Starting phenix.real_space_refine on Tue Feb 20 11:04:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6s_7349/02_2024/6c6s_7349_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6s_7349/02_2024/6c6s_7349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6s_7349/02_2024/6c6s_7349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6s_7349/02_2024/6c6s_7349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6s_7349/02_2024/6c6s_7349_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6s_7349/02_2024/6c6s_7349_neut.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 66 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 17161 2.51 5 N 4897 2.21 5 O 5454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 268": "NH1" <-> "NH2" Residue "I ARG 332": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27691 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 598 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "B" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 585 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "R" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 218 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "G" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1694 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Chain: "J" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10388 Classifications: {'peptide': 1335} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1277} Chain breaks: 2 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 79} Chain: "D" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1286 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 149} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15808 SG CYS J 70 54.471 119.572 61.785 1.00112.23 S ATOM 15822 SG CYS J 72 55.302 123.045 62.064 1.00120.53 S ATOM 15930 SG CYS J 85 52.204 122.460 60.311 1.00116.39 S ATOM 21642 SG CYS J 814 51.847 54.014 48.977 1.00 71.45 S ATOM 22207 SG CYS J 888 54.395 57.214 50.637 1.00 65.72 S ATOM 22258 SG CYS J 895 51.437 55.577 52.683 1.00 62.09 S ATOM 22279 SG CYS J 898 54.195 53.555 51.724 1.00 62.08 S Time building chain proxies: 14.74, per 1000 atoms: 0.53 Number of scatterers: 27691 At special positions: 0 Unit cell: (152.1, 153.4, 148.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 110 16.00 P 66 15.00 Mg 1 11.99 O 5454 8.00 N 4897 7.00 C 17161 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: 10.97 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " Number of angles added : 6 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6210 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 56 sheets defined 36.5% alpha, 15.4% beta 28 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 9.41 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.736A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 159 removed outlier: 4.255A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE G 159 " --> pdb=" O ALA G 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 154 through 159' Processing helix chain 'G' and resid 212 through 230 Processing helix chain 'H' and resid 34 through 50 removed outlier: 4.054A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.784A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 115 Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 42 through 46 removed outlier: 3.850A pdb=" N GLY I 45 " --> pdb=" O ASP I 42 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN I 46 " --> pdb=" O PRO I 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 42 through 46' Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.616A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 207 through 213 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.586A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 292 removed outlier: 3.630A pdb=" N TYR I 291 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE I 292 " --> pdb=" O VAL I 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 292' Processing helix chain 'I' and resid 318 through 329 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 removed outlier: 4.290A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 408 Processing helix chain 'I' and resid 421 through 438 removed outlier: 3.584A pdb=" N ILE I 425 " --> pdb=" O SER I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 480 Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 removed outlier: 3.537A pdb=" N GLU I 523 " --> pdb=" O ASN I 519 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.993A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 607 through 612 removed outlier: 3.580A pdb=" N GLU I 611 " --> pdb=" O SER I 607 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 607 through 612' Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 819 through 825 removed outlier: 4.177A pdb=" N VAL I 823 " --> pdb=" O SER I 819 " (cutoff:3.500A) Processing helix chain 'I' and resid 858 through 863 Processing helix chain 'I' and resid 896 through 906 Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.628A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.901A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.818A pdb=" N PHE I1164 " --> pdb=" O LEU I1161 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.653A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1310 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.714A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.590A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 180 through 191 removed outlier: 3.774A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 207 removed outlier: 3.998A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.560A pdb=" N GLN J 229 " --> pdb=" O GLU J 225 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 286 removed outlier: 3.553A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 337 through 342 removed outlier: 3.831A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 removed outlier: 3.883A pdb=" N ALA J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 417 removed outlier: 3.675A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.535A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 removed outlier: 3.720A pdb=" N SER J 539 " --> pdb=" O ARG J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 574 through 581 Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 598 through 613 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.829A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 671 Processing helix chain 'J' and resid 674 through 703 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 805 removed outlier: 3.814A pdb=" N GLY J 782 " --> pdb=" O GLY J 778 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.740A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.973A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1308 through 1313 removed outlier: 3.503A pdb=" N SER J1313 " --> pdb=" O ILE J1309 " (cutoff:3.500A) Processing helix chain 'J' and resid 1318 through 1324 removed outlier: 3.501A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1338 removed outlier: 3.801A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1361 through 1372 removed outlier: 4.339A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 removed outlier: 4.067A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 78 removed outlier: 3.601A pdb=" N LEU K 64 " --> pdb=" O ASN K 60 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA K 77 " --> pdb=" O GLN K 73 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 84 removed outlier: 3.523A pdb=" N THR K 84 " --> pdb=" O LEU K 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 24 Processing helix chain 'D' and resid 65 through 71 Processing helix chain 'D' and resid 89 through 96 removed outlier: 3.625A pdb=" N ILE D 93 " --> pdb=" O PRO D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 4.172A pdb=" N PHE D 123 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 4.996A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.515A pdb=" N LYS G 104 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.554A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 12 through 16 removed outlier: 3.881A pdb=" N GLU H 29 " --> pdb=" O ARG H 12 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL H 14 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR H 27 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE H 16 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LYS H 25 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 97 through 105 removed outlier: 3.512A pdb=" N VAL H 98 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'H' and resid 108 through 110 Processing sheet with id=AA9, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.489A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 59 through 60 removed outlier: 7.251A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 143 through 145 Processing sheet with id=AB4, first strand: chain 'I' and resid 147 through 148 removed outlier: 6.454A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'I' and resid 150 through 151 Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.137A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 296 through 297 removed outlier: 4.046A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 301 through 303 removed outlier: 7.225A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU I 308 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC5, first strand: chain 'I' and resid 616 through 617 removed outlier: 3.509A pdb=" N ILE I 616 " --> pdb=" O ARG I 637 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 748 through 752 removed outlier: 7.200A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AC9, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AD1, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 4.791A pdb=" N LYS I1065 " --> pdb=" O LEU I1235 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 830 through 832 Processing sheet with id=AD3, first strand: chain 'I' and resid 835 through 841 removed outlier: 6.323A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 882 through 884 Processing sheet with id=AD5, first strand: chain 'I' and resid 887 through 888 Processing sheet with id=AD6, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 3.638A pdb=" N SER J 353 " --> pdb=" O MET J 466 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD8, first strand: chain 'I' and resid 1268 through 1270 Processing sheet with id=AD9, first strand: chain 'I' and resid 1335 through 1339 removed outlier: 3.770A pdb=" N LYS J 21 " --> pdb=" O GLU I1338 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 103 through 112 removed outlier: 10.141A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 145 through 146 Processing sheet with id=AE3, first strand: chain 'J' and resid 253 through 254 removed outlier: 4.340A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 366 through 369 Processing sheet with id=AE5, first strand: chain 'J' and resid 547 through 549 Processing sheet with id=AE6, first strand: chain 'J' and resid 552 through 556 Processing sheet with id=AE7, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AE8, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE9, first strand: chain 'J' and resid 821 through 822 Processing sheet with id=AF1, first strand: chain 'J' and resid 825 through 826 removed outlier: 6.913A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 848 through 850 removed outlier: 6.408A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP J 855 " --> pdb=" O LYS J 850 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 957 through 961 Processing sheet with id=AF4, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AF5, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.678A pdb=" N ARG J1036 " --> pdb=" O LYS J1079 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 1046 through 1049 removed outlier: 3.760A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER J1058 " --> pdb=" O GLN J1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 1187 through 1190 Processing sheet with id=AF8, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 7.020A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 27 through 29 removed outlier: 3.622A pdb=" N ASN D 27 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 32 through 38 Processing sheet with id=AG2, first strand: chain 'D' and resid 150 through 154 1060 hydrogen bonds defined for protein. 2958 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 13.51 Time building geometry restraints manager: 11.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5359 1.32 - 1.44: 6543 1.44 - 1.57: 16030 1.57 - 1.69: 132 1.69 - 1.81: 190 Bond restraints: 28254 Sorted by residual: bond pdb=" CB VAL J 801 " pdb=" CG2 VAL J 801 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.31e+00 bond pdb=" CG LEU I 817 " pdb=" CD1 LEU I 817 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.69e+00 bond pdb=" CG LEU I1098 " pdb=" CD1 LEU I1098 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.91e+00 bond pdb=" C3' DA A 11 " pdb=" O3' DA A 11 " ideal model delta sigma weight residual 1.422 1.494 -0.072 3.00e-02 1.11e+03 5.84e+00 bond pdb=" C VAL I 550 " pdb=" N HIS I 551 " ideal model delta sigma weight residual 1.339 1.206 0.133 5.57e-02 3.22e+02 5.72e+00 ... (remaining 28249 not shown) Histogram of bond angle deviations from ideal: 93.95 - 102.93: 315 102.93 - 111.91: 13799 111.91 - 120.90: 15952 120.90 - 129.88: 8271 129.88 - 138.86: 129 Bond angle restraints: 38466 Sorted by residual: angle pdb=" C LYS I1158 " pdb=" N VAL I1159 " pdb=" CA VAL I1159 " ideal model delta sigma weight residual 121.97 132.34 -10.37 1.80e+00 3.09e-01 3.32e+01 angle pdb=" C SER J 503 " pdb=" N GLN J 504 " pdb=" CA GLN J 504 " ideal model delta sigma weight residual 121.54 110.82 10.72 1.91e+00 2.74e-01 3.15e+01 angle pdb=" C LEU J 903 " pdb=" N ALA J 904 " pdb=" CA ALA J 904 " ideal model delta sigma weight residual 126.32 136.05 -9.73 1.74e+00 3.30e-01 3.13e+01 angle pdb=" CB MET I 685 " pdb=" CG MET I 685 " pdb=" SD MET I 685 " ideal model delta sigma weight residual 112.70 97.95 14.75 3.00e+00 1.11e-01 2.42e+01 angle pdb=" C ALA J 426 " pdb=" N PRO J 427 " pdb=" CA PRO J 427 " ideal model delta sigma weight residual 119.84 113.72 6.12 1.25e+00 6.40e-01 2.40e+01 ... (remaining 38461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 16878 35.65 - 71.30: 311 71.30 - 106.95: 15 106.95 - 142.59: 0 142.59 - 178.24: 4 Dihedral angle restraints: 17208 sinusoidal: 7558 harmonic: 9650 Sorted by residual: dihedral pdb=" CA GLN I1157 " pdb=" C GLN I1157 " pdb=" N LYS I1158 " pdb=" CA LYS I1158 " ideal model delta harmonic sigma weight residual -180.00 -113.54 -66.46 0 5.00e+00 4.00e-02 1.77e+02 dihedral pdb=" CA THR I 595 " pdb=" C THR I 595 " pdb=" N ASP I 596 " pdb=" CA ASP I 596 " ideal model delta harmonic sigma weight residual -180.00 -131.57 -48.43 0 5.00e+00 4.00e-02 9.38e+01 dihedral pdb=" CA GLN J1326 " pdb=" C GLN J1326 " pdb=" N GLU J1327 " pdb=" CA GLU J1327 " ideal model delta harmonic sigma weight residual -180.00 -131.99 -48.01 0 5.00e+00 4.00e-02 9.22e+01 ... (remaining 17205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 4058 0.112 - 0.223: 327 0.223 - 0.335: 10 0.335 - 0.446: 0 0.446 - 0.558: 1 Chirality restraints: 4396 Sorted by residual: chirality pdb=" CB ILE I1079 " pdb=" CA ILE I1079 " pdb=" CG1 ILE I1079 " pdb=" CG2 ILE I1079 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.56 2.00e-01 2.50e+01 7.79e+00 chirality pdb=" CB ILE H 144 " pdb=" CA ILE H 144 " pdb=" CG1 ILE H 144 " pdb=" CG2 ILE H 144 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB ILE I 39 " pdb=" CA ILE I 39 " pdb=" CG1 ILE I 39 " pdb=" CG2 ILE I 39 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 4393 not shown) Planarity restraints: 4796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR I 595 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.45e+01 pdb=" C THR I 595 " -0.066 2.00e-02 2.50e+03 pdb=" O THR I 595 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP I 596 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 596 " -0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C ASP I 596 " 0.065 2.00e-02 2.50e+03 pdb=" O ASP I 596 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY I 597 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 29 " -0.056 5.00e-02 4.00e+02 8.54e-02 1.17e+01 pdb=" N PRO H 30 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO H 30 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO H 30 " -0.043 5.00e-02 4.00e+02 ... (remaining 4793 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 339 2.63 - 3.20: 23477 3.20 - 3.76: 42488 3.76 - 4.33: 57984 4.33 - 4.90: 94696 Nonbonded interactions: 218984 Sorted by model distance: nonbonded pdb=" O3' A R 20 " pdb="MG MG R1501 " model vdw 2.060 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG R1501 " model vdw 2.098 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG R1501 " model vdw 2.115 2.170 nonbonded pdb=" OG1 THR I 6 " pdb=" OD1 ASP I 781 " model vdw 2.242 2.440 nonbonded pdb=" OG SER J1321 " pdb=" OE2 GLU J1349 " model vdw 2.252 2.440 ... (remaining 218979 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 7 through 158 or resid 169 through 232)) selection = (chain 'H' and (resid 7 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.310 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 85.190 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.100 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 0.133 28254 Z= 0.582 Angle : 1.057 17.454 38466 Z= 0.567 Chirality : 0.061 0.558 4396 Planarity : 0.008 0.085 4796 Dihedral : 13.176 178.244 10998 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.32 % Favored : 91.50 % Rotamer: Outliers : 0.38 % Allowed : 2.52 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.16 % Twisted Proline : 0.71 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.11), residues: 3340 helix: -2.75 (0.11), residues: 1135 sheet: -2.26 (0.22), residues: 452 loop : -2.85 (0.12), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.005 TRP I 183 HIS 0.015 0.003 HIS G 23 PHE 0.043 0.004 PHE J 620 TYR 0.052 0.004 TYR I1229 ARG 0.023 0.001 ARG I1223 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 721 time to evaluate : 3.264 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: G 33 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7740 (ptm160) REVERT: G 145 LYS cc_start: 0.9070 (tttt) cc_final: 0.8707 (tttp) REVERT: H 214 GLU cc_start: 0.7689 (tt0) cc_final: 0.7221 (pp20) REVERT: I 302 ILE cc_start: 0.8296 (pp) cc_final: 0.7928 (mp) REVERT: I 311 CYS cc_start: 0.7772 (p) cc_final: 0.7225 (p) REVERT: I 330 HIS cc_start: 0.7068 (m-70) cc_final: 0.6737 (m90) REVERT: I 430 LYS cc_start: 0.9014 (mttt) cc_final: 0.8624 (mtmm) REVERT: I 439 LYS cc_start: 0.8822 (ptpt) cc_final: 0.8595 (mtmm) REVERT: I 475 VAL cc_start: 0.8707 (t) cc_final: 0.8486 (p) REVERT: I 805 MET cc_start: 0.8645 (ptm) cc_final: 0.8441 (ptm) REVERT: I 849 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8097 (tt0) REVERT: I 914 LYS cc_start: 0.5762 (ttpt) cc_final: 0.5269 (tptm) REVERT: I 918 LEU cc_start: 0.9054 (tp) cc_final: 0.8834 (tt) REVERT: I 1029 LEU cc_start: 0.8676 (tt) cc_final: 0.8391 (pp) REVERT: I 1109 ILE cc_start: 0.9226 (tp) cc_final: 0.8889 (tp) REVERT: I 1321 GLU cc_start: 0.7818 (tp30) cc_final: 0.7592 (tp30) REVERT: J 127 LEU cc_start: 0.9389 (tp) cc_final: 0.9099 (tt) REVERT: J 129 ASP cc_start: 0.7779 (t70) cc_final: 0.7282 (p0) REVERT: J 193 ASP cc_start: 0.7050 (t0) cc_final: 0.6764 (t0) REVERT: J 295 GLU cc_start: 0.8968 (tp30) cc_final: 0.8611 (mm-30) REVERT: J 681 LYS cc_start: 0.8573 (tptt) cc_final: 0.8337 (tppt) REVERT: J 953 LYS cc_start: 0.8364 (mtpt) cc_final: 0.7875 (ptpp) REVERT: J 981 GLU cc_start: 0.7730 (tt0) cc_final: 0.7410 (tm-30) REVERT: J 982 LEU cc_start: 0.8219 (tp) cc_final: 0.7172 (pp) REVERT: J 1219 ASP cc_start: 0.8305 (m-30) cc_final: 0.8050 (m-30) REVERT: K 45 LYS cc_start: 0.8230 (mttm) cc_final: 0.7966 (mttt) REVERT: K 63 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7816 (mt) REVERT: K 65 ASP cc_start: 0.8027 (m-30) cc_final: 0.7758 (m-30) REVERT: K 70 GLN cc_start: 0.8050 (tt0) cc_final: 0.7789 (mt0) REVERT: K 79 GLU cc_start: 0.5397 (tm-30) cc_final: 0.4933 (mm-30) REVERT: D 13 GLN cc_start: 0.8044 (mt0) cc_final: 0.7577 (mt0) REVERT: D 28 CYS cc_start: 0.7374 (m) cc_final: 0.6767 (m) REVERT: D 42 LYS cc_start: 0.8325 (mtpt) cc_final: 0.7774 (tptt) REVERT: D 43 ARG cc_start: 0.6838 (mtt180) cc_final: 0.6605 (mtt180) REVERT: D 84 SER cc_start: 0.9247 (t) cc_final: 0.9039 (m) REVERT: D 115 LYS cc_start: 0.8276 (mttt) cc_final: 0.7580 (pttm) outliers start: 11 outliers final: 3 residues processed: 729 average time/residue: 0.4675 time to fit residues: 507.4079 Evaluate side-chains 361 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 357 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain K residue 63 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 0.0000 chunk 256 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 265 optimal weight: 8.9990 chunk 102 optimal weight: 0.0870 chunk 161 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 307 optimal weight: 7.9990 overall best weight: 1.0168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 HIS I 69 GLN I 343 HIS ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 573 ASN I 604 HIS I 760 ASN I1116 HIS I1157 GLN I1220 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1313 HIS J 45 ASN ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 488 ASN J 792 ASN J 805 GLN J 817 HIS J1268 ASN J1326 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 GLN K 31 GLN D 20 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28254 Z= 0.189 Angle : 0.641 8.781 38466 Z= 0.335 Chirality : 0.044 0.223 4396 Planarity : 0.005 0.063 4796 Dihedral : 14.901 179.844 4438 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.66 % Favored : 94.28 % Rotamer: Outliers : 2.27 % Allowed : 9.20 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.13), residues: 3340 helix: -0.77 (0.14), residues: 1167 sheet: -1.87 (0.22), residues: 470 loop : -2.39 (0.13), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J1193 HIS 0.016 0.001 HIS I 165 PHE 0.029 0.001 PHE J1100 TYR 0.026 0.001 TYR G 185 ARG 0.009 0.001 ARG J1075 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 450 time to evaluate : 3.248 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: G 79 LEU cc_start: 0.8846 (tt) cc_final: 0.8641 (tp) REVERT: G 145 LYS cc_start: 0.9153 (tttt) cc_final: 0.8851 (tttp) REVERT: H 214 GLU cc_start: 0.7793 (tt0) cc_final: 0.7518 (pp20) REVERT: I 11 ILE cc_start: 0.9349 (tp) cc_final: 0.9036 (tt) REVERT: I 62 TYR cc_start: 0.5533 (m-10) cc_final: 0.5276 (m-80) REVERT: I 131 THR cc_start: 0.9474 (m) cc_final: 0.9197 (p) REVERT: I 247 ARG cc_start: 0.7914 (tpp-160) cc_final: 0.6741 (ttp80) REVERT: I 309 LEU cc_start: 0.9022 (tp) cc_final: 0.8497 (mp) REVERT: I 311 CYS cc_start: 0.7544 (p) cc_final: 0.7034 (p) REVERT: I 430 LYS cc_start: 0.8978 (mttt) cc_final: 0.8721 (ttmm) REVERT: I 503 LYS cc_start: 0.8832 (mmmm) cc_final: 0.8603 (ttpp) REVERT: I 521 LEU cc_start: 0.9340 (tp) cc_final: 0.9134 (tt) REVERT: I 696 ASP cc_start: 0.7916 (t0) cc_final: 0.7369 (t0) REVERT: I 739 ASP cc_start: 0.6339 (p0) cc_final: 0.6037 (p0) REVERT: I 740 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7427 (mt-10) REVERT: I 914 LYS cc_start: 0.5607 (ttpt) cc_final: 0.5206 (tptt) REVERT: I 918 LEU cc_start: 0.9116 (tp) cc_final: 0.8912 (tt) REVERT: I 992 LEU cc_start: 0.2914 (OUTLIER) cc_final: 0.2506 (tp) REVERT: I 1029 LEU cc_start: 0.8721 (tt) cc_final: 0.8508 (pp) REVERT: I 1229 TYR cc_start: 0.8987 (m-80) cc_final: 0.8745 (m-80) REVERT: I 1321 GLU cc_start: 0.7764 (tp30) cc_final: 0.7515 (tp30) REVERT: J 127 LEU cc_start: 0.9310 (tp) cc_final: 0.9106 (tt) REVERT: J 129 ASP cc_start: 0.7798 (t70) cc_final: 0.7172 (t70) REVERT: J 205 LEU cc_start: 0.7540 (tp) cc_final: 0.7274 (tt) REVERT: J 295 GLU cc_start: 0.8821 (tp30) cc_final: 0.8578 (mm-30) REVERT: J 453 VAL cc_start: 0.9443 (t) cc_final: 0.9215 (t) REVERT: J 681 LYS cc_start: 0.8572 (tptt) cc_final: 0.8351 (tppt) REVERT: J 759 ILE cc_start: 0.9267 (mm) cc_final: 0.9002 (mt) REVERT: J 870 ASP cc_start: 0.8711 (m-30) cc_final: 0.8467 (m-30) REVERT: J 981 GLU cc_start: 0.7688 (tt0) cc_final: 0.7412 (tm-30) REVERT: J 982 LEU cc_start: 0.8238 (tp) cc_final: 0.7892 (pp) REVERT: J 1146 GLU cc_start: 0.7908 (tp30) cc_final: 0.7334 (tp30) REVERT: J 1239 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7086 (t0) REVERT: J 1249 ASN cc_start: 0.8962 (t0) cc_final: 0.8700 (t0) REVERT: K 58 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7516 (pp) REVERT: K 65 ASP cc_start: 0.8116 (m-30) cc_final: 0.7797 (m-30) REVERT: K 79 GLU cc_start: 0.5601 (tm-30) cc_final: 0.5107 (mm-30) REVERT: D 13 GLN cc_start: 0.8186 (mt0) cc_final: 0.7555 (mt0) REVERT: D 32 MET cc_start: 0.7665 (mmm) cc_final: 0.7446 (mmm) REVERT: D 42 LYS cc_start: 0.8580 (mtpt) cc_final: 0.8237 (tptt) REVERT: D 43 ARG cc_start: 0.7163 (mtt180) cc_final: 0.6851 (mtt180) REVERT: D 115 LYS cc_start: 0.8373 (mttt) cc_final: 0.7936 (ttmt) outliers start: 65 outliers final: 36 residues processed: 497 average time/residue: 0.4096 time to fit residues: 321.1119 Evaluate side-chains 372 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 333 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 411 ILE Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 130 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 256 optimal weight: 0.8980 chunk 209 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 308 optimal weight: 8.9990 chunk 333 optimal weight: 30.0000 chunk 274 optimal weight: 0.0970 chunk 305 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 HIS ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 604 HIS I1010 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28254 Z= 0.212 Angle : 0.609 8.464 38466 Z= 0.316 Chirality : 0.043 0.185 4396 Planarity : 0.004 0.055 4796 Dihedral : 14.713 179.546 4435 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.50 % Favored : 93.44 % Rotamer: Outliers : 2.80 % Allowed : 11.08 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.14), residues: 3340 helix: 0.12 (0.15), residues: 1162 sheet: -1.64 (0.23), residues: 466 loop : -2.15 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J1193 HIS 0.015 0.001 HIS I 604 PHE 0.017 0.001 PHE I 230 TYR 0.024 0.001 TYR G 185 ARG 0.004 0.000 ARG I1106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 363 time to evaluate : 2.940 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: I 47 TYR cc_start: 0.5178 (m-80) cc_final: 0.4683 (m-80) REVERT: I 131 THR cc_start: 0.9347 (m) cc_final: 0.9118 (p) REVERT: I 247 ARG cc_start: 0.7793 (tpp-160) cc_final: 0.6627 (ttp-110) REVERT: I 285 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8562 (mp) REVERT: I 309 LEU cc_start: 0.8951 (tp) cc_final: 0.8512 (mp) REVERT: I 311 CYS cc_start: 0.7546 (p) cc_final: 0.6788 (p) REVERT: I 475 VAL cc_start: 0.8555 (t) cc_final: 0.7980 (p) REVERT: I 696 ASP cc_start: 0.7844 (t0) cc_final: 0.7412 (t0) REVERT: I 704 MET cc_start: 0.8341 (mmm) cc_final: 0.8130 (tpp) REVERT: I 740 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7185 (mt-10) REVERT: I 799 ASN cc_start: 0.9232 (OUTLIER) cc_final: 0.8718 (p0) REVERT: I 849 GLU cc_start: 0.7724 (tt0) cc_final: 0.7443 (tt0) REVERT: I 914 LYS cc_start: 0.5473 (ttpt) cc_final: 0.5111 (tptt) REVERT: I 918 LEU cc_start: 0.9105 (tp) cc_final: 0.8876 (tt) REVERT: I 992 LEU cc_start: 0.2949 (OUTLIER) cc_final: 0.2549 (tp) REVERT: I 1025 PHE cc_start: 0.7288 (t80) cc_final: 0.6979 (t80) REVERT: I 1029 LEU cc_start: 0.8715 (tt) cc_final: 0.8361 (pp) REVERT: I 1229 TYR cc_start: 0.8972 (m-80) cc_final: 0.8699 (m-10) REVERT: J 127 LEU cc_start: 0.9307 (tp) cc_final: 0.8988 (tt) REVERT: J 205 LEU cc_start: 0.7509 (tp) cc_final: 0.7261 (tt) REVERT: J 295 GLU cc_start: 0.8862 (tp30) cc_final: 0.8519 (mm-30) REVERT: J 681 LYS cc_start: 0.8604 (tptt) cc_final: 0.8354 (tppt) REVERT: J 759 ILE cc_start: 0.9277 (mm) cc_final: 0.9001 (mt) REVERT: J 870 ASP cc_start: 0.8719 (m-30) cc_final: 0.8490 (m-30) REVERT: J 981 GLU cc_start: 0.7715 (tt0) cc_final: 0.7400 (tm-30) REVERT: J 982 LEU cc_start: 0.8002 (tp) cc_final: 0.7754 (pp) REVERT: J 1146 GLU cc_start: 0.8061 (tp30) cc_final: 0.7527 (tp30) REVERT: J 1244 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7583 (mm110) REVERT: J 1249 ASN cc_start: 0.8943 (t0) cc_final: 0.8669 (t0) REVERT: K 58 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7927 (pp) REVERT: K 65 ASP cc_start: 0.8199 (m-30) cc_final: 0.7801 (m-30) REVERT: K 73 GLN cc_start: 0.6282 (pp30) cc_final: 0.6007 (pp30) REVERT: K 76 GLU cc_start: 0.7396 (mp0) cc_final: 0.7161 (pm20) REVERT: K 79 GLU cc_start: 0.5461 (tm-30) cc_final: 0.5025 (mm-30) REVERT: D 13 GLN cc_start: 0.8169 (mt0) cc_final: 0.7592 (mt0) REVERT: D 42 LYS cc_start: 0.8558 (mtpt) cc_final: 0.8186 (tptt) REVERT: D 43 ARG cc_start: 0.7194 (mtt180) cc_final: 0.6904 (mtt180) REVERT: D 115 LYS cc_start: 0.8374 (mttt) cc_final: 0.7892 (ttmt) outliers start: 80 outliers final: 54 residues processed: 417 average time/residue: 0.3842 time to fit residues: 257.3717 Evaluate side-chains 372 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 314 time to evaluate : 3.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 655 SER Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 130 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 304 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 147 optimal weight: 0.0170 chunk 207 optimal weight: 6.9990 chunk 309 optimal weight: 0.9990 chunk 327 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 293 optimal weight: 0.0040 chunk 88 optimal weight: 4.9990 overall best weight: 2.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 HIS ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 580 GLN I 604 HIS ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28254 Z= 0.263 Angle : 0.622 8.923 38466 Z= 0.321 Chirality : 0.044 0.240 4396 Planarity : 0.004 0.048 4796 Dihedral : 14.614 179.314 4435 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.41 % Favored : 93.53 % Rotamer: Outliers : 3.36 % Allowed : 12.59 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3340 helix: 0.53 (0.15), residues: 1155 sheet: -1.44 (0.23), residues: 477 loop : -1.97 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J1193 HIS 0.014 0.001 HIS I 604 PHE 0.014 0.001 PHE J 620 TYR 0.025 0.002 TYR G 185 ARG 0.009 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 338 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 29 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7700 (tm-30) REVERT: I 241 LEU cc_start: 0.7981 (tt) cc_final: 0.7736 (tp) REVERT: I 247 ARG cc_start: 0.7903 (tpp-160) cc_final: 0.6602 (ttp-110) REVERT: I 309 LEU cc_start: 0.9043 (tp) cc_final: 0.8604 (mp) REVERT: I 478 ARG cc_start: 0.8743 (tpp80) cc_final: 0.8521 (tpt90) REVERT: I 696 ASP cc_start: 0.7826 (t0) cc_final: 0.7521 (t70) REVERT: I 704 MET cc_start: 0.8470 (mmm) cc_final: 0.8213 (tpp) REVERT: I 740 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7465 (mt-10) REVERT: I 799 ASN cc_start: 0.9271 (OUTLIER) cc_final: 0.8788 (p0) REVERT: I 849 GLU cc_start: 0.7962 (tt0) cc_final: 0.7633 (tt0) REVERT: I 914 LYS cc_start: 0.5817 (ttpt) cc_final: 0.5350 (tptt) REVERT: I 918 LEU cc_start: 0.9104 (tp) cc_final: 0.8884 (tt) REVERT: I 1025 PHE cc_start: 0.7288 (t80) cc_final: 0.6973 (t80) REVERT: I 1029 LEU cc_start: 0.8772 (tt) cc_final: 0.8390 (pp) REVERT: I 1229 TYR cc_start: 0.8996 (m-80) cc_final: 0.8769 (m-10) REVERT: J 295 GLU cc_start: 0.8825 (tp30) cc_final: 0.8509 (mm-30) REVERT: J 681 LYS cc_start: 0.8623 (tptt) cc_final: 0.8403 (tppt) REVERT: J 759 ILE cc_start: 0.9346 (mm) cc_final: 0.9054 (mt) REVERT: J 870 ASP cc_start: 0.8746 (m-30) cc_final: 0.8538 (m-30) REVERT: J 982 LEU cc_start: 0.8045 (tp) cc_final: 0.7806 (pp) REVERT: J 1146 GLU cc_start: 0.8170 (tp30) cc_final: 0.7604 (tp30) REVERT: J 1174 ARG cc_start: 0.7545 (mtt90) cc_final: 0.6904 (tpp80) REVERT: J 1244 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7595 (mm110) REVERT: K 25 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7339 (ttt180) REVERT: K 56 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8427 (mm-30) REVERT: K 58 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7971 (pp) REVERT: K 65 ASP cc_start: 0.8223 (m-30) cc_final: 0.7850 (m-30) REVERT: K 79 GLU cc_start: 0.5315 (tm-30) cc_final: 0.4867 (mm-30) REVERT: D 42 LYS cc_start: 0.8575 (mtpt) cc_final: 0.8197 (tptt) REVERT: D 43 ARG cc_start: 0.7252 (mtt180) cc_final: 0.6923 (mtt180) REVERT: D 111 TYR cc_start: 0.4489 (m-80) cc_final: 0.4286 (m-80) REVERT: D 115 LYS cc_start: 0.8333 (mttt) cc_final: 0.7862 (ttmt) outliers start: 96 outliers final: 61 residues processed: 409 average time/residue: 0.3910 time to fit residues: 255.8491 Evaluate side-chains 366 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 302 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 362 ARG Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 655 SER Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 130 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 272 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 243 optimal weight: 0.7980 chunk 135 optimal weight: 0.7980 chunk 279 optimal weight: 10.0000 chunk 226 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 294 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 604 HIS ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28254 Z= 0.162 Angle : 0.586 13.784 38466 Z= 0.300 Chirality : 0.042 0.201 4396 Planarity : 0.004 0.049 4796 Dihedral : 14.434 179.076 4435 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.23 % Favored : 93.71 % Rotamer: Outliers : 2.97 % Allowed : 13.67 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 3340 helix: 0.79 (0.16), residues: 1160 sheet: -1.29 (0.23), residues: 472 loop : -1.86 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP J1193 HIS 0.019 0.001 HIS I 604 PHE 0.017 0.001 PHE I 230 TYR 0.030 0.001 TYR G 185 ARG 0.008 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 362 time to evaluate : 3.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 95 LYS cc_start: 0.8509 (tptm) cc_final: 0.8191 (tptp) REVERT: H 145 LYS cc_start: 0.8613 (tttt) cc_final: 0.8093 (tptm) REVERT: I 47 TYR cc_start: 0.5567 (m-80) cc_final: 0.5356 (m-80) REVERT: I 62 TYR cc_start: 0.5792 (m-10) cc_final: 0.5588 (m-80) REVERT: I 247 ARG cc_start: 0.7946 (tpp-160) cc_final: 0.6709 (ttp-110) REVERT: I 309 LEU cc_start: 0.9046 (tp) cc_final: 0.8645 (mp) REVERT: I 496 LYS cc_start: 0.8816 (tptt) cc_final: 0.8514 (tptt) REVERT: I 704 MET cc_start: 0.8394 (mmm) cc_final: 0.8166 (tpp) REVERT: I 914 LYS cc_start: 0.5703 (ttpt) cc_final: 0.5253 (tptt) REVERT: I 918 LEU cc_start: 0.9151 (tp) cc_final: 0.8928 (tt) REVERT: I 1025 PHE cc_start: 0.7308 (t80) cc_final: 0.7013 (t80) REVERT: I 1029 LEU cc_start: 0.8718 (tt) cc_final: 0.8376 (pp) REVERT: I 1156 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.5748 (mtm180) REVERT: I 1160 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.6032 (p0) REVERT: I 1229 TYR cc_start: 0.8864 (m-80) cc_final: 0.8346 (m-80) REVERT: I 1290 MET cc_start: 0.8590 (tpp) cc_final: 0.8136 (mmt) REVERT: J 295 GLU cc_start: 0.8765 (tp30) cc_final: 0.8392 (mm-30) REVERT: J 719 PHE cc_start: 0.8530 (m-10) cc_final: 0.8323 (m-80) REVERT: J 759 ILE cc_start: 0.9284 (mm) cc_final: 0.8954 (mt) REVERT: J 981 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6878 (tm-30) REVERT: J 1100 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.6213 (m-80) REVERT: J 1174 ARG cc_start: 0.7566 (mtt90) cc_final: 0.6944 (tpp80) REVERT: J 1244 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7543 (mm110) REVERT: K 65 ASP cc_start: 0.8211 (m-30) cc_final: 0.7785 (m-30) REVERT: K 79 GLU cc_start: 0.5522 (tm-30) cc_final: 0.5051 (mm-30) REVERT: D 13 GLN cc_start: 0.8200 (mt0) cc_final: 0.7764 (mt0) REVERT: D 42 LYS cc_start: 0.8357 (mtpt) cc_final: 0.7998 (tptt) REVERT: D 43 ARG cc_start: 0.7138 (mtt180) cc_final: 0.6884 (mtt180) REVERT: D 115 LYS cc_start: 0.8376 (mttt) cc_final: 0.7908 (ttmt) outliers start: 85 outliers final: 54 residues processed: 420 average time/residue: 0.4129 time to fit residues: 273.8651 Evaluate side-chains 374 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 316 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1156 ARG Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 981 GLU Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 98 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 110 optimal weight: 6.9990 chunk 295 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 192 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 327 optimal weight: 6.9990 chunk 272 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 41 ASN ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 573 ASN I 604 HIS I 799 ASN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28254 Z= 0.162 Angle : 0.587 13.956 38466 Z= 0.298 Chirality : 0.042 0.220 4396 Planarity : 0.004 0.045 4796 Dihedral : 14.320 179.125 4435 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.02 % Favored : 93.92 % Rotamer: Outliers : 3.22 % Allowed : 14.55 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3340 helix: 0.94 (0.16), residues: 1162 sheet: -1.18 (0.23), residues: 478 loop : -1.75 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J1193 HIS 0.012 0.001 HIS I 604 PHE 0.021 0.001 PHE I 230 TYR 0.028 0.001 TYR G 185 ARG 0.007 0.000 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 340 time to evaluate : 4.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 95 LYS cc_start: 0.8470 (tptm) cc_final: 0.8147 (tptp) REVERT: I 130 MET cc_start: 0.8862 (ttm) cc_final: 0.8533 (ttm) REVERT: I 239 MET cc_start: 0.5757 (tmm) cc_final: 0.5477 (tmm) REVERT: I 241 LEU cc_start: 0.7902 (tt) cc_final: 0.7380 (tp) REVERT: I 247 ARG cc_start: 0.8003 (tpp-160) cc_final: 0.6775 (ttm110) REVERT: I 272 ARG cc_start: 0.7551 (ttp-170) cc_final: 0.7332 (ptm-80) REVERT: I 309 LEU cc_start: 0.8984 (tp) cc_final: 0.8582 (mp) REVERT: I 434 ASP cc_start: 0.8464 (p0) cc_final: 0.8155 (p0) REVERT: I 490 GLN cc_start: 0.8210 (pm20) cc_final: 0.7873 (mm-40) REVERT: I 496 LYS cc_start: 0.8800 (tptt) cc_final: 0.8496 (tptt) REVERT: I 549 ASP cc_start: 0.7409 (t0) cc_final: 0.7197 (m-30) REVERT: I 704 MET cc_start: 0.8418 (mmm) cc_final: 0.8204 (tpp) REVERT: I 914 LYS cc_start: 0.5696 (ttpt) cc_final: 0.5261 (tptt) REVERT: I 918 LEU cc_start: 0.9150 (tp) cc_final: 0.8938 (tt) REVERT: I 1156 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.5607 (mtm180) REVERT: I 1160 ASP cc_start: 0.6449 (OUTLIER) cc_final: 0.5831 (p0) REVERT: I 1188 ASP cc_start: 0.8034 (t0) cc_final: 0.7813 (t0) REVERT: I 1229 TYR cc_start: 0.8811 (m-80) cc_final: 0.8288 (m-80) REVERT: I 1290 MET cc_start: 0.8591 (tpp) cc_final: 0.8370 (tpp) REVERT: J 295 GLU cc_start: 0.8741 (tp30) cc_final: 0.8378 (mm-30) REVERT: J 759 ILE cc_start: 0.9285 (mm) cc_final: 0.8994 (mt) REVERT: J 918 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8892 (pt) REVERT: J 981 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6878 (tm-30) REVERT: J 1100 PHE cc_start: 0.6999 (OUTLIER) cc_final: 0.6090 (m-80) REVERT: J 1174 ARG cc_start: 0.7585 (mtt90) cc_final: 0.6864 (tpp80) REVERT: J 1189 MET cc_start: 0.7839 (mmt) cc_final: 0.7399 (mmm) REVERT: K 7 GLN cc_start: 0.7829 (tp40) cc_final: 0.7627 (tp40) REVERT: K 65 ASP cc_start: 0.8216 (m-30) cc_final: 0.7804 (m-30) REVERT: K 79 GLU cc_start: 0.5518 (tm-30) cc_final: 0.5057 (mm-30) REVERT: D 13 GLN cc_start: 0.8166 (mt0) cc_final: 0.7954 (mm-40) REVERT: D 32 MET cc_start: 0.8055 (mmm) cc_final: 0.7075 (tpp) REVERT: D 42 LYS cc_start: 0.8371 (mtpt) cc_final: 0.8036 (tptt) REVERT: D 43 ARG cc_start: 0.6558 (mtt180) cc_final: 0.6047 (mtp85) REVERT: D 111 TYR cc_start: 0.4640 (m-80) cc_final: 0.4427 (m-80) REVERT: D 115 LYS cc_start: 0.8368 (mttt) cc_final: 0.7893 (ttmt) outliers start: 92 outliers final: 66 residues processed: 405 average time/residue: 0.3797 time to fit residues: 247.7573 Evaluate side-chains 379 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 309 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1156 ARG Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1100 PHE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 129 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 316 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 239 optimal weight: 0.4980 chunk 185 optimal weight: 0.1980 chunk 276 optimal weight: 40.0000 chunk 183 optimal weight: 10.0000 chunk 326 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 604 HIS I 799 ASN I1157 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 708 ASN ** J 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28254 Z= 0.240 Angle : 0.611 14.364 38466 Z= 0.310 Chirality : 0.043 0.227 4396 Planarity : 0.004 0.042 4796 Dihedral : 14.328 178.779 4435 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.47 % Favored : 93.47 % Rotamer: Outliers : 3.29 % Allowed : 14.76 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.14), residues: 3340 helix: 1.02 (0.16), residues: 1151 sheet: -1.12 (0.24), residues: 471 loop : -1.76 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 868 HIS 0.014 0.001 HIS I 604 PHE 0.025 0.001 PHE D 126 TYR 0.027 0.001 TYR G 185 ARG 0.008 0.000 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 302 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 247 ARG cc_start: 0.7982 (tpp-160) cc_final: 0.6864 (ttp-110) REVERT: I 285 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8583 (mp) REVERT: I 309 LEU cc_start: 0.8991 (tp) cc_final: 0.8584 (mp) REVERT: I 434 ASP cc_start: 0.8480 (p0) cc_final: 0.8163 (p0) REVERT: I 478 ARG cc_start: 0.8836 (tpp80) cc_final: 0.8448 (tpt90) REVERT: I 496 LYS cc_start: 0.8819 (tptt) cc_final: 0.8566 (tptt) REVERT: I 704 MET cc_start: 0.8519 (mmm) cc_final: 0.8281 (tpp) REVERT: I 914 LYS cc_start: 0.5786 (ttpt) cc_final: 0.5284 (tptt) REVERT: I 918 LEU cc_start: 0.9149 (tp) cc_final: 0.8918 (tt) REVERT: I 1156 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.5458 (mtm180) REVERT: I 1188 ASP cc_start: 0.8106 (t0) cc_final: 0.7779 (t0) REVERT: I 1229 TYR cc_start: 0.8858 (m-80) cc_final: 0.8332 (m-80) REVERT: I 1290 MET cc_start: 0.8700 (tpp) cc_final: 0.8342 (tpp) REVERT: J 295 GLU cc_start: 0.8789 (tp30) cc_final: 0.8395 (mm-30) REVERT: J 759 ILE cc_start: 0.9318 (mm) cc_final: 0.9016 (mt) REVERT: J 918 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8944 (pt) REVERT: J 981 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6840 (tm-30) REVERT: J 1174 ARG cc_start: 0.7629 (mtt90) cc_final: 0.6985 (tpp80) REVERT: K 7 GLN cc_start: 0.7924 (tp40) cc_final: 0.7678 (tp40) REVERT: K 65 ASP cc_start: 0.8159 (m-30) cc_final: 0.7779 (m-30) REVERT: K 79 GLU cc_start: 0.5653 (tm-30) cc_final: 0.5088 (mm-30) REVERT: D 42 LYS cc_start: 0.8389 (mtpt) cc_final: 0.8019 (tptt) REVERT: D 43 ARG cc_start: 0.6831 (mtt180) cc_final: 0.6521 (mtp85) REVERT: D 115 LYS cc_start: 0.8333 (mttt) cc_final: 0.7831 (ttmt) outliers start: 94 outliers final: 73 residues processed: 373 average time/residue: 0.3799 time to fit residues: 228.7548 Evaluate side-chains 366 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 290 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1156 ARG Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 362 ARG Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 655 SER Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 129 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 202 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 604 HIS ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28254 Z= 0.188 Angle : 0.596 14.341 38466 Z= 0.301 Chirality : 0.042 0.215 4396 Planarity : 0.004 0.051 4796 Dihedral : 14.262 178.831 4435 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.08 % Favored : 93.86 % Rotamer: Outliers : 3.01 % Allowed : 15.17 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3340 helix: 1.08 (0.16), residues: 1151 sheet: -1.10 (0.23), residues: 484 loop : -1.70 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J1193 HIS 0.009 0.001 HIS J 777 PHE 0.025 0.001 PHE D 126 TYR 0.030 0.001 TYR G 185 ARG 0.008 0.000 ARG I 801 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 309 time to evaluate : 4.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 95 LYS cc_start: 0.8335 (tptp) cc_final: 0.8108 (tptp) REVERT: I 247 ARG cc_start: 0.7961 (tpp-160) cc_final: 0.6733 (ttp-110) REVERT: I 285 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8505 (mp) REVERT: I 309 LEU cc_start: 0.8981 (tp) cc_final: 0.8585 (mp) REVERT: I 434 ASP cc_start: 0.8526 (p0) cc_final: 0.8149 (p0) REVERT: I 478 ARG cc_start: 0.8816 (tpp80) cc_final: 0.8388 (tpt90) REVERT: I 490 GLN cc_start: 0.8168 (pm20) cc_final: 0.7849 (mm-40) REVERT: I 496 LYS cc_start: 0.8791 (tptt) cc_final: 0.8559 (tptt) REVERT: I 604 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.7381 (m-70) REVERT: I 704 MET cc_start: 0.8487 (mmm) cc_final: 0.8258 (tpp) REVERT: I 914 LYS cc_start: 0.5903 (ttpt) cc_final: 0.5402 (tptt) REVERT: I 918 LEU cc_start: 0.9143 (tp) cc_final: 0.8920 (tt) REVERT: I 1156 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.5427 (mtm180) REVERT: I 1188 ASP cc_start: 0.8088 (t0) cc_final: 0.7715 (t0) REVERT: I 1229 TYR cc_start: 0.8876 (m-80) cc_final: 0.8317 (m-80) REVERT: I 1290 MET cc_start: 0.8609 (tpp) cc_final: 0.8330 (tpp) REVERT: J 295 GLU cc_start: 0.8746 (tp30) cc_final: 0.8485 (mm-30) REVERT: J 759 ILE cc_start: 0.9311 (mm) cc_final: 0.8983 (mt) REVERT: J 918 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8910 (pt) REVERT: J 981 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6817 (tm-30) REVERT: J 1174 ARG cc_start: 0.7599 (mtt90) cc_final: 0.7025 (tpp80) REVERT: K 7 GLN cc_start: 0.7877 (tp40) cc_final: 0.7636 (tp40) REVERT: K 65 ASP cc_start: 0.8152 (m-30) cc_final: 0.7771 (m-30) REVERT: K 79 GLU cc_start: 0.5599 (tm-30) cc_final: 0.5051 (mm-30) REVERT: D 32 MET cc_start: 0.8001 (mmm) cc_final: 0.7037 (tpp) REVERT: D 42 LYS cc_start: 0.8397 (mtpt) cc_final: 0.8045 (tptt) REVERT: D 43 ARG cc_start: 0.6625 (mtt180) cc_final: 0.6267 (mtp85) REVERT: D 115 LYS cc_start: 0.8296 (mttt) cc_final: 0.7809 (ttmt) outliers start: 86 outliers final: 72 residues processed: 371 average time/residue: 0.3834 time to fit residues: 228.7042 Evaluate side-chains 368 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 292 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1156 ARG Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 362 ARG Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 581 MET Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 129 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 297 optimal weight: 2.9990 chunk 313 optimal weight: 4.9990 chunk 285 optimal weight: 5.9990 chunk 304 optimal weight: 0.0970 chunk 312 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 275 optimal weight: 9.9990 chunk 287 optimal weight: 20.0000 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 127 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 604 HIS ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28254 Z= 0.190 Angle : 0.599 14.389 38466 Z= 0.302 Chirality : 0.043 0.220 4396 Planarity : 0.004 0.050 4796 Dihedral : 14.230 178.636 4435 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.14 % Favored : 93.80 % Rotamer: Outliers : 2.87 % Allowed : 15.66 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 3340 helix: 1.14 (0.16), residues: 1144 sheet: -1.11 (0.23), residues: 489 loop : -1.67 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J1193 HIS 0.008 0.001 HIS J 777 PHE 0.023 0.001 PHE I 230 TYR 0.030 0.001 TYR G 185 ARG 0.008 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 308 time to evaluate : 3.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 95 LYS cc_start: 0.8279 (tptp) cc_final: 0.8048 (tptp) REVERT: I 247 ARG cc_start: 0.7954 (tpp-160) cc_final: 0.6723 (ttp-110) REVERT: I 309 LEU cc_start: 0.8977 (tp) cc_final: 0.8613 (mp) REVERT: I 434 ASP cc_start: 0.8501 (p0) cc_final: 0.8151 (p0) REVERT: I 496 LYS cc_start: 0.8775 (tptt) cc_final: 0.8559 (tptt) REVERT: I 604 HIS cc_start: 0.7637 (OUTLIER) cc_final: 0.7289 (m-70) REVERT: I 704 MET cc_start: 0.8502 (mmm) cc_final: 0.8264 (tpp) REVERT: I 914 LYS cc_start: 0.5899 (ttpt) cc_final: 0.5407 (tptt) REVERT: I 918 LEU cc_start: 0.9146 (tp) cc_final: 0.8916 (tt) REVERT: I 1156 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.5332 (mtm180) REVERT: I 1188 ASP cc_start: 0.8070 (t0) cc_final: 0.7690 (t0) REVERT: I 1229 TYR cc_start: 0.8826 (m-80) cc_final: 0.8394 (m-80) REVERT: I 1290 MET cc_start: 0.8611 (tpp) cc_final: 0.8338 (tpp) REVERT: J 295 GLU cc_start: 0.8729 (tp30) cc_final: 0.8457 (mm-30) REVERT: J 759 ILE cc_start: 0.9309 (mm) cc_final: 0.8977 (mt) REVERT: J 918 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8912 (pt) REVERT: J 1174 ARG cc_start: 0.7575 (mtt90) cc_final: 0.7003 (tpp80) REVERT: K 7 GLN cc_start: 0.7897 (tp40) cc_final: 0.7651 (tp40) REVERT: K 58 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7901 (pp) REVERT: K 65 ASP cc_start: 0.8148 (m-30) cc_final: 0.7765 (m-30) REVERT: K 79 GLU cc_start: 0.5714 (tm-30) cc_final: 0.5172 (mm-30) REVERT: D 32 MET cc_start: 0.7901 (mmm) cc_final: 0.7146 (tpp) REVERT: D 42 LYS cc_start: 0.8302 (mtpt) cc_final: 0.8007 (tptt) REVERT: D 43 ARG cc_start: 0.6572 (mtt180) cc_final: 0.6164 (mtp85) REVERT: D 115 LYS cc_start: 0.8286 (mttt) cc_final: 0.7806 (ttmt) outliers start: 82 outliers final: 73 residues processed: 367 average time/residue: 0.3917 time to fit residues: 230.3300 Evaluate side-chains 369 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 292 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1156 ARG Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 362 ARG Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 655 SER Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 129 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 303 optimal weight: 0.7980 chunk 199 optimal weight: 5.9990 chunk 321 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 chunk 337 optimal weight: 2.9990 chunk 310 optimal weight: 0.7980 chunk 268 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 604 HIS ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN ** J 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28254 Z= 0.187 Angle : 0.602 14.204 38466 Z= 0.303 Chirality : 0.042 0.218 4396 Planarity : 0.004 0.067 4796 Dihedral : 14.200 178.569 4435 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.02 % Favored : 93.92 % Rotamer: Outliers : 2.87 % Allowed : 15.70 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.15), residues: 3340 helix: 1.14 (0.16), residues: 1148 sheet: -1.08 (0.23), residues: 489 loop : -1.61 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J1193 HIS 0.008 0.001 HIS J 777 PHE 0.019 0.001 PHE D 126 TYR 0.030 0.001 TYR G 185 ARG 0.008 0.000 ARG D 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 312 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6912 (tt0) REVERT: H 95 LYS cc_start: 0.8273 (tptp) cc_final: 0.8050 (tptp) REVERT: I 115 LYS cc_start: 0.6736 (pttt) cc_final: 0.6368 (ptpp) REVERT: I 247 ARG cc_start: 0.7951 (tpp-160) cc_final: 0.6720 (ttp-110) REVERT: I 309 LEU cc_start: 0.8965 (tp) cc_final: 0.8614 (mp) REVERT: I 434 ASP cc_start: 0.8486 (p0) cc_final: 0.8137 (p0) REVERT: I 490 GLN cc_start: 0.8088 (pm20) cc_final: 0.7809 (mm-40) REVERT: I 704 MET cc_start: 0.8502 (mmm) cc_final: 0.8262 (tpp) REVERT: I 914 LYS cc_start: 0.5895 (ttpt) cc_final: 0.5410 (tptt) REVERT: I 918 LEU cc_start: 0.9105 (tp) cc_final: 0.8892 (tt) REVERT: I 1156 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.6312 (ptt-90) REVERT: I 1188 ASP cc_start: 0.8075 (t0) cc_final: 0.7699 (t0) REVERT: I 1229 TYR cc_start: 0.8803 (m-80) cc_final: 0.8378 (m-80) REVERT: I 1290 MET cc_start: 0.8611 (tpp) cc_final: 0.8353 (tpp) REVERT: J 295 GLU cc_start: 0.8701 (tp30) cc_final: 0.8445 (mm-30) REVERT: J 759 ILE cc_start: 0.9304 (mm) cc_final: 0.8972 (mt) REVERT: J 918 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8911 (pt) REVERT: J 1174 ARG cc_start: 0.7564 (mtt90) cc_final: 0.7010 (tpp80) REVERT: K 7 GLN cc_start: 0.7719 (tp40) cc_final: 0.7481 (tp40) REVERT: K 58 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7907 (pp) REVERT: K 65 ASP cc_start: 0.8017 (m-30) cc_final: 0.7726 (m-30) REVERT: K 79 GLU cc_start: 0.5701 (tm-30) cc_final: 0.5016 (mm-30) REVERT: D 32 MET cc_start: 0.7946 (mmm) cc_final: 0.7189 (tpp) REVERT: D 42 LYS cc_start: 0.8289 (mtpt) cc_final: 0.8004 (tptt) REVERT: D 43 ARG cc_start: 0.6718 (mtt180) cc_final: 0.6461 (mtp85) REVERT: D 115 LYS cc_start: 0.8279 (mttt) cc_final: 0.7716 (ttmt) REVERT: D 124 GLU cc_start: 0.7236 (pm20) cc_final: 0.7014 (pm20) outliers start: 82 outliers final: 76 residues processed: 372 average time/residue: 0.3846 time to fit residues: 231.4399 Evaluate side-chains 376 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 297 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1156 ARG Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 362 ARG Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 655 SER Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1146 GLU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 129 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 164 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 286 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 chunk 74 optimal weight: 8.9990 chunk 269 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 276 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 604 HIS I 799 ASN I 955 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1295 ASN J1366 HIS D 156 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.117089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.088199 restraints weight = 58565.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.089075 restraints weight = 33081.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.088955 restraints weight = 27121.048| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 28254 Z= 0.317 Angle : 0.660 14.557 38466 Z= 0.334 Chirality : 0.044 0.202 4396 Planarity : 0.004 0.058 4796 Dihedral : 14.341 178.990 4435 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.22 % Favored : 92.72 % Rotamer: Outliers : 2.97 % Allowed : 15.84 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3340 helix: 0.94 (0.16), residues: 1160 sheet: -1.21 (0.23), residues: 471 loop : -1.66 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 183 HIS 0.022 0.001 HIS I 604 PHE 0.018 0.002 PHE D 126 TYR 0.024 0.002 TYR G 185 ARG 0.008 0.001 ARG D 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5746.81 seconds wall clock time: 105 minutes 27.57 seconds (6327.57 seconds total)