Starting phenix.real_space_refine on Sat Feb 24 21:24:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w64_8774/02_2024/5w64_8774.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w64_8774/02_2024/5w64_8774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w64_8774/02_2024/5w64_8774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w64_8774/02_2024/5w64_8774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w64_8774/02_2024/5w64_8774.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w64_8774/02_2024/5w64_8774.pdb" } resolution = 4.2 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= 0.012 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 Zn 6 6.06 5 P 99 5.49 5 S 205 5.16 5 C 29205 2.51 5 N 8042 2.21 5 O 8955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A ARG 1003": "NH1" <-> "NH2" Residue "A ARG 1015": "NH1" <-> "NH2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 280": "NH1" <-> "NH2" Residue "O ARG 407": "NH1" <-> "NH2" Residue "O ARG 419": "NH1" <-> "NH2" Residue "O ARG 472": "NH1" <-> "NH2" Residue "O ARG 484": "NH1" <-> "NH2" Residue "O ARG 542": "NH1" <-> "NH2" Residue "O GLU 664": "OE1" <-> "OE2" Residue "P ARG 305": "NH1" <-> "NH2" Residue "P ARG 324": "NH1" <-> "NH2" Residue "P ARG 350": "NH1" <-> "NH2" Residue "P GLU 371": "OE1" <-> "OE2" Residue "Q PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 3": "OE1" <-> "OE2" Residue "Q ARG 17": "NH1" <-> "NH2" Residue "Q ARG 30": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 166": "OE1" <-> "OE2" Residue "Q ARG 302": "NH1" <-> "NH2" Residue "Q GLU 363": "OE1" <-> "OE2" Residue "Q PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 46512 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 11542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1461, 11542 Classifications: {'peptide': 1461} Link IDs: {'PTRANS': 59, 'TRANS': 1401} Chain breaks: 7 Chain: "B" Number of atoms: 9351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1178, 9351 Classifications: {'peptide': 1178} Link IDs: {'PTRANS': 58, 'TRANS': 1119} Chain breaks: 2 Chain: "C" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2432 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 286} Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1760 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "H" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1071 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 479 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 811 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 841 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "N" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1254 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "O" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5063 Classifications: {'peptide': 640} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 19, 'TRANS': 620} Chain breaks: 4 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'UNK:plan-1': 53} Unresolved non-hydrogen planarities: 53 Chain: "P" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3238 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2923 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 2 Chain: "R" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna3p': 5} Chain: "S" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 875 Classifications: {'DNA': 42} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 41} Chain breaks: 1 Chain: "T" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1082 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 781 SG CYS A 102 178.656 82.727 78.840 1.00 0.00 S ATOM 806 SG CYS A 105 179.184 80.150 78.938 1.00 0.00 S ATOM 1605 SG CYS A 233 180.237 82.777 81.378 1.00 0.00 S ATOM 1627 SG CYS A 236 180.629 82.118 79.185 1.00 0.00 S ATOM 461 SG CYS A 62 131.998 64.491 79.271 1.00 0.00 S ATOM 480 SG CYS A 65 131.219 61.823 81.301 1.00 0.00 S ATOM 535 SG CYS A 72 130.124 63.736 82.231 1.00 0.00 S ATOM 20196 SG CYS B1104 145.151 57.313 87.204 1.00 0.00 S ATOM 20222 SG CYS B1107 145.563 60.028 88.059 1.00 0.00 S ATOM 20369 SG CYS B1128 144.613 58.261 85.487 1.00 0.00 S ATOM 20397 SG CYS B1131 146.391 56.083 85.595 1.00 0.00 S ATOM 28948 SG CYS I 10 162.559 150.943 85.754 1.00 0.00 S ATOM 28970 SG CYS I 13 159.662 149.034 84.867 1.00 0.00 S ATOM 29090 SG CYS I 30 162.050 147.959 83.845 1.00 0.00 S ATOM 29111 SG CYS I 33 162.275 150.622 84.187 1.00 0.00 S ATOM 29418 SG CYS J 7 91.006 99.175 128.458 1.00 0.00 S ATOM 29441 SG CYS J 10 88.745 98.160 129.875 1.00 0.00 S ATOM 29721 SG CYS J 45 90.583 99.696 131.584 1.00 0.00 S ATOM 29727 SG CYS J 46 87.728 100.544 130.829 1.00 0.00 S ATOM 30794 SG CYS L 31 88.979 105.101 84.474 1.00 0.00 S ATOM 30814 SG CYS L 34 86.036 105.370 84.091 1.00 0.00 S ATOM 30918 SG CYS L 48 86.899 105.080 82.106 1.00 0.00 S ATOM 30941 SG CYS L 51 88.955 106.519 82.405 1.00 0.00 S Residues with excluded nonbonded symmetry interactions: 102 residue: pdb=" N LYS A 991 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 991 " occ=0.00 residue: pdb=" N PRO A 992 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 992 " occ=0.00 residue: pdb=" N GLN A 993 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN A 993 " occ=0.00 residue: pdb=" N GLU A 994 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU A 994 " occ=0.00 residue: pdb=" N TYR A 995 " occ=0.00 ... (10 atoms not shown) pdb=" OH TYR A 995 " occ=0.00 residue: pdb=" N TYR A 996 " occ=0.00 ... (10 atoms not shown) pdb=" OH TYR A 996 " occ=0.00 residue: pdb=" N PHE A 997 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE A 997 " occ=0.00 residue: pdb=" N HIS A 998 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS A 998 " occ=0.00 residue: pdb=" N CYS A 999 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS A 999 " occ=0.00 residue: pdb=" N MET A1000 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET A1000 " occ=0.00 residue: pdb=" N ALA A1001 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A1001 " occ=0.00 residue: pdb=" N GLY A1002 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A1002 " occ=0.00 ... (remaining 90 not shown) Time building chain proxies: 23.43, per 1000 atoms: 0.50 Number of scatterers: 46512 At special positions: 0 Unit cell: (213.2, 193.7, 195, 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) Zn 6 29.99 S 205 16.00 P 99 15.00 O 8955 8.00 N 8042 7.00 C 29205 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: 20.23 Conformation dependent library (CDL) restraints added in 7.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 236 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 65 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 33 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " Number of angles added : 33 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10544 Finding SS restraints... Secondary structure from input PDB file: 215 helices and 60 sheets defined 42.5% alpha, 16.7% beta 31 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 17.57 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.705A pdb=" N SER A 101 " --> pdb=" O TYR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 127 Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 174 through 199 Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.819A pdb=" N ARG A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.608A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.885A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 380 through 406 Processing helix chain 'A' and resid 415 through 439 removed outlier: 3.886A pdb=" N ILE A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 498 through 505 Processing helix chain 'A' and resid 515 through 526 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.501A pdb=" N ILE A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 700 Processing helix chain 'A' and resid 701 through 705 Processing helix chain 'A' and resid 728 through 740 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 793 through 802 Processing helix chain 'A' and resid 802 through 825 Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 849 through 863 removed outlier: 3.644A pdb=" N THR A 853 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG A 855 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 Processing helix chain 'A' and resid 885 through 916 Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 923 through 932 Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 991 through 1013 removed outlier: 3.752A pdb=" N PHE A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1028 removed outlier: 3.744A pdb=" N GLY A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1064 removed outlier: 4.132A pdb=" N SER A1061 " --> pdb=" O ILE A1057 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N HIS A1062 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A1064 " --> pdb=" O GLU A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1080 Processing helix chain 'A' and resid 1081 through 1085 removed outlier: 3.851A pdb=" N ALA A1084 " --> pdb=" O ASN A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1108 Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.682A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 Processing helix chain 'A' and resid 1164 through 1176 Processing helix chain 'A' and resid 1184 through 1195 Processing helix chain 'A' and resid 1196 through 1199 Processing helix chain 'A' and resid 1217 through 1226 Processing helix chain 'A' and resid 1247 through 1259 Processing helix chain 'A' and resid 1264 through 1267 Processing helix chain 'A' and resid 1298 through 1307 Processing helix chain 'A' and resid 1309 through 1320 Processing helix chain 'A' and resid 1320 through 1337 Processing helix chain 'A' and resid 1440 through 1454 Processing helix chain 'A' and resid 1477 through 1481 Processing helix chain 'A' and resid 1484 through 1494 Processing helix chain 'A' and resid 1525 through 1531 removed outlier: 3.719A pdb=" N ASP A1531 " --> pdb=" O GLN A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1541 Processing helix chain 'A' and resid 1545 through 1554 Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.801A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.764A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1605 removed outlier: 4.335A pdb=" N THR A1605 " --> pdb=" O GLN A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1614 Processing helix chain 'A' and resid 1617 through 1629 Processing helix chain 'A' and resid 1636 through 1643 Processing helix chain 'A' and resid 1649 through 1652 Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 35 through 42 removed outlier: 4.275A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.690A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.604A pdb=" N LEU B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 170 through 175 removed outlier: 3.960A pdb=" N LYS B 174 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET B 175 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 219 through 225 removed outlier: 3.653A pdb=" N ALA B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.717A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 299 through 317 Processing helix chain 'B' and resid 322 through 335 Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 404 through 433 Processing helix chain 'B' and resid 442 through 451 Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.799A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.711A pdb=" N ASP B 477 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 4.142A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 512 removed outlier: 3.626A pdb=" N LEU B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.533A pdb=" N SER B 524 " --> pdb=" O LEU B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 569 Processing helix chain 'B' and resid 573 through 577 removed outlier: 3.901A pdb=" N PHE B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 573 through 577' Processing helix chain 'B' and resid 597 through 614 Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.774A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 698 through 704 Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 711 through 725 Processing helix chain 'B' and resid 731 through 736 removed outlier: 4.594A pdb=" N CYS B 734 " --> pdb=" O VAL B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 760 removed outlier: 4.126A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 833 through 839 Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.584A pdb=" N ARG B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.656A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 Processing helix chain 'B' and resid 1039 through 1044 Processing helix chain 'B' and resid 1072 through 1082 Processing helix chain 'B' and resid 1084 through 1093 Processing helix chain 'B' and resid 1173 through 1186 Proline residue: B1179 - end of helix removed outlier: 4.164A pdb=" N TYR B1184 " --> pdb=" O PHE B1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.588A pdb=" N LEU C 113 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.904A pdb=" N ASP C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 Processing helix chain 'D' and resid 32 through 49 removed outlier: 3.830A pdb=" N ASN D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.785A pdb=" N SER D 85 " --> pdb=" O ASN D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 27 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.554A pdb=" N CYS E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 59 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 142 removed outlier: 4.092A pdb=" N VAL E 142 " --> pdb=" O ALA E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'G' and resid 10 through 20 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 129 through 134 Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.778A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.720A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 54 Processing helix chain 'K' and resid 69 through 83 removed outlier: 4.380A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 98 Processing helix chain 'K' and resid 112 through 142 Processing helix chain 'M' and resid 67 through 72 Processing helix chain 'M' and resid 104 through 107 removed outlier: 3.505A pdb=" N ASN M 107 " --> pdb=" O SER M 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 104 through 107' Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 70 through 75 removed outlier: 3.759A pdb=" N ASP N 73 " --> pdb=" O LEU N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 154 Processing helix chain 'N' and resid 176 through 180 removed outlier: 3.618A pdb=" N ASP N 179 " --> pdb=" O ASP N 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 294 through 298 removed outlier: 3.914A pdb=" N ILE O 297 " --> pdb=" O PHE O 294 " (cutoff:3.500A) Processing helix chain 'O' and resid 571 through 576 removed outlier: 3.832A pdb=" N SER O 576 " --> pdb=" O PRO O 572 " (cutoff:3.500A) Processing helix chain 'O' and resid 577 through 579 No H-bonds generated for 'chain 'O' and resid 577 through 579' Processing helix chain 'O' and resid 582 through 614 removed outlier: 3.790A pdb=" N SER O 588 " --> pdb=" O ARG O 584 " (cutoff:3.500A) Processing helix chain 'O' and resid 618 through 644 Processing helix chain 'O' and resid 671 through 686 Processing helix chain 'O' and resid 695 through 704 removed outlier: 4.047A pdb=" N LEU O 699 " --> pdb=" O GLY O 695 " (cutoff:3.500A) Processing helix chain 'O' and resid 712 through 723 removed outlier: 3.582A pdb=" N ASN O 716 " --> pdb=" O ASP O 712 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN O 720 " --> pdb=" O ASN O 716 " (cutoff:3.500A) Processing helix chain 'O' and resid 732 through 744 removed outlier: 3.750A pdb=" N ILE O 736 " --> pdb=" O LEU O 732 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL O 737 " --> pdb=" O THR O 733 " (cutoff:3.500A) Processing helix chain 'O' and resid 752 through 764 Processing helix chain 'O' and resid 765 through 777 Processing helix chain 'P' and resid 96 through 124 Processing helix chain 'P' and resid 125 through 147 removed outlier: 3.757A pdb=" N GLU P 130 " --> pdb=" O PRO P 126 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR P 143 " --> pdb=" O LYS P 139 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP P 146 " --> pdb=" O LYS P 142 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN P 147 " --> pdb=" O THR P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 173 removed outlier: 3.846A pdb=" N THR P 161 " --> pdb=" O HIS P 157 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE P 162 " --> pdb=" O MET P 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 188 Processing helix chain 'P' and resid 201 through 206 Processing helix chain 'P' and resid 225 through 238 removed outlier: 3.668A pdb=" N ALA P 231 " --> pdb=" O TYR P 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 243 Processing helix chain 'P' and resid 249 through 260 removed outlier: 4.152A pdb=" N LEU P 253 " --> pdb=" O CYS P 249 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS P 260 " --> pdb=" O LEU P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 278 Processing helix chain 'P' and resid 301 through 319 Processing helix chain 'P' and resid 327 through 339 removed outlier: 4.145A pdb=" N LEU P 332 " --> pdb=" O LEU P 328 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER P 333 " --> pdb=" O LYS P 329 " (cutoff:3.500A) Processing helix chain 'P' and resid 345 through 355 Processing helix chain 'P' and resid 362 through 369 removed outlier: 3.554A pdb=" N PHE P 367 " --> pdb=" O SER P 363 " (cutoff:3.500A) Processing helix chain 'P' and resid 371 through 385 Processing helix chain 'P' and resid 405 through 417 Processing helix chain 'P' and resid 437 through 449 Processing helix chain 'P' and resid 470 through 491 Processing helix chain 'P' and resid 496 through 510 removed outlier: 3.593A pdb=" N LEU P 510 " --> pdb=" O LYS P 506 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 36 Processing helix chain 'Q' and resid 122 through 130 Processing helix chain 'Q' and resid 159 through 167 Processing helix chain 'Q' and resid 168 through 179 removed outlier: 4.033A pdb=" N ILE Q 175 " --> pdb=" O ARG Q 171 " (cutoff:3.500A) Proline residue: Q 176 - end of helix removed outlier: 4.028A pdb=" N HIS Q 179 " --> pdb=" O ILE Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 192 Processing helix chain 'Q' and resid 207 through 225 removed outlier: 3.666A pdb=" N THR Q 215 " --> pdb=" O ARG Q 211 " (cutoff:3.500A) Processing helix chain 'Q' and resid 228 through 242 removed outlier: 3.541A pdb=" N TYR Q 233 " --> pdb=" O TRP Q 229 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LYS Q 234 " --> pdb=" O SER Q 230 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG Q 241 " --> pdb=" O ALA Q 237 " (cutoff:3.500A) Processing helix chain 'Q' and resid 247 through 261 removed outlier: 4.116A pdb=" N VAL Q 255 " --> pdb=" O TRP Q 251 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU Q 256 " --> pdb=" O GLY Q 252 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU Q 258 " --> pdb=" O GLY Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 267 through 278 Processing helix chain 'Q' and resid 306 through 322 removed outlier: 3.502A pdb=" N LYS Q 322 " --> pdb=" O ILE Q 318 " (cutoff:3.500A) Processing helix chain 'Q' and resid 340 through 351 Processing helix chain 'Q' and resid 362 through 382 removed outlier: 3.803A pdb=" N LEU Q 379 " --> pdb=" O LYS Q 375 " (cutoff:3.500A) Processing helix chain 'Q' and resid 398 through 421 removed outlier: 3.532A pdb=" N THR Q 413 " --> pdb=" O HIS Q 409 " (cutoff:3.500A) Processing helix chain 'Q' and resid 427 through 443 removed outlier: 3.799A pdb=" N ILE Q 431 " --> pdb=" O PRO Q 427 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG Q 441 " --> pdb=" O SER Q 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 3.539A pdb=" N ASP A 15 " --> pdb=" O SER B1190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 243 through 245 removed outlier: 4.708A pdb=" N ILE A 251 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.751A pdb=" N GLU A 376 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 474 through 475 Processing sheet with id=AA8, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 5.542A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 506 through 510 removed outlier: 4.012A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 686 through 688 Processing sheet with id=AB2, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.340A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 826 through 827 removed outlier: 8.807A pdb=" N ILE B 947 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL B 772 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE B 949 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ALA B 774 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N MET B1013 " --> pdb=" O LEU B1022 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA B1024 " --> pdb=" O GLU B1011 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU B1011 " --> pdb=" O ALA B1024 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 826 through 827 removed outlier: 4.485A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N SER B 777 " --> pdb=" O ASP B1025 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N ASP B1025 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N MET B1013 " --> pdb=" O LEU B1022 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA B1024 " --> pdb=" O GLU B1011 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU B1011 " --> pdb=" O ALA B1024 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB6, first strand: chain 'A' and resid 1030 through 1032 removed outlier: 6.475A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1504 through 1508 removed outlier: 3.907A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.045A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1461 through 1462 Processing sheet with id=AC1, first strand: chain 'F' and resid 143 through 147 Processing sheet with id=AC2, first strand: chain 'B' and resid 71 through 74 removed outlier: 4.428A pdb=" N VAL B 97 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N SER B 144 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AC4, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC5, first strand: chain 'B' and resid 400 through 403 removed outlier: 6.834A pdb=" N MET B 205 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.565A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC8, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC9, first strand: chain 'B' and resid 571 through 572 removed outlier: 6.623A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 741 through 744 removed outlier: 7.740A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 741 through 744 removed outlier: 7.740A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AD4, first strand: chain 'B' and resid 857 through 863 removed outlier: 6.584A pdb=" N LYS B 872 " --> pdb=" O ILE B 858 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA B 860 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS B 870 " --> pdb=" O ALA B 860 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE B 862 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS B 868 " --> pdb=" O PHE B 862 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD6, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD7, first strand: chain 'B' and resid 1132 through 1134 Processing sheet with id=AD8, first strand: chain 'C' and resid 41 through 47 removed outlier: 5.387A pdb=" N VAL C 42 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE C 57 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE C 44 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASP C 55 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 10.652A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N PHE C 300 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N THR C 224 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N VAL C 302 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N VAL C 222 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.170A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLU C 201 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ASN C 87 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE2, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.676A pdb=" N VAL C 162 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AE4, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.894A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN G 121 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLY G 86 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR G 123 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR G 84 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N TRP G 125 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU G 82 " --> pdb=" O TRP G 125 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS G 72 " --> pdb=" O VAL G 81 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.257A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE7, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE8, first strand: chain 'G' and resid 132 through 141 removed outlier: 3.806A pdb=" N TYR G 136 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN G 140 " --> pdb=" O HIS G 144 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N HIS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.324A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF3, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AF4, first strand: chain 'M' and resid 95 through 97 removed outlier: 7.072A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 48 through 50 removed outlier: 4.758A pdb=" N THR M 37 " --> pdb=" O GLU M 56 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU M 56 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS M 99 " --> pdb=" O GLU M 63 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 48 through 50 Processing sheet with id=AF7, first strand: chain 'M' and resid 87 through 91 removed outlier: 3.651A pdb=" N SER M 87 " --> pdb=" O ASN M 82 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL M 77 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE N 56 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL N 53 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL N 139 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS N 57 " --> pdb=" O VAL N 139 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL N 136 " --> pdb=" O ASP N 92 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP N 92 " --> pdb=" O VAL N 136 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 57 through 60 removed outlier: 3.549A pdb=" N TYR O 548 " --> pdb=" O VAL O 539 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ASP O 536 " --> pdb=" O THR O 510 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N THR O 510 " --> pdb=" O ASP O 536 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU O 538 " --> pdb=" O ILE O 508 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE O 508 " --> pdb=" O LEU O 538 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS O 540 " --> pdb=" O THR O 506 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 201 through 205 removed outlier: 4.243A pdb=" N GLU O 201 " --> pdb=" O LEU O 219 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 242 through 245 removed outlier: 6.628A pdb=" N ILE O 264 " --> pdb=" O LYS O 243 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 305 through 306 Processing sheet with id=AG3, first strand: chain 'O' and resid 361 through 365 removed outlier: 3.732A pdb=" N GLU O 382 " --> pdb=" O THR O 391 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 402 through 405 removed outlier: 6.878A pdb=" N THR O 417 " --> pdb=" O ARG O 403 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 452 through 457 Processing sheet with id=AG6, first strand: chain 'O' and resid 452 through 457 1968 hydrogen bonds defined for protein. 5391 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 27.05 Time building geometry restraints manager: 21.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7773 1.32 - 1.44: 12844 1.44 - 1.57: 26463 1.57 - 1.69: 241 1.69 - 1.82: 326 Bond restraints: 47647 Sorted by residual: bond pdb=" N PRO B 78 " pdb=" CD PRO B 78 " ideal model delta sigma weight residual 1.473 1.324 0.149 1.40e-02 5.10e+03 1.14e+02 bond pdb=" CA GLU O 573 " pdb=" C GLU O 573 " ideal model delta sigma weight residual 1.523 1.642 -0.119 1.34e-02 5.57e+03 7.90e+01 bond pdb=" CA ILE O 297 " pdb=" C ILE O 297 " ideal model delta sigma weight residual 1.530 1.627 -0.097 1.12e-02 7.97e+03 7.47e+01 bond pdb=" CA LEU A 460 " pdb=" C LEU A 460 " ideal model delta sigma weight residual 1.522 1.634 -0.112 1.38e-02 5.25e+03 6.54e+01 bond pdb=" CA LEU P 262 " pdb=" C LEU P 262 " ideal model delta sigma weight residual 1.524 1.623 -0.099 1.26e-02 6.30e+03 6.16e+01 ... (remaining 47642 not shown) Histogram of bond angle deviations from ideal: 85.95 - 96.74: 23 96.74 - 107.54: 3049 107.54 - 118.33: 34892 118.33 - 129.12: 26520 129.12 - 139.91: 347 Bond angle restraints: 64831 Sorted by residual: angle pdb=" N HIS O 617 " pdb=" CA HIS O 617 " pdb=" C HIS O 617 " ideal model delta sigma weight residual 113.19 85.95 27.24 1.19e+00 7.06e-01 5.24e+02 angle pdb=" N VAL P 356 " pdb=" CA VAL P 356 " pdb=" C VAL P 356 " ideal model delta sigma weight residual 112.17 92.41 19.76 9.50e-01 1.11e+00 4.33e+02 angle pdb=" N HIS O 705 " pdb=" CA HIS O 705 " pdb=" C HIS O 705 " ideal model delta sigma weight residual 113.21 90.99 22.22 1.15e+00 7.56e-01 3.73e+02 angle pdb=" N ILE Q 152 " pdb=" CA ILE Q 152 " pdb=" C ILE Q 152 " ideal model delta sigma weight residual 113.20 95.13 18.07 9.60e-01 1.09e+00 3.54e+02 angle pdb=" C LYS B 77 " pdb=" N PRO B 78 " pdb=" CA PRO B 78 " ideal model delta sigma weight residual 120.11 100.39 19.72 1.12e+00 7.97e-01 3.10e+02 ... (remaining 64826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 27982 35.00 - 70.00: 721 70.00 - 105.00: 40 105.00 - 140.00: 0 140.00 - 175.00: 1 Dihedral angle restraints: 28744 sinusoidal: 12487 harmonic: 16257 Sorted by residual: dihedral pdb=" C LYS A 410 " pdb=" N LYS A 410 " pdb=" CA LYS A 410 " pdb=" CB LYS A 410 " ideal model delta harmonic sigma weight residual -122.60 -157.47 34.87 0 2.50e+00 1.60e-01 1.95e+02 dihedral pdb=" N LYS A 410 " pdb=" C LYS A 410 " pdb=" CA LYS A 410 " pdb=" CB LYS A 410 " ideal model delta harmonic sigma weight residual 122.80 157.09 -34.29 0 2.50e+00 1.60e-01 1.88e+02 dihedral pdb=" C GLN Q 147 " pdb=" N GLN Q 147 " pdb=" CA GLN Q 147 " pdb=" CB GLN Q 147 " ideal model delta harmonic sigma weight residual -122.60 -143.26 20.66 0 2.50e+00 1.60e-01 6.83e+01 ... (remaining 28741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.296: 7134 0.296 - 0.591: 107 0.591 - 0.887: 7 0.887 - 1.182: 3 1.182 - 1.478: 1 Chirality restraints: 7252 Sorted by residual: chirality pdb=" CA LYS A 410 " pdb=" N LYS A 410 " pdb=" C LYS A 410 " pdb=" CB LYS A 410 " both_signs ideal model delta sigma weight residual False 2.51 1.03 1.48 2.00e-01 2.50e+01 5.46e+01 chirality pdb=" CB ILE M 113 " pdb=" CA ILE M 113 " pdb=" CG1 ILE M 113 " pdb=" CG2 ILE M 113 " both_signs ideal model delta sigma weight residual False 2.64 1.59 1.05 2.00e-01 2.50e+01 2.78e+01 chirality pdb=" CA GLU P 122 " pdb=" N GLU P 122 " pdb=" C GLU P 122 " pdb=" CB GLU P 122 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.23e+01 ... (remaining 7249 not shown) Planarity restraints: 7976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 188 " 0.100 2.00e-02 2.50e+03 6.14e-02 6.60e+01 pdb=" CG PHE Q 188 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 188 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 188 " -0.054 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 188 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 188 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE Q 188 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS O 701 " -0.080 2.00e-02 2.50e+03 6.00e-02 5.40e+01 pdb=" CG HIS O 701 " 0.086 2.00e-02 2.50e+03 pdb=" ND1 HIS O 701 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 HIS O 701 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 HIS O 701 " -0.051 2.00e-02 2.50e+03 pdb=" NE2 HIS O 701 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 270 " 0.083 2.00e-02 2.50e+03 5.20e-02 4.72e+01 pdb=" CG PHE Q 270 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 270 " -0.062 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 270 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 270 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 270 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE Q 270 " 0.055 2.00e-02 2.50e+03 ... (remaining 7973 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.78: 224 1.78 - 2.56: 2359 2.56 - 3.34: 68380 3.34 - 4.12: 123881 4.12 - 4.90: 212911 Nonbonded interactions: 407755 Sorted by model distance: nonbonded pdb=" CA LEU O 732 " pdb=" OE2 GLU O 735 " model vdw 1.006 3.470 nonbonded pdb=" NZ LYS A 111 " pdb=" N GLU A 114 " model vdw 1.008 3.200 nonbonded pdb=" OE1 GLU O 614 " pdb=" CB ALA O 670 " model vdw 1.009 3.460 nonbonded pdb=" CD LYS Q 136 " pdb=" CG HIS Q 304 " model vdw 1.010 3.660 nonbonded pdb=" CE2 PHE N 23 " pdb=" CD1 ILE N 25 " model vdw 1.020 3.760 ... (remaining 407750 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.96 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 4.320 Check model and map are aligned: 0.710 Set scattering table: 0.450 Process input model: 148.500 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.149 47647 Z= 0.547 Angle : 1.558 27.236 64831 Z= 0.976 Chirality : 0.090 1.478 7252 Planarity : 0.011 0.122 7976 Dihedral : 15.064 175.004 18200 Min Nonbonded Distance : 1.006 Molprobity Statistics. All-atom Clashscore : 104.20 Ramachandran Plot: Outliers : 4.09 % Allowed : 8.80 % Favored : 87.11 % Rotamer: Outliers : 5.36 % Allowed : 5.11 % Favored : 89.53 % Cbeta Deviations : 1.10 % Peptide Plane: Cis-proline : 0.00 % 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: -3.53 (0.10), residues: 5432 helix: -1.96 (0.09), residues: 1918 sheet: -1.64 (0.17), residues: 750 loop : -2.87 (0.10), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.005 TRP Q 273 HIS 0.019 0.003 HIS A 998 PHE 0.100 0.004 PHE Q 188 TYR 0.096 0.007 TYR Q 443 ARG 0.096 0.011 ARG F 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1721 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1456 time to evaluate : 5.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 450 LYS cc_start: 0.5724 (OUTLIER) cc_final: 0.3149 (mttp) REVERT: A 460 LEU cc_start: 0.5431 (pp) cc_final: 0.4892 (pp) REVERT: A 472 MET cc_start: 0.7725 (mmp) cc_final: 0.7386 (mmt) REVERT: A 634 ASN cc_start: 0.6816 (m-40) cc_final: 0.6328 (m-40) REVERT: A 738 ASN cc_start: 0.6243 (t0) cc_final: 0.5673 (t0) REVERT: A 821 ILE cc_start: 0.7740 (mm) cc_final: 0.7520 (mm) REVERT: A 993 GLN cc_start: 0.1323 (mt0) cc_final: 0.0799 (mp10) REVERT: A 1000 MET cc_start: 0.1809 (mtt) cc_final: 0.1088 (mmt) REVERT: A 1004 GLU cc_start: -0.0679 (tm-30) cc_final: -0.1122 (pp20) REVERT: A 1007 ILE cc_start: 0.1135 (mt) cc_final: 0.0361 (mm) REVERT: A 1008 ASP cc_start: -0.0177 (t0) cc_final: -0.0404 (m-30) REVERT: A 1011 VAL cc_start: -0.2668 (m) cc_final: -0.3056 (p) REVERT: A 1012 LYS cc_start: 0.0317 (pttp) cc_final: -0.0252 (ttmt) REVERT: A 1013 THR cc_start: 0.2029 (m) cc_final: 0.0982 (t) REVERT: A 1089 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6157 (pt) REVERT: A 1170 MET cc_start: 0.5980 (mmm) cc_final: 0.5633 (mmm) REVERT: A 1188 ILE cc_start: 0.8709 (mt) cc_final: 0.8463 (mt) REVERT: B 63 LEU cc_start: 0.7606 (mt) cc_final: 0.6930 (mm) REVERT: B 80 ASN cc_start: -0.1405 (t0) cc_final: -0.2047 (t0) REVERT: B 110 ASN cc_start: 0.6106 (OUTLIER) cc_final: 0.5903 (p0) REVERT: B 231 HIS cc_start: 0.4801 (m-70) cc_final: 0.4579 (m-70) REVERT: B 411 MET cc_start: 0.7052 (mtp) cc_final: 0.6719 (mtm) REVERT: B 496 PHE cc_start: 0.7945 (t80) cc_final: 0.7506 (t80) REVERT: B 733 LEU cc_start: 0.7551 (mt) cc_final: 0.7001 (mp) REVERT: B 813 LEU cc_start: 0.4890 (OUTLIER) cc_final: 0.3259 (pp) REVERT: B 905 TYR cc_start: 0.6497 (m-10) cc_final: 0.5893 (m-10) REVERT: B 1086 PHE cc_start: 0.6711 (m-80) cc_final: 0.6440 (m-80) REVERT: C 71 MET cc_start: 0.7219 (mtm) cc_final: 0.6659 (mtm) REVERT: D 25 THR cc_start: 0.7519 (p) cc_final: 0.7271 (p) REVERT: F 137 TYR cc_start: 0.6316 (m-80) cc_final: 0.5958 (m-80) REVERT: F 145 ASP cc_start: 0.6916 (m-30) cc_final: 0.5919 (m-30) REVERT: G 96 SER cc_start: 0.5451 (OUTLIER) cc_final: 0.5056 (p) REVERT: G 110 ASP cc_start: 0.6624 (p0) cc_final: 0.5594 (p0) REVERT: I 11 LEU cc_start: 0.5621 (tp) cc_final: 0.4907 (mt) REVERT: J 48 ARG cc_start: 0.7914 (ptt90) cc_final: 0.7344 (ptt90) REVERT: J 49 MET cc_start: 0.8064 (tpp) cc_final: 0.7389 (tpp) REVERT: J 54 VAL cc_start: 0.9206 (t) cc_final: 0.8978 (p) REVERT: K 103 ILE cc_start: 0.7620 (tt) cc_final: 0.7327 (tt) REVERT: L 46 VAL cc_start: 0.8593 (t) cc_final: 0.8255 (p) REVERT: L 57 LEU cc_start: 0.6429 (tp) cc_final: 0.6092 (tt) REVERT: M 66 THR cc_start: 0.6982 (OUTLIER) cc_final: 0.6379 (p) REVERT: M 74 ASN cc_start: 0.7779 (t0) cc_final: 0.6717 (t0) REVERT: O 485 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8572 (mmtm) REVERT: O 634 THR cc_start: 0.6785 (p) cc_final: 0.6576 (p) REVERT: O 747 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7308 (mt) REVERT: P 254 LEU cc_start: 0.7757 (tp) cc_final: 0.7541 (tp) REVERT: P 291 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7264 (m-30) REVERT: P 512 ARG cc_start: 0.0245 (OUTLIER) cc_final: -0.0114 (mpp80) REVERT: Q 166 GLU cc_start: 0.7667 (tt0) cc_final: 0.6793 (tt0) REVERT: Q 204 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: Q 271 LEU cc_start: 0.9052 (mt) cc_final: 0.8633 (mt) outliers start: 265 outliers final: 130 residues processed: 1676 average time/residue: 0.6084 time to fit residues: 1638.6949 Evaluate side-chains 975 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 834 time to evaluate : 5.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 469 optimal weight: 8.9990 chunk 421 optimal weight: 20.0000 chunk 233 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 284 optimal weight: 6.9990 chunk 225 optimal weight: 8.9990 chunk 435 optimal weight: 30.0000 chunk 168 optimal weight: 9.9990 chunk 264 optimal weight: 9.9990 chunk 324 optimal weight: 8.9990 chunk 504 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 93 GLN A 107 HIS A 116 HIS A 221 HIS A 224 HIS A 332 GLN A 344 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 HIS A 553 GLN A 580 HIS A 636 HIS A 656 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1314 GLN ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 HIS A1532 GLN ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 282 HIS ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS B 683 ASN B1010 ASN B1038 HIS B1089 GLN ** B1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN E 3 GLN E 5 ASN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 GLN N 132 GLN O 215 ASN O 267 ASN O 301 GLN O 308 ASN ** O 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 490 GLN O 579 ASN O 580 ASN ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 259 GLN ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 449 GLN Q 184 ASN Q 287 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 47647 Z= 0.397 Angle : 1.014 28.124 64831 Z= 0.527 Chirality : 0.054 0.404 7252 Planarity : 0.007 0.100 7976 Dihedral : 13.972 176.474 7147 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 32.26 Ramachandran Plot: Outliers : 1.49 % Allowed : 7.79 % Favored : 90.72 % Rotamer: Outliers : 0.44 % Allowed : 3.64 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.11), residues: 5432 helix: -0.57 (0.11), residues: 1968 sheet: -1.22 (0.17), residues: 742 loop : -2.10 (0.11), residues: 2722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP O 324 HIS 0.030 0.002 HIS P 157 PHE 0.067 0.003 PHE P 125 TYR 0.037 0.003 TYR Q 131 ARG 0.012 0.001 ARG M 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1115 time to evaluate : 5.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 101 SER cc_start: 0.5322 (m) cc_final: 0.4999 (p) REVERT: A 228 LEU cc_start: 0.8012 (pp) cc_final: 0.7590 (pp) REVERT: A 434 VAL cc_start: 0.7135 (t) cc_final: 0.6932 (t) REVERT: A 472 MET cc_start: 0.7510 (mmp) cc_final: 0.7280 (mmm) REVERT: A 818 THR cc_start: 0.7667 (p) cc_final: 0.7449 (p) REVERT: A 821 ILE cc_start: 0.7818 (mm) cc_final: 0.7589 (mm) REVERT: A 925 MET cc_start: 0.7101 (tpt) cc_final: 0.6691 (tmm) REVERT: A 994 GLU cc_start: 0.0734 (mt-10) cc_final: -0.0010 (mt-10) REVERT: A 1000 MET cc_start: 0.2394 (mtt) cc_final: 0.1967 (mmm) REVERT: A 1011 VAL cc_start: -0.2742 (m) cc_final: -0.3247 (p) REVERT: A 1013 THR cc_start: 0.1799 (m) cc_final: 0.0458 (t) REVERT: A 1019 LEU cc_start: -0.0500 (tp) cc_final: -0.0970 (tp) REVERT: A 1185 VAL cc_start: 0.8741 (m) cc_final: 0.8228 (m) REVERT: A 1192 SER cc_start: 0.8923 (m) cc_final: 0.8220 (t) REVERT: A 1642 VAL cc_start: 0.9090 (t) cc_final: 0.8782 (t) REVERT: A 1647 ASN cc_start: 0.8564 (t0) cc_final: 0.7971 (t0) REVERT: B 38 LEU cc_start: 0.7768 (mm) cc_final: 0.7286 (mm) REVERT: B 258 VAL cc_start: 0.7531 (t) cc_final: 0.7299 (t) REVERT: B 259 THR cc_start: 0.7866 (p) cc_final: 0.7619 (p) REVERT: B 276 ILE cc_start: 0.7773 (mp) cc_final: 0.7517 (mp) REVERT: B 309 LEU cc_start: 0.6472 (mt) cc_final: 0.6111 (mt) REVERT: B 355 ASP cc_start: 0.6834 (m-30) cc_final: 0.6294 (t0) REVERT: B 496 PHE cc_start: 0.7857 (t80) cc_final: 0.7513 (t80) REVERT: B 1079 LEU cc_start: 0.8232 (mt) cc_final: 0.8023 (mt) REVERT: B 1176 VAL cc_start: 0.8522 (t) cc_final: 0.8255 (t) REVERT: D 25 THR cc_start: 0.7402 (p) cc_final: 0.7135 (p) REVERT: E 140 LEU cc_start: 0.6950 (mm) cc_final: 0.6737 (mm) REVERT: F 115 THR cc_start: 0.8813 (p) cc_final: 0.8577 (p) REVERT: F 137 TYR cc_start: 0.6521 (m-80) cc_final: 0.6296 (m-80) REVERT: G 47 VAL cc_start: 0.6324 (m) cc_final: 0.6121 (m) REVERT: G 110 ASP cc_start: 0.6407 (p0) cc_final: 0.5533 (p0) REVERT: I 65 SER cc_start: 0.7297 (p) cc_final: 0.6943 (t) REVERT: J 16 ASP cc_start: 0.6571 (p0) cc_final: 0.6328 (p0) REVERT: J 32 GLU cc_start: 0.5921 (mp0) cc_final: 0.5614 (mp0) REVERT: J 48 ARG cc_start: 0.7504 (ptt90) cc_final: 0.7046 (ptt90) REVERT: J 49 MET cc_start: 0.7925 (tpp) cc_final: 0.7108 (tpp) REVERT: J 54 VAL cc_start: 0.9204 (t) cc_final: 0.8965 (p) REVERT: K 100 LEU cc_start: 0.7032 (mt) cc_final: 0.6713 (mp) REVERT: O 436 ILE cc_start: 0.6216 (OUTLIER) cc_final: 0.5887 (mp) REVERT: O 471 MET cc_start: 0.7427 (mtt) cc_final: 0.6254 (mtm) outliers start: 22 outliers final: 6 residues processed: 1132 average time/residue: 0.5927 time to fit residues: 1102.1206 Evaluate side-chains 777 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 770 time to evaluate : 5.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 280 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 420 optimal weight: 50.0000 chunk 343 optimal weight: 10.0000 chunk 139 optimal weight: 0.9980 chunk 505 optimal weight: 3.9990 chunk 546 optimal weight: 6.9990 chunk 450 optimal weight: 30.0000 chunk 501 optimal weight: 20.0000 chunk 172 optimal weight: 10.0000 chunk 405 optimal weight: 0.6980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN A 656 GLN A 738 ASN A 798 HIS A 950 GLN A1036 ASN A1088 HIS A1113 HIS A1319 ASN ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN B 462 GLN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN B 755 ASN B 975 HIS ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 113 GLN F 100 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN J 26 GLN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN N 132 GLN ** O 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 454 GLN O 461 HIS O 613 HIS ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 728 GLN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 511 HIS ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 409 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 47647 Z= 0.287 Angle : 0.850 21.099 64831 Z= 0.440 Chirality : 0.049 0.387 7252 Planarity : 0.006 0.113 7976 Dihedral : 14.118 177.585 7147 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 26.26 Ramachandran Plot: Outliers : 1.14 % Allowed : 7.64 % Favored : 91.22 % Rotamer: Outliers : 0.20 % Allowed : 3.96 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % Twisted General : 0.15 % 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: -1.49 (0.11), residues: 5432 helix: 0.04 (0.11), residues: 1967 sheet: -1.05 (0.17), residues: 749 loop : -1.76 (0.12), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP O 324 HIS 0.014 0.001 HIS P 157 PHE 0.073 0.003 PHE P 125 TYR 0.034 0.002 TYR P 227 ARG 0.013 0.001 ARG O 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1012 time to evaluate : 5.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 472 MET cc_start: 0.7322 (mmp) cc_final: 0.7045 (mmm) REVERT: A 590 ASN cc_start: 0.8925 (t0) cc_final: 0.8691 (t0) REVERT: A 633 MET cc_start: 0.8056 (mtm) cc_final: 0.7825 (mtm) REVERT: A 674 ILE cc_start: 0.8971 (mt) cc_final: 0.8763 (mt) REVERT: A 925 MET cc_start: 0.7020 (tpt) cc_final: 0.6741 (tmm) REVERT: A 994 GLU cc_start: 0.0589 (mt-10) cc_final: -0.0403 (mt-10) REVERT: A 1000 MET cc_start: 0.1934 (mtt) cc_final: 0.1402 (mmm) REVERT: A 1008 ASP cc_start: 0.1158 (t0) cc_final: 0.0908 (m-30) REVERT: A 1027 LEU cc_start: 0.2155 (mt) cc_final: 0.1395 (mt) REVERT: A 1050 TYR cc_start: 0.6774 (t80) cc_final: 0.6490 (t80) REVERT: A 1185 VAL cc_start: 0.8783 (m) cc_final: 0.8263 (t) REVERT: A 1188 ILE cc_start: 0.8248 (mt) cc_final: 0.7740 (mt) REVERT: A 1192 SER cc_start: 0.8953 (m) cc_final: 0.8248 (t) REVERT: A 1603 MET cc_start: 0.5682 (tpt) cc_final: 0.4823 (mmm) REVERT: A 1647 ASN cc_start: 0.8605 (t0) cc_final: 0.8401 (t0) REVERT: B 166 GLN cc_start: 0.7409 (mp10) cc_final: 0.7006 (mp10) REVERT: B 413 LEU cc_start: 0.7741 (mt) cc_final: 0.7400 (mt) REVERT: B 496 PHE cc_start: 0.8002 (t80) cc_final: 0.7541 (t80) REVERT: B 514 THR cc_start: 0.7399 (p) cc_final: 0.7189 (p) REVERT: B 640 LEU cc_start: 0.8133 (tp) cc_final: 0.7892 (tp) REVERT: B 697 LEU cc_start: 0.8342 (mm) cc_final: 0.8114 (mm) REVERT: B 733 LEU cc_start: 0.7367 (mp) cc_final: 0.7118 (mp) REVERT: B 898 LEU cc_start: 0.5814 (tp) cc_final: 0.5373 (tp) REVERT: B 934 ILE cc_start: 0.8613 (pt) cc_final: 0.8368 (pt) REVERT: C 95 GLU cc_start: 0.6637 (mm-30) cc_final: 0.5233 (mm-30) REVERT: E 116 ILE cc_start: 0.6786 (pt) cc_final: 0.5828 (pt) REVERT: F 92 ARG cc_start: 0.7681 (tpt-90) cc_final: 0.7420 (tpt-90) REVERT: F 137 TYR cc_start: 0.6309 (m-80) cc_final: 0.5875 (m-80) REVERT: F 151 LEU cc_start: 0.6960 (tp) cc_final: 0.6209 (tp) REVERT: G 47 VAL cc_start: 0.6799 (m) cc_final: 0.6462 (m) REVERT: G 110 ASP cc_start: 0.6411 (p0) cc_final: 0.5522 (p0) REVERT: J 49 MET cc_start: 0.7739 (tpp) cc_final: 0.7243 (tpp) REVERT: J 52 THR cc_start: 0.8663 (p) cc_final: 0.8419 (p) REVERT: J 54 VAL cc_start: 0.9219 (t) cc_final: 0.8857 (p) REVERT: K 81 MET cc_start: 0.5083 (mmt) cc_final: 0.4856 (mmt) REVERT: K 100 LEU cc_start: 0.7149 (mt) cc_final: 0.6920 (mp) REVERT: N 81 THR cc_start: 0.4998 (m) cc_final: 0.4680 (m) REVERT: P 304 LEU cc_start: 0.7420 (mp) cc_final: 0.6823 (mp) outliers start: 10 outliers final: 2 residues processed: 1019 average time/residue: 0.6047 time to fit residues: 1021.2343 Evaluate side-chains 723 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 721 time to evaluate : 5.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 499 optimal weight: 7.9990 chunk 380 optimal weight: 20.0000 chunk 262 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 241 optimal weight: 4.9990 chunk 339 optimal weight: 50.0000 chunk 507 optimal weight: 4.9990 chunk 537 optimal weight: 0.9990 chunk 265 optimal weight: 20.0000 chunk 481 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 GLN A1151 ASN ** A1320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 248 ASN B 351 GLN B 473 GLN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 454 GLN ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 720 GLN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 260 ASN Q 319 ASN Q 409 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 47647 Z= 0.263 Angle : 0.798 21.056 64831 Z= 0.414 Chirality : 0.047 0.385 7252 Planarity : 0.006 0.104 7976 Dihedral : 14.153 178.897 7147 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.94 % Allowed : 7.55 % Favored : 91.51 % Rotamer: Outliers : 0.10 % Allowed : 3.54 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.11 % 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: -1.20 (0.11), residues: 5432 helix: 0.30 (0.11), residues: 1961 sheet: -0.90 (0.18), residues: 763 loop : -1.60 (0.12), residues: 2708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP N 54 HIS 0.012 0.001 HIS E 99 PHE 0.080 0.002 PHE P 125 TYR 0.037 0.002 TYR A 478 ARG 0.010 0.001 ARG O 377 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 965 time to evaluate : 5.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 472 MET cc_start: 0.7385 (mmp) cc_final: 0.7042 (mmm) REVERT: A 590 ASN cc_start: 0.9003 (t0) cc_final: 0.8695 (t0) REVERT: A 618 TYR cc_start: 0.8545 (m-80) cc_final: 0.8233 (m-10) REVERT: A 633 MET cc_start: 0.8137 (mtm) cc_final: 0.7839 (mtm) REVERT: A 634 ASN cc_start: 0.6919 (m-40) cc_final: 0.5947 (m-40) REVERT: A 674 ILE cc_start: 0.8960 (mt) cc_final: 0.8734 (mt) REVERT: A 925 MET cc_start: 0.6982 (tpt) cc_final: 0.6704 (tmm) REVERT: A 960 MET cc_start: 0.6239 (mtp) cc_final: 0.5681 (mtm) REVERT: A 994 GLU cc_start: 0.0660 (mt-10) cc_final: -0.0177 (mt-10) REVERT: A 1000 MET cc_start: 0.2079 (mtt) cc_final: 0.1589 (mmm) REVERT: A 1008 ASP cc_start: 0.1260 (t0) cc_final: 0.0730 (m-30) REVERT: A 1009 THR cc_start: 0.0449 (m) cc_final: -0.0287 (m) REVERT: A 1019 LEU cc_start: 0.0662 (tp) cc_final: -0.0338 (tp) REVERT: A 1050 TYR cc_start: 0.6788 (t80) cc_final: 0.6553 (t80) REVERT: A 1185 VAL cc_start: 0.8660 (m) cc_final: 0.8193 (t) REVERT: A 1192 SER cc_start: 0.9014 (m) cc_final: 0.8206 (t) REVERT: A 1614 SER cc_start: 0.7898 (p) cc_final: 0.7626 (p) REVERT: A 1647 ASN cc_start: 0.8678 (t0) cc_final: 0.8371 (t0) REVERT: B 276 ILE cc_start: 0.7901 (mp) cc_final: 0.7610 (mp) REVERT: B 413 LEU cc_start: 0.7726 (mt) cc_final: 0.7406 (mt) REVERT: B 414 LYS cc_start: 0.7588 (tttp) cc_final: 0.7297 (ttpp) REVERT: B 496 PHE cc_start: 0.8073 (t80) cc_final: 0.7589 (t80) REVERT: B 697 LEU cc_start: 0.8411 (mm) cc_final: 0.8097 (mm) REVERT: B 898 LEU cc_start: 0.5709 (tp) cc_final: 0.5342 (tp) REVERT: C 95 GLU cc_start: 0.6771 (mm-30) cc_final: 0.5367 (mm-30) REVERT: D 25 THR cc_start: 0.7252 (p) cc_final: 0.7033 (p) REVERT: F 136 ARG cc_start: 0.6804 (mtt180) cc_final: 0.6526 (mtt180) REVERT: F 137 TYR cc_start: 0.6277 (m-80) cc_final: 0.5980 (m-80) REVERT: F 145 ASP cc_start: 0.5746 (m-30) cc_final: 0.5268 (m-30) REVERT: G 47 VAL cc_start: 0.6645 (m) cc_final: 0.6379 (m) REVERT: G 110 ASP cc_start: 0.6066 (p0) cc_final: 0.5596 (p0) REVERT: J 16 ASP cc_start: 0.6646 (p0) cc_final: 0.6445 (p0) REVERT: J 49 MET cc_start: 0.7843 (tpp) cc_final: 0.7584 (tpp) REVERT: J 54 VAL cc_start: 0.9228 (t) cc_final: 0.8880 (p) REVERT: N 75 GLU cc_start: 0.5629 (mm-30) cc_final: 0.5103 (mm-30) REVERT: P 388 THR cc_start: 0.7782 (m) cc_final: 0.7554 (m) REVERT: Q 157 MET cc_start: 0.5704 (ttt) cc_final: 0.4237 (tpp) outliers start: 5 outliers final: 1 residues processed: 968 average time/residue: 0.5767 time to fit residues: 933.8915 Evaluate side-chains 699 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 698 time to evaluate : 5.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 447 optimal weight: 9.9990 chunk 305 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 400 optimal weight: 5.9990 chunk 221 optimal weight: 0.0370 chunk 458 optimal weight: 0.9990 chunk 371 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 274 optimal weight: 0.0370 chunk 482 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 overall best weight: 3.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1320 GLN ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS M 89 GLN ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 720 GLN P 98 HIS ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 194 GLN ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 449 GLN ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 409 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 47647 Z= 0.247 Angle : 0.764 18.264 64831 Z= 0.394 Chirality : 0.046 0.344 7252 Planarity : 0.005 0.110 7976 Dihedral : 14.079 176.713 7147 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 23.50 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.75 % Favored : 91.42 % Rotamer: Outliers : 0.06 % Allowed : 3.11 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.10 % 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: -1.03 (0.11), residues: 5432 helix: 0.46 (0.11), residues: 1960 sheet: -0.82 (0.18), residues: 757 loop : -1.50 (0.12), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP N 54 HIS 0.011 0.001 HIS K 95 PHE 0.072 0.002 PHE P 125 TYR 0.030 0.002 TYR A 478 ARG 0.033 0.001 ARG Q 302 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 933 time to evaluate : 5.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 PHE cc_start: 0.6549 (t80) cc_final: 0.6176 (t80) REVERT: A 438 ILE cc_start: 0.6470 (OUTLIER) cc_final: 0.6242 (mp) REVERT: A 595 LEU cc_start: 0.8566 (mt) cc_final: 0.8242 (mt) REVERT: A 618 TYR cc_start: 0.8451 (m-80) cc_final: 0.8177 (m-10) REVERT: A 633 MET cc_start: 0.8145 (mtm) cc_final: 0.7858 (mtm) REVERT: A 947 LEU cc_start: 0.7399 (mp) cc_final: 0.7156 (mp) REVERT: A 994 GLU cc_start: 0.0448 (mt-10) cc_final: 0.0218 (mt-10) REVERT: A 1000 MET cc_start: 0.1991 (mtt) cc_final: 0.1531 (mmm) REVERT: A 1008 ASP cc_start: 0.1176 (t0) cc_final: 0.0906 (m-30) REVERT: A 1027 LEU cc_start: 0.2708 (mt) cc_final: 0.2304 (mt) REVERT: A 1185 VAL cc_start: 0.8564 (m) cc_final: 0.8155 (t) REVERT: A 1192 SER cc_start: 0.8820 (m) cc_final: 0.8267 (t) REVERT: A 1647 ASN cc_start: 0.8639 (t0) cc_final: 0.8314 (t0) REVERT: B 61 LEU cc_start: 0.8375 (mt) cc_final: 0.8128 (mt) REVERT: B 276 ILE cc_start: 0.7969 (mp) cc_final: 0.7723 (mp) REVERT: B 413 LEU cc_start: 0.7728 (mt) cc_final: 0.7357 (mt) REVERT: B 496 PHE cc_start: 0.8078 (t80) cc_final: 0.7616 (t80) REVERT: B 556 SER cc_start: 0.6355 (p) cc_final: 0.5553 (t) REVERT: B 783 MET cc_start: 0.6563 (mmm) cc_final: 0.6342 (mmt) REVERT: B 898 LEU cc_start: 0.5648 (tp) cc_final: 0.5204 (tp) REVERT: B 928 SER cc_start: 0.9143 (p) cc_final: 0.8811 (t) REVERT: B 959 THR cc_start: 0.9241 (p) cc_final: 0.9015 (p) REVERT: B 962 MET cc_start: 0.7401 (ttm) cc_final: 0.7180 (ttm) REVERT: C 95 GLU cc_start: 0.6862 (mm-30) cc_final: 0.5335 (mm-30) REVERT: F 137 TYR cc_start: 0.6307 (m-80) cc_final: 0.6061 (m-80) REVERT: G 110 ASP cc_start: 0.6357 (p0) cc_final: 0.5454 (p0) REVERT: H 46 LEU cc_start: 0.7439 (mt) cc_final: 0.7171 (mt) REVERT: I 7 LEU cc_start: 0.6231 (mp) cc_final: 0.5983 (mt) REVERT: J 54 VAL cc_start: 0.9137 (t) cc_final: 0.8891 (p) REVERT: M 10 ILE cc_start: 0.3236 (tp) cc_final: 0.2890 (tp) REVERT: N 81 THR cc_start: 0.4760 (m) cc_final: 0.4542 (m) REVERT: O 416 LEU cc_start: 0.6682 (mt) cc_final: 0.5855 (mp) REVERT: P 388 THR cc_start: 0.7979 (m) cc_final: 0.7725 (m) REVERT: Q 157 MET cc_start: 0.5188 (ttt) cc_final: 0.4029 (tpp) outliers start: 3 outliers final: 1 residues processed: 935 average time/residue: 0.6007 time to fit residues: 942.4790 Evaluate side-chains 698 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 696 time to evaluate : 5.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 180 optimal weight: 5.9990 chunk 483 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 315 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 537 optimal weight: 0.2980 chunk 446 optimal weight: 0.9980 chunk 249 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 282 optimal weight: 8.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1314 GLN ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN B 673 ASN ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 720 GLN ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 769 GLN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 351 ASN ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 286 GLN Q 319 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 409 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 47647 Z= 0.230 Angle : 0.760 16.576 64831 Z= 0.388 Chirality : 0.046 0.443 7252 Planarity : 0.005 0.105 7976 Dihedral : 14.000 176.537 7147 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.64 % Favored : 91.66 % Rotamer: Outliers : 0.10 % Allowed : 2.06 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.11), residues: 5432 helix: 0.55 (0.11), residues: 1964 sheet: -0.81 (0.18), residues: 738 loop : -1.42 (0.12), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP N 54 HIS 0.013 0.001 HIS L 53 PHE 0.060 0.002 PHE P 125 TYR 0.030 0.002 TYR B 905 ARG 0.018 0.001 ARG O 475 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 929 time to evaluate : 5.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7955 (ttpp) cc_final: 0.7736 (ttmt) REVERT: A 466 LEU cc_start: 0.7095 (tt) cc_final: 0.6870 (tt) REVERT: A 589 MET cc_start: 0.7070 (mmm) cc_final: 0.6866 (mmp) REVERT: A 633 MET cc_start: 0.8259 (mtm) cc_final: 0.8018 (mtm) REVERT: A 634 ASN cc_start: 0.7028 (m-40) cc_final: 0.6819 (m-40) REVERT: A 925 MET cc_start: 0.7217 (tpt) cc_final: 0.7010 (tmm) REVERT: A 943 ILE cc_start: 0.8234 (pt) cc_final: 0.7745 (pt) REVERT: A 947 LEU cc_start: 0.7340 (mp) cc_final: 0.7078 (mp) REVERT: A 960 MET cc_start: 0.6301 (mtp) cc_final: 0.5876 (mtm) REVERT: A 994 GLU cc_start: 0.0252 (mt-10) cc_final: -0.0306 (mt-10) REVERT: A 1000 MET cc_start: 0.1880 (mtt) cc_final: 0.1237 (mmm) REVERT: A 1008 ASP cc_start: 0.1305 (t0) cc_final: 0.0779 (m-30) REVERT: A 1009 THR cc_start: 0.1162 (m) cc_final: 0.0322 (m) REVERT: A 1027 LEU cc_start: 0.2477 (mt) cc_final: 0.2263 (mt) REVERT: A 1050 TYR cc_start: 0.6656 (t80) cc_final: 0.6427 (t80) REVERT: A 1185 VAL cc_start: 0.8584 (m) cc_final: 0.7864 (t) REVERT: A 1647 ASN cc_start: 0.8627 (t0) cc_final: 0.8364 (t0) REVERT: B 26 ILE cc_start: 0.7416 (pt) cc_final: 0.7193 (mm) REVERT: B 242 ASP cc_start: 0.7652 (p0) cc_final: 0.6604 (p0) REVERT: B 276 ILE cc_start: 0.7968 (mp) cc_final: 0.7734 (mp) REVERT: B 413 LEU cc_start: 0.7719 (mt) cc_final: 0.7352 (mt) REVERT: B 496 PHE cc_start: 0.8095 (t80) cc_final: 0.7544 (t80) REVERT: B 556 SER cc_start: 0.6143 (p) cc_final: 0.5332 (t) REVERT: B 668 GLU cc_start: 0.7473 (pt0) cc_final: 0.6940 (pt0) REVERT: B 898 LEU cc_start: 0.5607 (tp) cc_final: 0.5277 (tp) REVERT: B 959 THR cc_start: 0.9193 (p) cc_final: 0.8985 (p) REVERT: B 1086 PHE cc_start: 0.6598 (m-80) cc_final: 0.5531 (m-80) REVERT: B 1174 THR cc_start: 0.7545 (p) cc_final: 0.6138 (p) REVERT: C 95 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6091 (mm-30) REVERT: F 136 ARG cc_start: 0.6698 (mtt180) cc_final: 0.6353 (mtt180) REVERT: F 137 TYR cc_start: 0.6485 (m-80) cc_final: 0.6101 (m-80) REVERT: F 151 LEU cc_start: 0.6686 (tp) cc_final: 0.6451 (tp) REVERT: H 46 LEU cc_start: 0.7295 (mt) cc_final: 0.6976 (mt) REVERT: I 7 LEU cc_start: 0.6734 (mp) cc_final: 0.6200 (mt) REVERT: I 16 LEU cc_start: 0.4704 (tp) cc_final: 0.4436 (tp) REVERT: J 16 ASP cc_start: 0.6253 (p0) cc_final: 0.6039 (p0) REVERT: J 54 VAL cc_start: 0.9162 (t) cc_final: 0.8856 (p) REVERT: K 71 THR cc_start: 0.8411 (p) cc_final: 0.8140 (p) REVERT: O 416 LEU cc_start: 0.6916 (mt) cc_final: 0.5881 (mp) REVERT: O 443 ASP cc_start: 0.7562 (m-30) cc_final: 0.7337 (m-30) REVERT: P 405 ASP cc_start: 0.5271 (p0) cc_final: 0.4794 (p0) REVERT: Q 157 MET cc_start: 0.4967 (ttt) cc_final: 0.4053 (tpp) outliers start: 5 outliers final: 3 residues processed: 932 average time/residue: 0.5750 time to fit residues: 896.9946 Evaluate side-chains 705 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 702 time to evaluate : 5.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 518 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 306 optimal weight: 0.0050 chunk 392 optimal weight: 20.0000 chunk 304 optimal weight: 8.9990 chunk 452 optimal weight: 20.0000 chunk 300 optimal weight: 5.9990 chunk 535 optimal weight: 6.9990 chunk 335 optimal weight: 30.0000 chunk 326 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 overall best weight: 2.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 382 GLN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1320 GLN B 62 ASN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN ** B 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN ** O 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 720 GLN ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 209 ASN ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 351 ASN ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6016 moved from start: 0.6612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 47647 Z= 0.234 Angle : 0.745 15.253 64831 Z= 0.381 Chirality : 0.046 0.341 7252 Planarity : 0.005 0.140 7976 Dihedral : 13.940 177.112 7147 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.49 % Favored : 91.84 % Rotamer: Outliers : 0.06 % Allowed : 1.48 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.11), residues: 5432 helix: 0.63 (0.11), residues: 1971 sheet: -0.77 (0.18), residues: 745 loop : -1.33 (0.12), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP Q 251 HIS 0.019 0.001 HIS B1038 PHE 0.060 0.002 PHE P 125 TYR 0.039 0.002 TYR B 905 ARG 0.014 0.001 ARG O 475 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 901 time to evaluate : 5.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 589 MET cc_start: 0.7199 (mmm) cc_final: 0.6988 (mmp) REVERT: A 618 TYR cc_start: 0.8464 (m-80) cc_final: 0.8065 (m-80) REVERT: A 925 MET cc_start: 0.7084 (tpt) cc_final: 0.6865 (tmm) REVERT: A 947 LEU cc_start: 0.7341 (mp) cc_final: 0.7092 (mp) REVERT: A 994 GLU cc_start: 0.0169 (mt-10) cc_final: -0.0288 (mt-10) REVERT: A 1000 MET cc_start: 0.1752 (mtt) cc_final: 0.1250 (mmm) REVERT: A 1008 ASP cc_start: 0.1371 (t0) cc_final: 0.0798 (m-30) REVERT: A 1009 THR cc_start: 0.0485 (m) cc_final: 0.0186 (m) REVERT: A 1027 LEU cc_start: 0.2870 (mt) cc_final: 0.2456 (mt) REVERT: A 1050 TYR cc_start: 0.6696 (t80) cc_final: 0.6379 (t80) REVERT: A 1185 VAL cc_start: 0.8614 (m) cc_final: 0.7848 (t) REVERT: A 1610 PHE cc_start: 0.6236 (m-80) cc_final: 0.5975 (m-80) REVERT: A 1642 VAL cc_start: 0.8701 (t) cc_final: 0.8462 (t) REVERT: A 1647 ASN cc_start: 0.8560 (t0) cc_final: 0.8315 (t0) REVERT: B 276 ILE cc_start: 0.7947 (mp) cc_final: 0.7705 (mp) REVERT: B 411 MET cc_start: 0.6764 (mmt) cc_final: 0.6425 (mmt) REVERT: B 413 LEU cc_start: 0.7713 (mt) cc_final: 0.7242 (mt) REVERT: B 556 SER cc_start: 0.6195 (p) cc_final: 0.5449 (t) REVERT: B 668 GLU cc_start: 0.7480 (pt0) cc_final: 0.6965 (pt0) REVERT: B 720 GLN cc_start: 0.7593 (mm110) cc_final: 0.7028 (mm-40) REVERT: B 783 MET cc_start: 0.6446 (mmm) cc_final: 0.6040 (mmm) REVERT: B 898 LEU cc_start: 0.5602 (tp) cc_final: 0.5307 (tp) REVERT: B 959 THR cc_start: 0.9143 (p) cc_final: 0.8936 (p) REVERT: B 1086 PHE cc_start: 0.6349 (m-80) cc_final: 0.5490 (m-80) REVERT: C 95 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6430 (mm-30) REVERT: E 75 MET cc_start: 0.3807 (ppp) cc_final: 0.3158 (tmm) REVERT: F 137 TYR cc_start: 0.6449 (m-80) cc_final: 0.6212 (m-80) REVERT: I 7 LEU cc_start: 0.6816 (mp) cc_final: 0.6558 (mp) REVERT: I 16 LEU cc_start: 0.4861 (tp) cc_final: 0.4496 (tp) REVERT: J 54 VAL cc_start: 0.9195 (t) cc_final: 0.8917 (p) REVERT: M 100 VAL cc_start: 0.5757 (t) cc_final: 0.5458 (t) REVERT: O 416 LEU cc_start: 0.6866 (mt) cc_final: 0.5970 (mp) REVERT: O 538 LEU cc_start: 0.7844 (mp) cc_final: 0.7601 (mt) REVERT: P 254 LEU cc_start: 0.8205 (tp) cc_final: 0.7914 (tp) REVERT: Q 1 MET cc_start: 0.6256 (tmm) cc_final: 0.4600 (tmm) REVERT: Q 157 MET cc_start: 0.4976 (ttt) cc_final: 0.4131 (tpp) outliers start: 3 outliers final: 1 residues processed: 903 average time/residue: 0.5648 time to fit residues: 850.0729 Evaluate side-chains 685 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 684 time to evaluate : 5.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 331 optimal weight: 0.4980 chunk 214 optimal weight: 9.9990 chunk 320 optimal weight: 1.9990 chunk 161 optimal weight: 0.0770 chunk 105 optimal weight: 7.9990 chunk 103 optimal weight: 40.0000 chunk 340 optimal weight: 50.0000 chunk 365 optimal weight: 0.0000 chunk 264 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 421 optimal weight: 50.0000 overall best weight: 1.7146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN ** B 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN E 99 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 270 GLN O 337 ASN ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 720 GLN ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 434 HIS ** P 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.6810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 47647 Z= 0.216 Angle : 0.743 14.597 64831 Z= 0.378 Chirality : 0.046 0.321 7252 Planarity : 0.005 0.110 7976 Dihedral : 13.866 176.827 7147 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.38 % Favored : 91.96 % Rotamer: Outliers : 0.06 % Allowed : 0.99 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.12), residues: 5432 helix: 0.72 (0.12), residues: 1973 sheet: -0.73 (0.18), residues: 742 loop : -1.28 (0.13), residues: 2717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP P 118 HIS 0.011 0.001 HIS Q 304 PHE 0.055 0.002 PHE P 125 TYR 0.024 0.002 TYR P 177 ARG 0.010 0.001 ARG Q 302 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 913 time to evaluate : 5.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 466 LEU cc_start: 0.6898 (tt) cc_final: 0.6627 (tt) REVERT: A 947 LEU cc_start: 0.7296 (mp) cc_final: 0.7083 (mp) REVERT: A 960 MET cc_start: 0.6038 (mtp) cc_final: 0.5616 (mtp) REVERT: A 994 GLU cc_start: 0.0190 (mt-10) cc_final: -0.0073 (mt-10) REVERT: A 1000 MET cc_start: 0.1631 (mtt) cc_final: 0.0975 (mmm) REVERT: A 1008 ASP cc_start: 0.1316 (t0) cc_final: 0.0925 (m-30) REVERT: A 1009 THR cc_start: 0.0653 (m) cc_final: 0.0377 (m) REVERT: A 1027 LEU cc_start: 0.3028 (mt) cc_final: 0.2644 (mt) REVERT: A 1185 VAL cc_start: 0.8642 (m) cc_final: 0.8056 (t) REVERT: A 1610 PHE cc_start: 0.6231 (m-80) cc_final: 0.6007 (m-80) REVERT: A 1642 VAL cc_start: 0.8558 (t) cc_final: 0.8332 (t) REVERT: B 276 ILE cc_start: 0.7888 (mp) cc_final: 0.7545 (mp) REVERT: B 413 LEU cc_start: 0.7733 (mt) cc_final: 0.7143 (mt) REVERT: B 462 GLN cc_start: 0.7697 (pp30) cc_final: 0.7455 (pp30) REVERT: B 496 PHE cc_start: 0.8022 (t80) cc_final: 0.7593 (t80) REVERT: B 668 GLU cc_start: 0.7370 (pt0) cc_final: 0.6861 (pt0) REVERT: B 898 LEU cc_start: 0.5693 (tp) cc_final: 0.5384 (tp) REVERT: B 1075 GLU cc_start: 0.6212 (mp0) cc_final: 0.6010 (mp0) REVERT: B 1086 PHE cc_start: 0.6432 (m-80) cc_final: 0.5707 (m-80) REVERT: C 95 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6780 (mm-30) REVERT: E 75 MET cc_start: 0.4047 (ppp) cc_final: 0.3212 (tmm) REVERT: F 137 TYR cc_start: 0.6504 (m-80) cc_final: 0.6290 (m-80) REVERT: G 52 MET cc_start: 0.6360 (ptm) cc_final: 0.5724 (ppp) REVERT: I 7 LEU cc_start: 0.6800 (mp) cc_final: 0.6598 (mp) REVERT: I 16 LEU cc_start: 0.4804 (tp) cc_final: 0.4469 (tp) REVERT: J 54 VAL cc_start: 0.9174 (t) cc_final: 0.8851 (p) REVERT: K 46 LYS cc_start: 0.6552 (tptt) cc_final: 0.6091 (tptm) REVERT: P 405 ASP cc_start: 0.5693 (p0) cc_final: 0.5176 (p0) REVERT: P 491 PHE cc_start: 0.5823 (m-10) cc_final: 0.5404 (m-10) REVERT: Q 157 MET cc_start: 0.4916 (ttt) cc_final: 0.4178 (tpp) outliers start: 3 outliers final: 1 residues processed: 914 average time/residue: 0.5748 time to fit residues: 875.0452 Evaluate side-chains 702 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 701 time to evaluate : 5.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 487 optimal weight: 6.9990 chunk 513 optimal weight: 7.9990 chunk 468 optimal weight: 40.0000 chunk 499 optimal weight: 30.0000 chunk 300 optimal weight: 4.9990 chunk 217 optimal weight: 7.9990 chunk 392 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 chunk 451 optimal weight: 50.0000 chunk 472 optimal weight: 0.0870 chunk 497 optimal weight: 40.0000 overall best weight: 5.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN B 824 HIS ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 720 GLN ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 434 HIS ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 319 ASN ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.6939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 47647 Z= 0.298 Angle : 0.775 13.544 64831 Z= 0.398 Chirality : 0.047 0.519 7252 Planarity : 0.005 0.112 7976 Dihedral : 13.881 177.920 7147 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 24.63 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.86 % Favored : 91.53 % Rotamer: Outliers : 0.02 % Allowed : 0.51 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.12), residues: 5432 helix: 0.68 (0.12), residues: 1968 sheet: -0.74 (0.18), residues: 734 loop : -1.33 (0.12), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP P 118 HIS 0.013 0.001 HIS Q 304 PHE 0.055 0.002 PHE B 577 TYR 0.034 0.002 TYR B 905 ARG 0.010 0.001 ARG H 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 876 time to evaluate : 5.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 LEU cc_start: 0.6917 (tt) cc_final: 0.6663 (tt) REVERT: A 925 MET cc_start: 0.6848 (tpt) cc_final: 0.6583 (mmm) REVERT: A 947 LEU cc_start: 0.7361 (mp) cc_final: 0.7159 (mp) REVERT: A 1000 MET cc_start: 0.1734 (mtt) cc_final: 0.1285 (mmm) REVERT: A 1008 ASP cc_start: 0.1341 (t0) cc_final: 0.0671 (m-30) REVERT: A 1009 THR cc_start: 0.0529 (m) cc_final: 0.0128 (m) REVERT: A 1042 ASP cc_start: 0.6824 (p0) cc_final: 0.6419 (p0) REVERT: A 1185 VAL cc_start: 0.8601 (m) cc_final: 0.8200 (t) REVERT: B 104 ILE cc_start: 0.8674 (tp) cc_final: 0.8444 (tp) REVERT: B 411 MET cc_start: 0.6791 (mmt) cc_final: 0.6412 (mmt) REVERT: B 413 LEU cc_start: 0.7559 (mt) cc_final: 0.7048 (mt) REVERT: B 415 GLU cc_start: 0.6597 (tp30) cc_final: 0.6348 (tp30) REVERT: B 496 PHE cc_start: 0.8148 (t80) cc_final: 0.7614 (t80) REVERT: B 556 SER cc_start: 0.6475 (p) cc_final: 0.5836 (t) REVERT: B 557 ASP cc_start: 0.5712 (m-30) cc_final: 0.5358 (m-30) REVERT: B 697 LEU cc_start: 0.8263 (mm) cc_final: 0.7999 (mm) REVERT: B 965 GLU cc_start: 0.7574 (pp20) cc_final: 0.7274 (pp20) REVERT: B 1086 PHE cc_start: 0.6301 (m-80) cc_final: 0.5441 (m-80) REVERT: C 95 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6949 (mm-30) REVERT: E 75 MET cc_start: 0.4481 (ppp) cc_final: 0.3857 (tmm) REVERT: F 90 ARG cc_start: 0.7662 (ptm-80) cc_final: 0.7298 (ttp80) REVERT: F 137 TYR cc_start: 0.6454 (m-80) cc_final: 0.5455 (m-80) REVERT: F 145 ASP cc_start: 0.5881 (m-30) cc_final: 0.5454 (m-30) REVERT: I 16 LEU cc_start: 0.4786 (tp) cc_final: 0.4553 (tp) REVERT: J 54 VAL cc_start: 0.9243 (t) cc_final: 0.8959 (p) REVERT: O 443 ASP cc_start: 0.8148 (m-30) cc_final: 0.7804 (m-30) REVERT: P 405 ASP cc_start: 0.5955 (p0) cc_final: 0.5422 (p0) REVERT: P 491 PHE cc_start: 0.6101 (m-10) cc_final: 0.5764 (m-80) REVERT: Q 157 MET cc_start: 0.5086 (ttt) cc_final: 0.4289 (tpp) outliers start: 1 outliers final: 1 residues processed: 877 average time/residue: 0.5914 time to fit residues: 865.3560 Evaluate side-chains 660 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 659 time to evaluate : 5.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 327 optimal weight: 40.0000 chunk 528 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 250 optimal weight: 0.0060 chunk 367 optimal weight: 7.9990 chunk 553 optimal weight: 20.0000 chunk 509 optimal weight: 6.9990 chunk 441 optimal weight: 8.9990 chunk 45 optimal weight: 0.0000 chunk 340 optimal weight: 50.0000 chunk 270 optimal weight: 0.9980 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN ** B 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS F 100 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 ASN ** O 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 720 GLN ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 351 ASN P 434 HIS ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6030 moved from start: 0.7150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 47647 Z= 0.225 Angle : 0.753 13.025 64831 Z= 0.382 Chirality : 0.047 0.464 7252 Planarity : 0.005 0.114 7976 Dihedral : 13.842 177.166 7147 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.42 % Favored : 91.99 % Rotamer: Outliers : 0.04 % Allowed : 0.28 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.12), residues: 5432 helix: 0.74 (0.12), residues: 1955 sheet: -0.74 (0.18), residues: 747 loop : -1.26 (0.13), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP P 118 HIS 0.011 0.001 HIS B1038 PHE 0.048 0.002 PHE P 125 TYR 0.030 0.002 TYR B 409 ARG 0.008 0.001 ARG E 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 889 time to evaluate : 5.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 LEU cc_start: 0.6823 (tt) cc_final: 0.6500 (tt) REVERT: A 925 MET cc_start: 0.6732 (tpt) cc_final: 0.6516 (mmm) REVERT: A 960 MET cc_start: 0.5736 (mtp) cc_final: 0.5170 (mtp) REVERT: A 994 GLU cc_start: -0.0638 (pt0) cc_final: -0.1220 (pt0) REVERT: A 1000 MET cc_start: 0.1727 (mtt) cc_final: 0.1232 (mmm) REVERT: A 1008 ASP cc_start: 0.1249 (t0) cc_final: 0.0549 (m-30) REVERT: A 1027 LEU cc_start: 0.2693 (mt) cc_final: 0.2382 (mt) REVERT: A 1042 ASP cc_start: 0.6846 (p0) cc_final: 0.6470 (p0) REVERT: A 1185 VAL cc_start: 0.8724 (m) cc_final: 0.7919 (t) REVERT: A 1656 VAL cc_start: 0.8449 (t) cc_final: 0.8235 (p) REVERT: B 61 LEU cc_start: 0.8362 (mt) cc_final: 0.8121 (mt) REVERT: B 276 ILE cc_start: 0.8067 (mp) cc_final: 0.7769 (mp) REVERT: B 378 ILE cc_start: 0.8176 (mm) cc_final: 0.7935 (mm) REVERT: B 411 MET cc_start: 0.6754 (mmt) cc_final: 0.6333 (mmt) REVERT: B 413 LEU cc_start: 0.7467 (mt) cc_final: 0.7066 (mt) REVERT: B 470 LEU cc_start: 0.8187 (mp) cc_final: 0.7864 (mt) REVERT: B 496 PHE cc_start: 0.8030 (t80) cc_final: 0.7541 (t80) REVERT: B 668 GLU cc_start: 0.7684 (pt0) cc_final: 0.7477 (pt0) REVERT: B 697 LEU cc_start: 0.8253 (mm) cc_final: 0.8033 (mm) REVERT: B 733 LEU cc_start: 0.7393 (mp) cc_final: 0.6935 (mp) REVERT: B 794 ASP cc_start: 0.7348 (p0) cc_final: 0.6971 (p0) REVERT: B 1086 PHE cc_start: 0.6267 (m-80) cc_final: 0.5482 (m-80) REVERT: C 95 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6708 (mm-30) REVERT: E 75 MET cc_start: 0.4133 (ppp) cc_final: 0.3718 (tmm) REVERT: F 145 ASP cc_start: 0.5572 (m-30) cc_final: 0.5342 (m-30) REVERT: J 16 ASP cc_start: 0.5659 (p0) cc_final: 0.5410 (p0) REVERT: J 54 VAL cc_start: 0.9269 (t) cc_final: 0.8946 (p) REVERT: O 443 ASP cc_start: 0.8098 (m-30) cc_final: 0.7733 (m-30) REVERT: P 405 ASP cc_start: 0.5925 (p0) cc_final: 0.5450 (p0) REVERT: P 491 PHE cc_start: 0.5911 (m-10) cc_final: 0.5430 (m-10) REVERT: Q 157 MET cc_start: 0.5110 (ttt) cc_final: 0.4272 (tpp) outliers start: 2 outliers final: 1 residues processed: 890 average time/residue: 0.5909 time to fit residues: 881.8962 Evaluate side-chains 679 residues out of total 4950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 678 time to evaluate : 5.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 350 optimal weight: 30.0000 chunk 469 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 406 optimal weight: 50.0000 chunk 65 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 441 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 chunk 453 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN ** B 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN E 99 HIS ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN N 51 GLN ** O 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 395 GLN ** O 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 720 GLN ** O 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 351 ASN P 434 HIS ** Q 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.088241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.068419 restraints weight = 247770.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.070200 restraints weight = 136044.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.071382 restraints weight = 88090.963| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.7225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 47647 Z= 0.393 Angle : 0.840 15.283 64831 Z= 0.435 Chirality : 0.048 0.451 7252 Planarity : 0.006 0.114 7976 Dihedral : 14.019 179.492 7147 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 29.82 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.65 % Favored : 90.76 % Rotamer: Outliers : 0.02 % Allowed : 0.46 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.24 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.11), residues: 5432 helix: 0.51 (0.12), residues: 1959 sheet: -0.97 (0.18), residues: 755 loop : -1.38 (0.12), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.003 TRP Q 273 HIS 0.015 0.002 HIS Q 304 PHE 0.047 0.003 PHE Q 358 TYR 0.033 0.003 TYR B 409 ARG 0.011 0.001 ARG E 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14481.28 seconds wall clock time: 261 minutes 16.82 seconds (15676.82 seconds total)