: 1 outliers final: 0 residues processed: 584 average time/residue: 0.5261 time to fit residues: 536.1187 Evaluate side-chains 444 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 4.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 354 optimal weight: 0.0570 chunk 459 optimal weight: 0.0970 chunk 616 optimal weight: 8.9990 chunk 177 optimal weight: 0.0000 chunk 533 optimal weight: 0.0980 chunk 85 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 579 optimal weight: 20.0000 chunk 242 optimal weight: 1.9990 chunk 594 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 overall best weight: 0.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 991 ASN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 HIS B1120 GLN C 501 GLN C 544 GLN C 767 ASN ** C 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN D1054 GLN ** D1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 ASN F 4 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 337 HIS G 379 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.090797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.077902 restraints weight = 170921.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.079795 restraints weight = 96590.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.081091 restraints weight = 62806.862| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.106 57634 Z= 0.152 Angle : 0.759 82.671 78081 Z= 0.314 Chirality : 0.050 1.521 8693 Planarity : 0.003 0.053 10217 Dihedral : 5.070 160.075 8145 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.05 % Allowed : 0.17 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -1.04 (0.10), residues: 7290 helix: 0.81 (0.11), residues: 2495 sheet: -0.93 (0.18), residues: 870 loop : -1.68 (0.09), residues: 3925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 69 HIS 0.007 0.001 HIS C 796 PHE 0.024 0.001 PHE C1439 TYR 0.010 0.001 TYR A 561 ARG 0.009 0.000 ARG C 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9723.57 seconds wall clock time: 173 minutes 23.25 seconds (10403.25 seconds total)