Starting phenix.real_space_refine on Mon Sep 14 03:59:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c6s_7349/09_2026/6c6s_7349_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c6s_7349/09_2026/6c6s_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/cci-nas-00/data/ceres_data/6c6s_7349/09_2026/6c6s_7349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c6s_7349/09_2026/6c6s_7349.map" model { file = "/net/cci-nas-00/data/ceres_data/6c6s_7349/09_2026/6c6s_7349_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c6s_7349/09_2026/6c6s_7349_neut.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'ARG:plan': 1, 'GLN:plan1': 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: 5.24, per 1000 atoms: 0.19 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 - 3.00 Amino acid : True - 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: 2.22 Conformation dependent library (CDL) restraints added in 945.1 milliseconds 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: 3.22 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: 6.64 Time building geometry restraints manager: 2.96 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=" C3' DA A 11 " pdb=" O3' DA A 11 " ideal model delta sigma weight residual 1.435 1.494 -0.059 1.30e-02 5.92e+03 2.09e+01 bond pdb=" C3' DC B 11 " pdb=" O3' DC B 11 " ideal model delta sigma weight residual 1.435 1.382 0.053 1.30e-02 5.92e+03 1.67e+01 bond pdb=" C3' DG A 8 " pdb=" O3' DG A 8 " ideal model delta sigma weight residual 1.435 1.487 -0.052 1.30e-02 5.92e+03 1.58e+01 bond pdb=" C3' DC B 17 " pdb=" O3' DC B 17 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.40e+01 bond pdb=" C3' DG A 16 " pdb=" O3' DG A 16 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.39e+01 ... (remaining 28249 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 37916 3.49 - 6.98: 491 6.98 - 10.47: 50 10.47 - 13.96: 7 13.96 - 17.45: 2 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=" O4' DA B 16 " pdb=" C4' DA B 16 " pdb=" C3' DA B 16 " ideal model delta sigma weight residual 106.00 102.61 3.39 6.00e-01 2.78e+00 3.18e+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=" O4' DC B 18 " pdb=" C4' DC B 18 " pdb=" C3' DC B 18 " ideal model delta sigma weight residual 106.00 102.78 3.22 6.00e-01 2.78e+00 2.88e+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: 4038 0.112 - 0.223: 345 0.223 - 0.335: 12 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=" C3' DG A 8 " pdb=" C4' DG A 8 " pdb=" O3' DG A 8 " pdb=" C2' DG A 8 " both_signs ideal model delta sigma weight residual False -2.73 -2.46 -0.27 2.00e-01 2.50e+01 1.88e+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 3.040 nonbonded pdb=" OG SER J1321 " pdb=" OE2 GLU J1349 " model vdw 2.252 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 1.030 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 30.650 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 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 : 0.010 0.244 28261 Z= 0.463 Angle : 1.082 22.014 38472 Z= 0.610 Chirality : 0.062 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.023 0.001 ARG I1223 TYR 0.052 0.004 TYR I1229 PHE 0.043 0.004 PHE J 620 TRP 0.047 0.005 TRP I 183 HIS 0.015 0.003 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00916 / 0.45 (28254) covalent geometry : angle 1.07107 / 0.61 (38466) hydrogen bonds : bond 0.16193 / 18.40 ( 1127) hydrogen bonds : angle 7.50183 / 8.82 ( 3100) metal coordination : bond 0.16649 / 16.40 ( 7) metal coordination : angle 12.45635 / 24.11 ( 6) *********************** 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 to be fit. rotamer outliers: 11 poor density : 721 time to evaluate : 1.037 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: G 33 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7740 (ptm160) REVERT: G 145 LYS cc_start: 0.9070 (tttt) cc_final: 0.8708 (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: 0.7929 (mp) REVERT: I 311 CYS cc_start: 0.7772 (p) cc_final: 0.7226 (p) REVERT: I 330 HIS cc_start: 0.7068 (m-70) cc_final: 0.6736 (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: 0.8487 (p) REVERT: I 805 MET cc_start: 0.8645 (ptm) cc_final: 0.8440 (ptm) REVERT: I 849 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8098 (tt0) REVERT: I 914 LYS cc_start: 0.5762 (ttpt) cc_final: 0.5269 (tptm) REVERT: I 918 LEU cc_start: 0.9053 (tp) cc_final: 0.8833 (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: 0.8890 (tp) REVERT: I 1321 GLU cc_start: 0.7819 (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: 0.8610 (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: 0.8051 (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: 0.7788 (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: 0.6768 (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: 0.9037 (m) REVERT: D 115 LYS cc_start: 0.8276 (mttt) cc_final: 0.7581 (pttm) outliers start: 11 outliers final: 3 residues processed: 729 average time/residue: 0.2148 time to fit residues: 236.0358 Evaluate side-chains 360 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 356 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN I 343 HIS I 604 HIS I 760 ASN I1116 HIS I1157 GLN I1220 GLN I1236 ASN I1313 HIS J 45 ASN ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS J 792 ASN J 805 GLN J 817 HIS J1268 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 GLN K 31 GLN D 20 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.119797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.091504 restraints weight = 58374.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.092303 restraints weight = 30885.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.094500 restraints weight = 21894.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.094581 restraints weight = 19358.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.094370 restraints weight = 15443.715| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28261 Z= 0.158 Angle : 0.726 14.105 38472 Z= 0.382 Chirality : 0.047 0.288 4396 Planarity : 0.006 0.080 4796 Dihedral : 15.128 175.130 4438 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.38 % Favored : 93.53 % Rotamer: Outliers : 2.06 % Allowed : 9.34 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.13), residues: 3340 helix: -0.99 (0.14), residues: 1152 sheet: -1.97 (0.22), residues: 502 loop : -2.49 (0.13), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J1075 TYR 0.026 0.002 TYR G 185 PHE 0.026 0.002 PHE J1100 TRP 0.021 0.002 TRP J1193 HIS 0.008 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (28254) covalent geometry : angle 0.72510 / 0.38 (38466) hydrogen bonds : bond 0.05034 / 5.70 ( 1127) hydrogen bonds : angle 5.81339 / 6.73 ( 3100) metal coordination : bond 0.00639 / 0.75 ( 7) metal coordination : angle 2.53222 / 4.98 ( 6) *********************** 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 485 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 426 time to evaluate : 1.032 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: G 79 LEU cc_start: 0.8914 (tt) cc_final: 0.8686 (tp) REVERT: H 214 GLU cc_start: 0.7751 (tt0) cc_final: 0.7420 (pp20) REVERT: I 247 ARG cc_start: 0.7886 (tpp-160) cc_final: 0.6933 (ttp-110) REVERT: I 311 CYS cc_start: 0.7547 (p) cc_final: 0.7215 (p) REVERT: I 430 LYS cc_start: 0.8898 (mttt) cc_final: 0.8585 (ttmm) REVERT: I 704 MET cc_start: 0.7918 (tpp) cc_final: 0.7702 (tpp) REVERT: I 739 ASP cc_start: 0.6375 (p0) cc_final: 0.6151 (p0) REVERT: I 914 LYS cc_start: 0.5589 (ttpt) cc_final: 0.5199 (tptt) REVERT: I 930 ASP cc_start: 0.7520 (t70) cc_final: 0.7309 (t0) REVERT: I 992 LEU cc_start: 0.2908 (OUTLIER) cc_final: 0.2466 (tp) REVERT: I 1114 GLU cc_start: 0.8130 (tt0) cc_final: 0.7911 (tt0) REVERT: I 1297 ASP cc_start: 0.8170 (t0) cc_final: 0.7701 (t0) REVERT: I 1321 GLU cc_start: 0.7862 (tp30) cc_final: 0.7475 (tp30) REVERT: J 127 LEU cc_start: 0.9373 (tp) cc_final: 0.9163 (tt) REVERT: J 129 ASP cc_start: 0.7782 (t70) cc_final: 0.7162 (t70) REVERT: J 180 MET cc_start: 0.8397 (ttm) cc_final: 0.8162 (ttt) REVERT: J 205 LEU cc_start: 0.7532 (tp) cc_final: 0.7244 (tt) REVERT: J 681 LYS cc_start: 0.8522 (tptt) cc_final: 0.8309 (tppt) REVERT: J 759 ILE cc_start: 0.9173 (mm) cc_final: 0.8925 (mt) REVERT: J 870 ASP cc_start: 0.8705 (m-30) cc_final: 0.8455 (m-30) REVERT: J 981 GLU cc_start: 0.7579 (tt0) cc_final: 0.7353 (tm-30) REVERT: J 982 LEU cc_start: 0.8265 (tp) cc_final: 0.7682 (pp) REVERT: J 1239 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7159 (t0) REVERT: J 1249 ASN cc_start: 0.8976 (t0) cc_final: 0.8769 (t0) REVERT: K 58 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7694 (pp) REVERT: K 65 ASP cc_start: 0.8172 (m-30) cc_final: 0.7776 (m-30) REVERT: K 79 GLU cc_start: 0.5648 (tm-30) cc_final: 0.5076 (mm-30) REVERT: D 42 LYS cc_start: 0.8567 (mtpt) cc_final: 0.8229 (tptt) REVERT: D 43 ARG cc_start: 0.6799 (mtt180) cc_final: 0.6528 (mtt180) REVERT: D 115 LYS cc_start: 0.8380 (mttt) cc_final: 0.7746 (pttm) outliers start: 59 outliers final: 31 residues processed: 469 average time/residue: 0.1935 time to fit residues: 142.9727 Evaluate side-chains 369 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 335 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 156 SER 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 309 LEU Chi-restraints excluded: chain I residue 468 LEU 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 992 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL 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 362 ARG 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 655 SER 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 48 VAL Chi-restraints excluded: chain K residue 58 LEU 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 240 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 257 optimal weight: 0.9990 chunk 280 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 97 optimal weight: 0.0970 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 132 HIS ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 604 HIS I1010 GLN I1136 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** J1023 HIS ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.119345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.090242 restraints weight = 58787.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.091555 restraints weight = 31938.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.092885 restraints weight = 22371.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.092944 restraints weight = 19706.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.092906 restraints weight = 17055.221| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28261 Z= 0.151 Angle : 0.665 10.532 38472 Z= 0.350 Chirality : 0.046 0.297 4396 Planarity : 0.005 0.070 4796 Dihedral : 14.865 174.885 4436 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.59 % Favored : 93.35 % Rotamer: Outliers : 2.38 % Allowed : 10.63 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.14), residues: 3340 helix: -0.25 (0.15), residues: 1161 sheet: -1.78 (0.22), residues: 490 loop : -2.23 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 478 TYR 0.026 0.001 TYR G 185 PHE 0.017 0.001 PHE I1025 TRP 0.030 0.002 TRP J1193 HIS 0.006 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (28254) covalent geometry : angle 0.66443 / 0.35 (38466) hydrogen bonds : bond 0.04572 / 5.18 ( 1127) hydrogen bonds : angle 5.37251 / 6.18 ( 3100) metal coordination : bond 0.00491 / 0.52 ( 7) metal coordination : angle 1.74311 / 3.44 ( 6) *********************** 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 to be fit. rotamer outliers: 68 poor density : 375 time to evaluate : 1.086 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: G 79 LEU cc_start: 0.8930 (tt) cc_final: 0.8695 (tp) REVERT: H 214 GLU cc_start: 0.7744 (tt0) cc_final: 0.7465 (pp20) REVERT: I 47 TYR cc_start: 0.5288 (m-80) cc_final: 0.4747 (m-80) REVERT: I 311 CYS cc_start: 0.7325 (p) cc_final: 0.6736 (p) REVERT: I 459 MET cc_start: 0.8974 (mtp) cc_final: 0.8772 (mtp) REVERT: I 478 ARG cc_start: 0.8786 (tpp80) cc_final: 0.8484 (ttt90) REVERT: I 487 LEU cc_start: 0.4696 (pp) cc_final: 0.3899 (pp) REVERT: I 503 LYS cc_start: 0.8927 (mmmm) cc_final: 0.8640 (ttpp) REVERT: I 704 MET cc_start: 0.8038 (tpp) cc_final: 0.7755 (tpp) REVERT: I 849 GLU cc_start: 0.7877 (tt0) cc_final: 0.7672 (tt0) REVERT: I 914 LYS cc_start: 0.5488 (ttpt) cc_final: 0.5092 (tptt) REVERT: I 930 ASP cc_start: 0.7385 (t70) cc_final: 0.7180 (t0) REVERT: I 943 LYS cc_start: 0.7659 (tptp) cc_final: 0.6970 (mmmt) REVERT: I 992 LEU cc_start: 0.2935 (OUTLIER) cc_final: 0.2500 (tp) REVERT: I 1114 GLU cc_start: 0.8127 (tt0) cc_final: 0.7907 (tt0) REVERT: I 1229 TYR cc_start: 0.9058 (m-80) cc_final: 0.8639 (m-80) REVERT: I 1297 ASP cc_start: 0.7907 (t0) cc_final: 0.7481 (t0) REVERT: I 1321 GLU cc_start: 0.7736 (tp30) cc_final: 0.7352 (tp30) REVERT: J 127 LEU cc_start: 0.9361 (tp) cc_final: 0.9160 (tt) REVERT: J 129 ASP cc_start: 0.7780 (t70) cc_final: 0.7157 (t70) REVERT: J 180 MET cc_start: 0.8421 (ttm) cc_final: 0.8216 (ttt) REVERT: J 205 LEU cc_start: 0.7443 (tp) cc_final: 0.7199 (tt) REVERT: J 582 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9081 (tp) REVERT: J 681 LYS cc_start: 0.8522 (tptt) cc_final: 0.8284 (tppt) REVERT: J 759 ILE cc_start: 0.9184 (mm) cc_final: 0.8939 (mt) REVERT: J 870 ASP cc_start: 0.8742 (m-30) cc_final: 0.8505 (m-30) REVERT: J 981 GLU cc_start: 0.7655 (tt0) cc_final: 0.7387 (tm-30) REVERT: J 982 LEU cc_start: 0.8177 (tp) cc_final: 0.7843 (pp) REVERT: J 1239 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6985 (t0) REVERT: J 1249 ASN cc_start: 0.8978 (t0) cc_final: 0.8673 (t0) REVERT: K 7 GLN cc_start: 0.8108 (tp40) cc_final: 0.7738 (tp40) REVERT: K 58 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7723 (pp) REVERT: K 65 ASP cc_start: 0.8169 (m-30) cc_final: 0.7835 (m-30) REVERT: K 76 GLU cc_start: 0.7146 (mp0) cc_final: 0.6928 (pm20) REVERT: K 79 GLU cc_start: 0.5557 (tm-30) cc_final: 0.5027 (mm-30) REVERT: D 13 GLN cc_start: 0.8220 (mt0) cc_final: 0.7614 (mt0) REVERT: D 42 LYS cc_start: 0.8452 (mtpt) cc_final: 0.8059 (tptt) REVERT: D 43 ARG cc_start: 0.7145 (mtt180) cc_final: 0.6842 (mtt180) REVERT: D 115 LYS cc_start: 0.8437 (mttt) cc_final: 0.7989 (ttmt) outliers start: 68 outliers final: 45 residues processed: 423 average time/residue: 0.1887 time to fit residues: 127.6102 Evaluate side-chains 353 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 304 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 I residue 21 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 472 GLU 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 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1273 MET 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 362 ARG 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 548 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 614 LEU 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 746 LEU Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 1023 HIS 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 39 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 63 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 310 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 331 optimal weight: 9.9990 chunk 260 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 314 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 HIS I 150 HIS ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1157 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1299 ASN ** J 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1326 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.115947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.086654 restraints weight = 58453.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.088538 restraints weight = 33766.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.088215 restraints weight = 22960.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.088792 restraints weight = 22758.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.088671 restraints weight = 18782.569| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 28261 Z= 0.255 Angle : 0.717 13.356 38472 Z= 0.373 Chirality : 0.047 0.293 4396 Planarity : 0.005 0.066 4796 Dihedral : 14.796 174.794 4435 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.16 % Favored : 92.78 % Rotamer: Outliers : 3.32 % Allowed : 11.61 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.14), residues: 3340 helix: 0.09 (0.15), residues: 1160 sheet: -1.74 (0.22), residues: 482 loop : -2.17 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 352 TYR 0.024 0.002 TYR G 185 PHE 0.026 0.002 PHE I 230 TRP 0.024 0.002 TRP J1193 HIS 0.015 0.001 HIS J1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.25 (28254) covalent geometry : angle 0.71632 / 0.37 (38466) hydrogen bonds : bond 0.04691 / 5.35 ( 1127) hydrogen bonds : angle 5.27995 / 6.03 ( 3100) metal coordination : bond 0.00954 / 0.98 ( 7) metal coordination : angle 2.30170 / 4.59 ( 6) *********************** 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 407 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 312 time to evaluate : 1.087 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: G 79 LEU cc_start: 0.9041 (tt) cc_final: 0.8810 (tp) REVERT: H 214 GLU cc_start: 0.7782 (tt0) cc_final: 0.7521 (pp20) REVERT: I 47 TYR cc_start: 0.5363 (m-80) cc_final: 0.4879 (m-80) REVERT: I 131 THR cc_start: 0.9431 (m) cc_final: 0.9193 (p) REVERT: I 247 ARG cc_start: 0.8061 (tpp-160) cc_final: 0.6853 (ttp-110) REVERT: I 704 MET cc_start: 0.8339 (tpp) cc_final: 0.8066 (tpp) REVERT: I 849 GLU cc_start: 0.7997 (tt0) cc_final: 0.7671 (tt0) REVERT: I 851 THR cc_start: 0.8637 (t) cc_final: 0.8416 (t) REVERT: I 914 LYS cc_start: 0.5867 (ttpt) cc_final: 0.5355 (tptt) REVERT: I 930 ASP cc_start: 0.7682 (t70) cc_final: 0.7255 (t0) REVERT: I 992 LEU cc_start: 0.3125 (OUTLIER) cc_final: 0.2673 (tp) REVERT: I 1114 GLU cc_start: 0.8358 (tt0) cc_final: 0.8113 (tt0) REVERT: I 1297 ASP cc_start: 0.8130 (t0) cc_final: 0.7807 (t0) REVERT: I 1321 GLU cc_start: 0.7999 (tp30) cc_final: 0.7612 (tp30) REVERT: J 127 LEU cc_start: 0.9388 (tp) cc_final: 0.9134 (tt) REVERT: J 180 MET cc_start: 0.8654 (ttm) cc_final: 0.8432 (ttt) REVERT: J 532 GLU cc_start: 0.8316 (pt0) cc_final: 0.8069 (tt0) REVERT: J 582 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9131 (tp) REVERT: J 681 LYS cc_start: 0.8648 (tptt) cc_final: 0.8409 (tppt) REVERT: J 981 GLU cc_start: 0.7732 (tt0) cc_final: 0.7379 (tm-30) REVERT: J 982 LEU cc_start: 0.8266 (tp) cc_final: 0.7860 (pp) REVERT: J 1239 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7328 (t0) REVERT: J 1249 ASN cc_start: 0.9056 (t0) cc_final: 0.8768 (t0) REVERT: K 7 GLN cc_start: 0.8033 (tp40) cc_final: 0.7811 (tp40) REVERT: K 65 ASP cc_start: 0.8294 (m-30) cc_final: 0.7874 (m-30) REVERT: K 79 GLU cc_start: 0.5484 (tm-30) cc_final: 0.5015 (mm-30) REVERT: D 13 GLN cc_start: 0.8409 (mt0) cc_final: 0.8058 (mm-40) REVERT: D 42 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8181 (tptt) REVERT: D 43 ARG cc_start: 0.7223 (mtt180) cc_final: 0.6922 (mtt180) REVERT: D 111 TYR cc_start: 0.4470 (m-80) cc_final: 0.4258 (m-80) REVERT: D 115 LYS cc_start: 0.8385 (mttt) cc_final: 0.7911 (ttmt) outliers start: 95 outliers final: 70 residues processed: 383 average time/residue: 0.1869 time to fit residues: 115.6722 Evaluate side-chains 362 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 289 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1292 THR 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 362 ARG 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 453 VAL 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 534 GLU Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 582 ILE 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 697 MET 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 885 VAL 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 1239 ASP Chi-restraints excluded: chain J residue 1253 ILE Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1353 VAL 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 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 94 optimal weight: 1.9990 chunk 324 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 231 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 287 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 155 optimal weight: 0.0070 chunk 124 optimal weight: 7.9990 chunk 314 optimal weight: 1.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 41 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1236 ASN J 488 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.118924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.089495 restraints weight = 58523.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.091195 restraints weight = 33035.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.091389 restraints weight = 22215.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.091807 restraints weight = 21320.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.091886 restraints weight = 18976.012| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28261 Z= 0.134 Angle : 0.632 12.791 38472 Z= 0.329 Chirality : 0.045 0.292 4396 Planarity : 0.004 0.067 4796 Dihedral : 14.588 175.451 4435 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.17 % Favored : 93.80 % Rotamer: Outliers : 2.59 % Allowed : 13.11 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.14), residues: 3340 helix: 0.39 (0.15), residues: 1159 sheet: -1.54 (0.23), residues: 468 loop : -2.01 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 133 TYR 0.027 0.001 TYR G 185 PHE 0.024 0.001 PHE I 230 TRP 0.033 0.002 TRP J1193 HIS 0.005 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (28254) covalent geometry : angle 0.63240 / 0.33 (38466) hydrogen bonds : bond 0.04207 / 4.77 ( 1127) hydrogen bonds : angle 5.00285 / 5.69 ( 3100) metal coordination : bond 0.00327 / 0.35 ( 7) metal coordination : angle 1.05127 / 2.06 ( 6) *********************** 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 442 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 368 time to evaluate : 1.043 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: H 29 GLU cc_start: 0.6772 (pm20) cc_final: 0.6492 (pm20) REVERT: H 95 LYS cc_start: 0.8487 (tptm) cc_final: 0.8136 (tptm) REVERT: H 214 GLU cc_start: 0.7685 (tt0) cc_final: 0.7464 (pp20) REVERT: I 241 LEU cc_start: 0.8485 (tp) cc_final: 0.8097 (tt) REVERT: I 247 ARG cc_start: 0.8054 (tpp-160) cc_final: 0.6795 (ttp-110) REVERT: I 704 MET cc_start: 0.8225 (tpp) cc_final: 0.8006 (tpp) REVERT: I 849 GLU cc_start: 0.7972 (tt0) cc_final: 0.7688 (tt0) REVERT: I 851 THR cc_start: 0.8564 (t) cc_final: 0.8349 (t) REVERT: I 914 LYS cc_start: 0.5771 (ttpt) cc_final: 0.5293 (tptt) REVERT: I 930 ASP cc_start: 0.7468 (t70) cc_final: 0.7121 (t0) REVERT: I 992 LEU cc_start: 0.3048 (OUTLIER) cc_final: 0.2597 (tp) REVERT: I 1114 GLU cc_start: 0.8165 (tt0) cc_final: 0.7849 (tt0) REVERT: I 1229 TYR cc_start: 0.9028 (m-80) cc_final: 0.8629 (m-80) REVERT: I 1297 ASP cc_start: 0.8049 (t0) cc_final: 0.7791 (t0) REVERT: I 1321 GLU cc_start: 0.7840 (tp30) cc_final: 0.7343 (tp30) REVERT: J 127 LEU cc_start: 0.9240 (tp) cc_final: 0.8988 (tt) REVERT: J 180 MET cc_start: 0.8560 (ttm) cc_final: 0.8324 (ttt) REVERT: J 532 GLU cc_start: 0.8288 (pt0) cc_final: 0.8087 (tt0) REVERT: J 582 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9098 (tp) REVERT: J 681 LYS cc_start: 0.8530 (tptt) cc_final: 0.8318 (tppt) REVERT: J 759 ILE cc_start: 0.9292 (mm) cc_final: 0.8973 (mt) REVERT: J 981 GLU cc_start: 0.7632 (tt0) cc_final: 0.7353 (tm-30) REVERT: J 1239 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.7065 (t0) REVERT: J 1244 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7857 (mm110) REVERT: J 1349 GLU cc_start: 0.7838 (mp0) cc_final: 0.7510 (mt-10) REVERT: K 7 GLN cc_start: 0.8015 (tp40) cc_final: 0.7774 (tp40) REVERT: K 58 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7785 (pp) REVERT: K 65 ASP cc_start: 0.8209 (m-30) cc_final: 0.7719 (m-30) REVERT: K 79 GLU cc_start: 0.5522 (tm-30) cc_final: 0.5081 (mm-30) REVERT: D 13 GLN cc_start: 0.8395 (mt0) cc_final: 0.7980 (mt0) REVERT: D 42 LYS cc_start: 0.8435 (mtpt) cc_final: 0.8098 (tptt) REVERT: D 43 ARG cc_start: 0.7159 (mtt180) cc_final: 0.6947 (mtt180) REVERT: D 115 LYS cc_start: 0.8376 (mttt) cc_final: 0.7927 (ttmt) outliers start: 74 outliers final: 58 residues processed: 420 average time/residue: 0.1791 time to fit residues: 121.1136 Evaluate side-chains 375 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 313 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 550 VAL 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 992 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1225 VAL 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 249 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 362 ARG Chi-restraints excluded: chain J residue 442 ILE 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 548 VAL Chi-restraints excluded: chain J residue 582 ILE 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 807 LEU Chi-restraints excluded: chain J residue 1023 HIS 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 1239 ASP 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 98 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 130 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 167 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 297 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 281 optimal weight: 0.0370 chunk 144 optimal weight: 0.9990 chunk 206 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 overall best weight: 1.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 41 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.117703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.088564 restraints weight = 58127.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.090244 restraints weight = 31226.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.090758 restraints weight = 21467.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.091164 restraints weight = 19957.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.091659 restraints weight = 17277.447| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28261 Z= 0.161 Angle : 0.640 14.473 38472 Z= 0.333 Chirality : 0.045 0.285 4396 Planarity : 0.004 0.058 4796 Dihedral : 14.489 178.026 4435 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.59 % Favored : 93.38 % Rotamer: Outliers : 3.18 % Allowed : 13.43 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.14), residues: 3340 helix: 0.52 (0.15), residues: 1160 sheet: -1.42 (0.23), residues: 461 loop : -1.93 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 67 TYR 0.027 0.001 TYR G 185 PHE 0.025 0.001 PHE D 126 TRP 0.031 0.002 TRP J1193 HIS 0.005 0.001 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (28254) covalent geometry : angle 0.63979 / 0.33 (38466) hydrogen bonds : bond 0.04215 / 4.80 ( 1127) hydrogen bonds : angle 4.93415 / 5.62 ( 3100) metal coordination : bond 0.00535 / 0.55 ( 7) metal coordination : angle 1.44137 / 2.87 ( 6) *********************** 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 421 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 330 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 241 LEU cc_start: 0.8240 (tp) cc_final: 0.7873 (tt) REVERT: I 247 ARG cc_start: 0.7977 (tpp-160) cc_final: 0.6803 (ttp-110) REVERT: I 434 ASP cc_start: 0.8426 (p0) cc_final: 0.8086 (p0) REVERT: I 549 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7456 (m-30) REVERT: I 704 MET cc_start: 0.8308 (tpp) cc_final: 0.8072 (tpp) REVERT: I 756 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.8202 (m-10) REVERT: I 914 LYS cc_start: 0.5824 (ttpt) cc_final: 0.5344 (tptt) REVERT: I 930 ASP cc_start: 0.7504 (t70) cc_final: 0.7138 (t0) REVERT: I 1114 GLU cc_start: 0.8224 (tt0) cc_final: 0.7875 (tt0) REVERT: I 1229 TYR cc_start: 0.8991 (m-80) cc_final: 0.8605 (m-80) REVERT: I 1297 ASP cc_start: 0.8104 (t0) cc_final: 0.7757 (t0) REVERT: J 127 LEU cc_start: 0.9295 (tp) cc_final: 0.9080 (tt) REVERT: J 582 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9111 (tp) REVERT: J 759 ILE cc_start: 0.9290 (mm) cc_final: 0.8983 (mt) REVERT: J 918 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8967 (pt) REVERT: J 982 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8026 (pp) REVERT: J 1244 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7894 (mm110) REVERT: J 1349 GLU cc_start: 0.7850 (mp0) cc_final: 0.7520 (mt-10) REVERT: K 58 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7975 (pp) REVERT: K 65 ASP cc_start: 0.8095 (m-30) cc_final: 0.7729 (m-30) REVERT: K 79 GLU cc_start: 0.5520 (tm-30) cc_final: 0.5113 (mm-30) REVERT: D 42 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8147 (tptt) REVERT: D 115 LYS cc_start: 0.8399 (mttt) cc_final: 0.7935 (ttmt) outliers start: 91 outliers final: 64 residues processed: 397 average time/residue: 0.1846 time to fit residues: 117.8600 Evaluate side-chains 370 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 300 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 133 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 I residue 21 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 311 CYS 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 472 GLU Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 549 ASP 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 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 756 TYR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL 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 242 LEU Chi-restraints excluded: chain J residue 255 LEU 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 429 LEU 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 582 ILE Chi-restraints excluded: chain J residue 644 MET 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 807 LEU Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1023 HIS 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 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 98 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 130 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 227 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 309 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 41 ASN H 66 HIS ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1220 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.118686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.089420 restraints weight = 58413.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.090557 restraints weight = 32727.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.091049 restraints weight = 22517.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.091409 restraints weight = 20828.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.092868 restraints weight = 18883.225| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28261 Z= 0.145 Angle : 0.639 14.255 38472 Z= 0.330 Chirality : 0.044 0.281 4396 Planarity : 0.004 0.052 4796 Dihedral : 14.418 178.420 4435 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.44 % Favored : 93.53 % Rotamer: Outliers : 2.83 % Allowed : 14.62 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.14), residues: 3340 helix: 0.64 (0.15), residues: 1165 sheet: -1.36 (0.23), residues: 461 loop : -1.87 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 542 TYR 0.030 0.001 TYR G 185 PHE 0.033 0.001 PHE D 126 TRP 0.022 0.001 TRP J1193 HIS 0.005 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (28254) covalent geometry : angle 0.63911 / 0.33 (38466) hydrogen bonds : bond 0.04100 / 4.67 ( 1127) hydrogen bonds : angle 4.84081 / 5.49 ( 3100) metal coordination : bond 0.00428 / 0.44 ( 7) metal coordination : angle 0.98957 / 1.96 ( 6) *********************** 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 407 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 326 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 29 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7549 (tm-30) REVERT: H 95 LYS cc_start: 0.8475 (tptm) cc_final: 0.8244 (tptp) REVERT: I 62 TYR cc_start: 0.5673 (m-10) cc_final: 0.5403 (m-80) REVERT: I 241 LEU cc_start: 0.8324 (tp) cc_final: 0.7890 (tt) REVERT: I 247 ARG cc_start: 0.7976 (tpp-160) cc_final: 0.6767 (ttp-110) REVERT: I 370 MET cc_start: 0.8780 (tpp) cc_final: 0.8579 (tpt) REVERT: I 434 ASP cc_start: 0.8388 (p0) cc_final: 0.8115 (p0) REVERT: I 542 ARG cc_start: 0.7386 (mmp80) cc_final: 0.7082 (mmp80) REVERT: I 549 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7397 (m-30) REVERT: I 704 MET cc_start: 0.8303 (tpp) cc_final: 0.8075 (tpp) REVERT: I 756 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.8072 (m-10) REVERT: I 914 LYS cc_start: 0.5823 (ttpt) cc_final: 0.5335 (tptt) REVERT: I 930 ASP cc_start: 0.7499 (t70) cc_final: 0.7102 (t0) REVERT: I 1114 GLU cc_start: 0.8192 (tt0) cc_final: 0.7855 (tt0) REVERT: I 1229 TYR cc_start: 0.8978 (m-80) cc_final: 0.8561 (m-80) REVERT: I 1321 GLU cc_start: 0.7788 (tp30) cc_final: 0.7280 (tp30) REVERT: J 312 ARG cc_start: 0.8278 (mmp80) cc_final: 0.7636 (mmp-170) REVERT: J 582 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9156 (tp) REVERT: J 759 ILE cc_start: 0.9270 (mm) cc_final: 0.8973 (mt) REVERT: J 1244 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7862 (mm110) REVERT: J 1349 GLU cc_start: 0.7852 (mp0) cc_final: 0.7491 (mt-10) REVERT: K 7 GLN cc_start: 0.8045 (tp40) cc_final: 0.7837 (tp-100) REVERT: K 65 ASP cc_start: 0.8085 (m-30) cc_final: 0.7736 (m-30) REVERT: K 79 GLU cc_start: 0.5509 (tm-30) cc_final: 0.5107 (mm-30) REVERT: D 42 LYS cc_start: 0.8359 (mtpt) cc_final: 0.8080 (tptt) REVERT: D 111 TYR cc_start: 0.5122 (m-80) cc_final: 0.4685 (m-80) REVERT: D 115 LYS cc_start: 0.8401 (mttt) cc_final: 0.7932 (ttmt) REVERT: D 158 GLU cc_start: 0.5612 (pm20) cc_final: 0.5385 (pm20) outliers start: 81 outliers final: 66 residues processed: 383 average time/residue: 0.1829 time to fit residues: 112.4893 Evaluate side-chains 362 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 293 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 39 LEU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 292 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 472 GLU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 549 ASP 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 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 756 TYR Chi-restraints excluded: chain I residue 826 ASP 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 1184 THR Chi-restraints excluded: chain I residue 1225 VAL 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 242 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 362 ARG Chi-restraints excluded: chain J residue 429 LEU 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 582 ILE Chi-restraints excluded: chain J residue 644 MET 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 807 LEU Chi-restraints excluded: chain J residue 1023 HIS 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 1353 VAL 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 98 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 130 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 138 optimal weight: 0.3980 chunk 155 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 309 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 41 ASN ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.118231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.088659 restraints weight = 58513.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.089874 restraints weight = 33614.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.090485 restraints weight = 23048.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.090941 restraints weight = 20867.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.091004 restraints weight = 18534.251| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28261 Z= 0.155 Angle : 0.639 14.382 38472 Z= 0.330 Chirality : 0.045 0.280 4396 Planarity : 0.004 0.052 4796 Dihedral : 14.372 179.976 4435 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.35 % Favored : 93.62 % Rotamer: Outliers : 2.80 % Allowed : 15.17 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.14), residues: 3340 helix: 0.67 (0.15), residues: 1161 sheet: -1.32 (0.23), residues: 472 loop : -1.82 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 860 TYR 0.029 0.002 TYR G 185 PHE 0.031 0.001 PHE D 126 TRP 0.032 0.002 TRP J1193 HIS 0.005 0.001 HIS I1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (28254) covalent geometry : angle 0.63758 / 0.33 (38466) hydrogen bonds : bond 0.04090 / 4.67 ( 1127) hydrogen bonds : angle 4.79437 / 5.45 ( 3100) metal coordination : bond 0.00855 / 0.88 ( 7) metal coordination : angle 3.53800 / 6.85 ( 6) *********************** 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 387 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 307 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 29 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7588 (tm-30) REVERT: H 95 LYS cc_start: 0.8456 (tptm) cc_final: 0.8177 (tptm) REVERT: I 194 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9021 (tp) REVERT: I 241 LEU cc_start: 0.8336 (tp) cc_final: 0.7786 (tt) REVERT: I 247 ARG cc_start: 0.7966 (tpp-160) cc_final: 0.6709 (ttp-110) REVERT: I 285 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8526 (mp) REVERT: I 434 ASP cc_start: 0.8375 (p0) cc_final: 0.7991 (p0) REVERT: I 549 ASP cc_start: 0.7791 (t0) cc_final: 0.7443 (m-30) REVERT: I 704 MET cc_start: 0.8335 (tpp) cc_final: 0.8116 (tpp) REVERT: I 756 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.8173 (m-10) REVERT: I 914 LYS cc_start: 0.5890 (ttpt) cc_final: 0.5365 (tptt) REVERT: I 930 ASP cc_start: 0.7517 (t70) cc_final: 0.7127 (t0) REVERT: I 1109 ILE cc_start: 0.9128 (tp) cc_final: 0.8918 (tp) REVERT: I 1114 GLU cc_start: 0.8139 (tt0) cc_final: 0.7830 (tt0) REVERT: I 1229 TYR cc_start: 0.8949 (m-80) cc_final: 0.8546 (m-80) REVERT: I 1321 GLU cc_start: 0.7869 (tp30) cc_final: 0.7523 (tp30) REVERT: J 312 ARG cc_start: 0.8216 (mmp80) cc_final: 0.7713 (mmp-170) REVERT: J 582 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9158 (tp) REVERT: J 759 ILE cc_start: 0.9272 (mm) cc_final: 0.8944 (mt) REVERT: J 918 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8916 (pt) REVERT: J 1244 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7846 (mm110) REVERT: J 1349 GLU cc_start: 0.7864 (mp0) cc_final: 0.7479 (mt-10) REVERT: K 65 ASP cc_start: 0.8138 (m-30) cc_final: 0.7751 (m-30) REVERT: K 79 GLU cc_start: 0.5479 (tm-30) cc_final: 0.5060 (mm-30) REVERT: D 42 LYS cc_start: 0.8341 (mtpt) cc_final: 0.8038 (tptt) REVERT: D 111 TYR cc_start: 0.5048 (m-80) cc_final: 0.4614 (m-80) REVERT: D 115 LYS cc_start: 0.8367 (mttt) cc_final: 0.7872 (ttmt) REVERT: D 158 GLU cc_start: 0.5663 (pm20) cc_final: 0.5431 (pm20) outliers start: 80 outliers final: 72 residues processed: 363 average time/residue: 0.1816 time to fit residues: 106.8083 Evaluate side-chains 365 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 288 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 70 THR 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 157 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 292 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 424 ASP Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 499 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 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 756 TYR Chi-restraints excluded: chain I residue 826 ASP 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 1160 ASP Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1225 VAL 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 242 LEU Chi-restraints excluded: chain J residue 249 LEU 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 429 LEU 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 582 ILE 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 740 LEU 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 885 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1023 HIS 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 1353 VAL 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 98 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 130 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 268 optimal weight: 9.9990 chunk 274 optimal weight: 3.9990 chunk 290 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 304 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 319 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1010 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.117225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.087718 restraints weight = 58821.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.088977 restraints weight = 32856.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.089782 restraints weight = 22376.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.090107 restraints weight = 20312.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.090202 restraints weight = 18593.708| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28261 Z= 0.186 Angle : 0.657 14.553 38472 Z= 0.338 Chirality : 0.045 0.268 4396 Planarity : 0.004 0.053 4796 Dihedral : 14.369 179.027 4435 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.65 % Favored : 93.32 % Rotamer: Outliers : 3.15 % Allowed : 15.17 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.14), residues: 3340 helix: 0.69 (0.15), residues: 1162 sheet: -1.31 (0.23), residues: 471 loop : -1.80 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 23 TYR 0.027 0.002 TYR G 185 PHE 0.025 0.001 PHE D 126 TRP 0.020 0.002 TRP J1193 HIS 0.005 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (28254) covalent geometry : angle 0.65467 / 0.34 (38466) hydrogen bonds : bond 0.04173 / 4.78 ( 1127) hydrogen bonds : angle 4.81102 / 5.45 ( 3100) metal coordination : bond 0.01157 / 1.25 ( 7) metal coordination : angle 4.24787 / 8.43 ( 6) *********************** 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 388 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 298 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 29 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7551 (tm-30) REVERT: H 95 LYS cc_start: 0.8386 (tptm) cc_final: 0.8093 (tptm) REVERT: I 241 LEU cc_start: 0.8344 (tp) cc_final: 0.7781 (tt) REVERT: I 247 ARG cc_start: 0.7888 (tpp-160) cc_final: 0.6688 (ttp-110) REVERT: I 285 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8512 (mp) REVERT: I 319 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7322 (mp) REVERT: I 434 ASP cc_start: 0.8416 (p0) cc_final: 0.8062 (p0) REVERT: I 549 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: I 704 MET cc_start: 0.8403 (tpp) cc_final: 0.8176 (tpp) REVERT: I 756 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.8081 (m-10) REVERT: I 914 LYS cc_start: 0.5892 (ttpt) cc_final: 0.5331 (tptt) REVERT: I 930 ASP cc_start: 0.7608 (t70) cc_final: 0.7202 (t0) REVERT: I 1114 GLU cc_start: 0.8215 (tt0) cc_final: 0.7901 (tt0) REVERT: I 1156 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.5672 (mtm180) REVERT: I 1229 TYR cc_start: 0.8957 (m-80) cc_final: 0.8525 (m-80) REVERT: J 312 ARG cc_start: 0.8201 (mmp80) cc_final: 0.7921 (mmp-170) REVERT: J 582 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9151 (tp) REVERT: J 759 ILE cc_start: 0.9269 (mm) cc_final: 0.8989 (mt) REVERT: J 918 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8948 (pt) REVERT: J 1244 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7848 (mm110) REVERT: J 1349 GLU cc_start: 0.7865 (mp0) cc_final: 0.7553 (mt-10) REVERT: K 65 ASP cc_start: 0.8113 (m-30) cc_final: 0.7742 (m-30) REVERT: K 79 GLU cc_start: 0.5434 (tm-30) cc_final: 0.4961 (mm-30) REVERT: D 32 MET cc_start: 0.7823 (mmm) cc_final: 0.7520 (mmm) REVERT: D 42 LYS cc_start: 0.8338 (mtpt) cc_final: 0.8046 (tptt) REVERT: D 115 LYS cc_start: 0.8377 (mttt) cc_final: 0.7884 (ttmt) REVERT: D 124 GLU cc_start: 0.7327 (pm20) cc_final: 0.6995 (pm20) REVERT: D 158 GLU cc_start: 0.5612 (pm20) cc_final: 0.5374 (pm20) outliers start: 90 outliers final: 75 residues processed: 360 average time/residue: 0.1753 time to fit residues: 102.5091 Evaluate side-chains 366 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 284 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 THR 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 78 ILE 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 I residue 21 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 319 LEU 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 424 ASP Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 756 TYR 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 1138 VAL 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 1225 VAL 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 135 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 249 LEU 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 429 LEU 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 582 ILE 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 697 MET 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 918 ILE Chi-restraints excluded: chain J residue 1023 HIS 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 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 98 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 130 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 6 optimal weight: 7.9990 chunk 249 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 282 optimal weight: 20.0000 chunk 310 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.117791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.089452 restraints weight = 58881.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.089715 restraints weight = 33643.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.090095 restraints weight = 26194.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.090333 restraints weight = 24872.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.090480 restraints weight = 21927.656| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28261 Z= 0.156 Angle : 0.653 14.293 38472 Z= 0.335 Chirality : 0.044 0.264 4396 Planarity : 0.004 0.053 4796 Dihedral : 14.335 178.751 4435 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.41 % Favored : 93.56 % Rotamer: Outliers : 2.97 % Allowed : 15.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.14), residues: 3340 helix: 0.72 (0.15), residues: 1161 sheet: -1.28 (0.24), residues: 462 loop : -1.76 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG I 542 TYR 0.030 0.002 TYR G 185 PHE 0.024 0.001 PHE D 126 TRP 0.023 0.002 TRP J1193 HIS 0.005 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (28254) covalent geometry : angle 0.65232 / 0.33 (38466) hydrogen bonds : bond 0.04077 / 4.65 ( 1127) hydrogen bonds : angle 4.74867 / 5.38 ( 3100) metal coordination : bond 0.00711 / 0.78 ( 7) metal coordination : angle 3.10288 / 6.17 ( 6) ********************** 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 388 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 303 time to evaluate : 1.098 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: H 29 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7502 (tm-30) REVERT: H 145 LYS cc_start: 0.8624 (tttt) cc_final: 0.8378 (tptm) REVERT: I 241 LEU cc_start: 0.8236 (tp) cc_final: 0.7710 (tt) REVERT: I 247 ARG cc_start: 0.7843 (tpp-160) cc_final: 0.6633 (ttp-110) REVERT: I 285 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8528 (mp) REVERT: I 434 ASP cc_start: 0.8466 (p0) cc_final: 0.8112 (p0) REVERT: I 490 GLN cc_start: 0.7976 (pm20) cc_final: 0.7615 (mm-40) REVERT: I 549 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7341 (m-30) REVERT: I 704 MET cc_start: 0.8387 (tpp) cc_final: 0.8177 (tpp) REVERT: I 756 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.8021 (m-10) REVERT: I 914 LYS cc_start: 0.5921 (ttpt) cc_final: 0.5373 (tptt) REVERT: I 930 ASP cc_start: 0.7554 (t70) cc_final: 0.7185 (t0) REVERT: I 1114 GLU cc_start: 0.8208 (tt0) cc_final: 0.7935 (tt0) REVERT: I 1156 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.5699 (mtm180) REVERT: I 1229 TYR cc_start: 0.8943 (m-80) cc_final: 0.8523 (m-80) REVERT: J 312 ARG cc_start: 0.8221 (mmp80) cc_final: 0.7800 (mmp-170) REVERT: J 582 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9150 (tp) REVERT: J 759 ILE cc_start: 0.9247 (mm) cc_final: 0.8982 (mt) REVERT: J 1244 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7808 (mm110) REVERT: J 1349 GLU cc_start: 0.7824 (mp0) cc_final: 0.7501 (mt-10) REVERT: K 65 ASP cc_start: 0.7953 (m-30) cc_final: 0.7687 (m-30) REVERT: K 79 GLU cc_start: 0.5761 (tm-30) cc_final: 0.5281 (mm-30) REVERT: D 32 MET cc_start: 0.7873 (mmm) cc_final: 0.7526 (mmm) REVERT: D 42 LYS cc_start: 0.8348 (mtpt) cc_final: 0.8057 (tptt) REVERT: D 100 LYS cc_start: 0.5979 (mttm) cc_final: 0.5737 (mttm) REVERT: D 115 LYS cc_start: 0.8373 (mttt) cc_final: 0.7879 (ttmt) REVERT: D 124 GLU cc_start: 0.7339 (pm20) cc_final: 0.7055 (pm20) REVERT: D 158 GLU cc_start: 0.5575 (pm20) cc_final: 0.5336 (pm20) outliers start: 85 outliers final: 71 residues processed: 365 average time/residue: 0.1807 time to fit residues: 106.7830 Evaluate side-chains 363 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 287 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 133 LEU 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 78 ILE Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 756 TYR 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 1138 VAL 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 1225 VAL 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 221 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 249 LEU 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 429 LEU 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 582 ILE 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 1023 HIS 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 1353 VAL 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 98 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 130 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 70 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 264 optimal weight: 8.9990 chunk 168 optimal weight: 0.4980 chunk 243 optimal weight: 2.9990 chunk 256 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 199 optimal weight: 0.0020 chunk 188 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 41 ASN H 127 GLN ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.118882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.090735 restraints weight = 58355.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.090930 restraints weight = 34440.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.091710 restraints weight = 25069.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.091968 restraints weight = 22457.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.092037 restraints weight = 20867.626| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28261 Z= 0.127 Angle : 0.636 13.988 38472 Z= 0.326 Chirality : 0.044 0.256 4396 Planarity : 0.004 0.056 4796 Dihedral : 14.277 178.494 4435 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.20 % Favored : 93.77 % Rotamer: Outliers : 2.80 % Allowed : 15.70 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3340 helix: 0.85 (0.16), residues: 1151 sheet: -1.28 (0.23), residues: 469 loop : -1.70 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 860 TYR 0.031 0.001 TYR G 185 PHE 0.020 0.001 PHE D 126 TRP 0.031 0.002 TRP J1193 HIS 0.005 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (28254) covalent geometry : angle 0.63504 / 0.33 (38466) hydrogen bonds : bond 0.03950 / 4.51 ( 1127) hydrogen bonds : angle 4.68943 / 5.31 ( 3100) metal coordination : bond 0.00510 / 0.56 ( 7) metal coordination : angle 2.72841 / 5.41 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4440.14 seconds wall clock time: 77 minutes 39.80 seconds (4659.80 seconds total)