Starting phenix.real_space_refine on Wed Mar 20 02:26:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xug_33468/03_2024/7xug_33468.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xug_33468/03_2024/7xug_33468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xug_33468/03_2024/7xug_33468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xug_33468/03_2024/7xug_33468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xug_33468/03_2024/7xug_33468.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xug_33468/03_2024/7xug_33468.pdb" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 59 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16125 2.51 5 N 4601 2.21 5 O 5132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 97": "OE1" <-> "OE2" Residue "G GLU 181": "OE1" <-> "OE2" Residue "G GLU 206": "OE1" <-> "OE2" Residue "G GLU 215": "OE1" <-> "OE2" Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "H GLU 181": "OE1" <-> "OE2" Residue "H GLU 206": "OE1" <-> "OE2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "I GLU 40": "OE1" <-> "OE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 231": "OE1" <-> "OE2" Residue "I GLU 244": "OE1" <-> "OE2" Residue "I ARG 268": "NH1" <-> "NH2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I GLU 382": "OE1" <-> "OE2" Residue "I GLU 392": "OE1" <-> "OE2" Residue "I GLU 413": "OE1" <-> "OE2" Residue "I GLU 461": "OE1" <-> "OE2" Residue "I ASP 696": "OD1" <-> "OD2" Residue "I GLU 745": "OE1" <-> "OE2" Residue "I GLU 813": "OE1" <-> "OE2" Residue "I GLU 947": "OE1" <-> "OE2" Residue "I GLU 950": "OE1" <-> "OE2" Residue "I GLU 1026": "OE1" <-> "OE2" Residue "I GLU 1083": "OE1" <-> "OE2" Residue "I ASP 1154": "OD1" <-> "OD2" Residue "I GLU 1194": "OE1" <-> "OE2" Residue "I GLU 1219": "OE1" <-> "OE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 207": "OE1" <-> "OE2" Residue "J GLU 235": "OE1" <-> "OE2" Residue "J GLU 295": "OE1" <-> "OE2" Residue "J GLU 386": "OE1" <-> "OE2" Residue "J GLU 418": "OE1" <-> "OE2" Residue "J GLU 497": "OE1" <-> "OE2" Residue "J GLU 523": "OE1" <-> "OE2" Residue "J GLU 652": "OE1" <-> "OE2" Residue "J GLU 656": "OE1" <-> "OE2" Residue "J GLU 658": "OE1" <-> "OE2" Residue "J GLU 660": "OE1" <-> "OE2" Residue "J GLU 714": "OE1" <-> "OE2" Residue "J GLU 765": "OE1" <-> "OE2" Residue "J GLU 833": "OE1" <-> "OE2" Residue "J GLU 866": "OE1" <-> "OE2" Residue "J GLU 874": "OE1" <-> "OE2" Residue "J GLU 1009": "OE1" <-> "OE2" Residue "J GLU 1015": "OE1" <-> "OE2" Residue "J GLU 1215": "OE1" <-> "OE2" Residue "J GLU 1236": "OE1" <-> "OE2" Residue "J GLU 1278": "OE1" <-> "OE2" Residue "J GLU 1281": "OE1" <-> "OE2" Residue "J GLU 1317": "OE1" <-> "OE2" Residue "J PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 42": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26026 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 421 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain breaks: 1 Chain: "B" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 606 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 206 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "G" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1686 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1315, 10372 Classifications: {'peptide': 1315} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1259} Chain breaks: 1 Chain: "J" Number of atoms: 10414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10414 Classifications: {'peptide': 1339} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1283} Chain breaks: 2 Chain: "K" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 631 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15427 SG CYS J 70 53.069 120.026 62.720 1.00 99.60 S ATOM 15441 SG CYS J 72 54.012 123.479 62.554 1.00103.88 S ATOM 15549 SG CYS J 85 51.704 122.159 59.861 1.00103.61 S ATOM 15573 SG CYS J 88 55.120 120.719 59.764 1.00100.15 S ATOM 21261 SG CYS J 814 50.534 53.596 48.938 1.00 63.68 S ATOM 21826 SG CYS J 888 52.909 56.131 50.397 1.00 54.43 S ATOM 21877 SG CYS J 895 50.353 54.594 52.692 1.00 45.78 S ATOM 21898 SG CYS J 898 53.214 52.612 51.518 1.00 48.56 S Time building chain proxies: 13.80, per 1000 atoms: 0.53 Number of scatterers: 26026 At special positions: 0 Unit cell: (149.46, 139.92, 148.4, 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 106 16.00 P 59 15.00 Mg 1 11.99 O 5132 8.00 N 4601 7.00 C 16125 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.33 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb=" ZN J1502 " 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 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " Number of angles added : 12 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5854 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 49 sheets defined 37.1% alpha, 15.9% beta 28 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 8.91 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 4.005A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.845A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) 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 158 Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'G' and resid 230 through 232 No H-bonds generated for 'chain 'G' and resid 230 through 232' Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.747A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.540A pdb=" N LYS H 86 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.816A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE I 39 " --> pdb=" O PHE I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.607A 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 206 through 212 removed outlier: 4.195A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.953A 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 293 removed outlier: 3.788A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.952A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) 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 390 removed outlier: 4.212A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 480 removed outlier: 3.598A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 483 through 487 Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 520 through 528 removed outlier: 3.868A pdb=" N ARG I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 704 through 711 Processing helix chain 'I' and resid 820 through 825 removed outlier: 3.559A pdb=" N GLU I 825 " --> pdb=" O ARG I 821 " (cutoff:3.500A) Processing helix chain 'I' and resid 860 through 865 removed outlier: 3.728A pdb=" N SER I 863 " --> pdb=" O ALA I 860 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS I 864 " --> pdb=" O ALA I 861 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU I 865 " --> pdb=" O LEU I 862 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 860 through 865' Processing helix chain 'I' and resid 942 through 963 Processing helix chain 'I' and resid 966 through 979 Processing helix chain 'I' and resid 986 through 990 removed outlier: 3.646A pdb=" N LEU I 989 " --> pdb=" O ALA I 986 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP I 990 " --> pdb=" O GLU I 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 986 through 990' Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.607A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS I1028 " --> pdb=" O GLU I1024 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA I1031 " --> pdb=" O LYS I1027 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS I1032 " --> pdb=" O LYS I1028 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG I1033 " --> pdb=" O LEU I1029 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG I1034 " --> pdb=" O GLU I1030 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.426A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.573A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1175 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 1282 removed outlier: 3.531A pdb=" N VAL I1275 " --> pdb=" O GLY I1271 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.761A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1322 through 1332 removed outlier: 3.958A pdb=" N LEU I1326 " --> pdb=" O SER I1322 " (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: 3.531A 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 122 through 128 Processing helix chain 'J' and resid 131 through 140 removed outlier: 3.605A pdb=" N ILE J 135 " --> pdb=" O PRO J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 194 through 207 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 removed outlier: 3.503A pdb=" N LEU J 249 " --> pdb=" O PRO J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 263 through 286 removed outlier: 3.545A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.525A pdb=" N VAL J 292 " --> pdb=" O PRO J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 332 Processing helix chain 'J' and resid 336 through 341 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 Processing helix chain 'J' and resid 406 through 416 removed outlier: 4.541A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (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 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 538 Processing helix chain 'J' and resid 574 through 581 Processing helix chain 'J' and resid 588 through 593 removed outlier: 3.666A pdb=" N ASN J 593 " --> pdb=" O SER J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 removed outlier: 3.628A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.588A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.526A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.020A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.610A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.623A pdb=" N GLY J 782 " --> pdb=" O GLY J 778 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.767A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1068 through 1072 Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 removed outlier: 3.533A pdb=" N ILE J1220 " --> pdb=" O ALA J1216 " (cutoff:3.500A) Processing helix chain 'J' and resid 1226 through 1243 removed outlier: 3.505A 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 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1324 removed outlier: 3.695A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1362 through 1373 Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.873A 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 80 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 16 removed outlier: 7.001A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU G 198 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 98 through 105 removed outlier: 3.767A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 91 removed outlier: 3.516A pdb=" N ARG G 91 " --> pdb=" O GLU G 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 153 removed outlier: 3.548A pdb=" N ALA G 175 " --> pdb=" O VAL G 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 16 through 20 removed outlier: 6.344A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 16 through 20 removed outlier: 6.344A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 97 through 104 removed outlier: 7.553A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN H 147 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA H 55 " --> pdb=" O GLN H 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB1, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AB2, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.578A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'I' and resid 66 through 75 removed outlier: 5.344A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'I' and resid 451 through 453 removed outlier: 3.586A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AB8, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB9, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AC1, first strand: chain 'I' and resid 249 through 250 removed outlier: 3.678A pdb=" N GLU I 249 " --> pdb=" O ILE I 269 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.017A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.577A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) 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 580 through 581 Processing sheet with id=AC6, first strand: chain 'I' and resid 634 through 637 Processing sheet with id=AC7, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.565A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET I 768 " --> pdb=" O ASP I 785 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 749 through 751 removed outlier: 6.493A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 757 through 758 removed outlier: 3.562A pdb=" N THR I 757 " --> pdb=" O ILE I 765 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.542A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.361A 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 831 Processing sheet with id=AD3, first strand: chain 'I' and resid 834 through 841 removed outlier: 5.677A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD5, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.665A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AD7, first strand: chain 'J' and resid 103 through 112 removed outlier: 6.649A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 9.739A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 159 through 160 removed outlier: 3.651A pdb=" N VAL J 145 " --> pdb=" O LYS J 179 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS J 179 " --> pdb=" O VAL J 145 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 253 through 254 removed outlier: 4.194A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA J 261 " --> pdb=" O VAL J 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'J' and resid 350 through 357 Processing sheet with id=AE2, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE3, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AE4, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE5, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE6, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.652A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 958 through 961 removed outlier: 6.787A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AE9, first strand: chain 'J' and resid 1024 through 1026 removed outlier: 4.368A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id=AF2, first strand: chain 'J' and resid 1156 through 1157 removed outlier: 3.607A pdb=" N ALA J1157 " --> pdb=" O ASP J1208 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP J1208 " --> pdb=" O ALA J1157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'J' and resid 1162 through 1168 removed outlier: 5.340A pdb=" N ARG J1174 " --> pdb=" O GLY J1166 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU J1168 " --> pdb=" O LYS J1172 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS J1172 " --> pdb=" O GLU J1168 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.218A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) 1015 hydrogen bonds defined for protein. 2838 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 13.66 Time building geometry restraints manager: 11.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7318 1.33 - 1.45: 4423 1.45 - 1.57: 14494 1.57 - 1.70: 115 1.70 - 1.82: 184 Bond restraints: 26534 Sorted by residual: bond pdb=" C ILE I 145 " pdb=" N VAL I 146 " ideal model delta sigma weight residual 1.334 1.297 0.036 1.24e-02 6.50e+03 8.49e+00 bond pdb=" CA SER J 590 " pdb=" C SER J 590 " ideal model delta sigma weight residual 1.522 1.483 0.039 1.38e-02 5.25e+03 8.03e+00 bond pdb=" N VAL I1155 " pdb=" CA VAL I1155 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.83e+00 bond pdb=" N THR I 754 " pdb=" CA THR I 754 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.33e-02 5.65e+03 6.55e+00 bond pdb=" C LYS I 17 " pdb=" N ARG I 18 " ideal model delta sigma weight residual 1.328 1.287 0.041 1.67e-02 3.59e+03 6.03e+00 ... (remaining 26529 not shown) Histogram of bond angle deviations from ideal: 97.23 - 104.59: 606 104.59 - 111.95: 12782 111.95 - 119.32: 9667 119.32 - 126.68: 12634 126.68 - 134.04: 402 Bond angle restraints: 36091 Sorted by residual: angle pdb=" C VAL I1103 " pdb=" CA VAL I1103 " pdb=" CB VAL I1103 " ideal model delta sigma weight residual 114.00 108.62 5.38 1.31e+00 5.83e-01 1.69e+01 angle pdb=" CA ARG I 201 " pdb=" CB ARG I 201 " pdb=" CG ARG I 201 " ideal model delta sigma weight residual 114.10 121.89 -7.79 2.00e+00 2.50e-01 1.52e+01 angle pdb=" CA TYR I1018 " pdb=" CB TYR I1018 " pdb=" CG TYR I1018 " ideal model delta sigma weight residual 113.90 120.48 -6.58 1.80e+00 3.09e-01 1.34e+01 angle pdb=" CA TYR I 756 " pdb=" C TYR I 756 " pdb=" O TYR I 756 " ideal model delta sigma weight residual 122.45 117.71 4.74 1.30e+00 5.92e-01 1.33e+01 angle pdb=" CB ARG G 170 " pdb=" CG ARG G 170 " pdb=" CD ARG G 170 " ideal model delta sigma weight residual 111.30 118.82 -7.52 2.30e+00 1.89e-01 1.07e+01 ... (remaining 36086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.71: 15513 30.71 - 61.42: 669 61.42 - 92.12: 62 92.12 - 122.83: 0 122.83 - 153.54: 1 Dihedral angle restraints: 16245 sinusoidal: 7144 harmonic: 9101 Sorted by residual: dihedral pdb=" CA SER I1295 " pdb=" C SER I1295 " pdb=" N ASP I1296 " pdb=" CA ASP I1296 " ideal model delta harmonic sigma weight residual -180.00 -151.51 -28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ASN I 519 " pdb=" C ASN I 519 " pdb=" N PRO I 520 " pdb=" CA PRO I 520 " ideal model delta harmonic sigma weight residual 180.00 153.31 26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA PRO J 502 " pdb=" C PRO J 502 " pdb=" N SER J 503 " pdb=" CA SER J 503 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 16242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2703 0.045 - 0.089: 1064 0.089 - 0.134: 301 0.134 - 0.179: 52 0.179 - 0.223: 9 Chirality restraints: 4129 Sorted by residual: chirality pdb=" CB VAL J 415 " pdb=" CA VAL J 415 " pdb=" CG1 VAL J 415 " pdb=" CG2 VAL J 415 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB ILE I 765 " pdb=" CA ILE I 765 " pdb=" CG1 ILE I 765 " pdb=" CG2 ILE I 765 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA GLN J 504 " pdb=" N GLN J 504 " pdb=" C GLN J 504 " pdb=" CB GLN J 504 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 4126 not shown) Planarity restraints: 4519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I 519 " 0.046 5.00e-02 4.00e+02 6.99e-02 7.81e+00 pdb=" N PRO I 520 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO I 520 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO I 520 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 189 " 0.044 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO I 190 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO I 190 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO I 190 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR I1018 " 0.026 2.00e-02 2.50e+03 1.72e-02 5.91e+00 pdb=" CG TYR I1018 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR I1018 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR I1018 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR I1018 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR I1018 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR I1018 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR I1018 " 0.001 2.00e-02 2.50e+03 ... (remaining 4516 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 193 2.53 - 3.12: 21054 3.12 - 3.72: 38463 3.72 - 4.31: 53490 4.31 - 4.90: 90717 Nonbonded interactions: 203917 Sorted by model distance: nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1503 " model vdw 1.938 2.170 nonbonded pdb=" OG1 THR I 91 " pdb=" O ILE I 138 " model vdw 1.958 2.440 nonbonded pdb=" OD2 ASP G 62 " pdb=" OG SER G 141 " model vdw 1.988 2.440 nonbonded pdb=" OG1 THR I 216 " pdb=" OE1 GLN I 219 " model vdw 1.992 2.440 nonbonded pdb=" OG SER J1318 " pdb=" OD1 ASP J1342 " model vdw 2.038 2.440 ... (remaining 203912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 7 through 158 or resid 169 through 232)) selection = (chain 'H' and (resid 7 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 0.020 Extract box with map and model: 6.760 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 81.970 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 26534 Z= 0.577 Angle : 0.869 8.144 36091 Z= 0.485 Chirality : 0.051 0.223 4129 Planarity : 0.005 0.070 4519 Dihedral : 16.496 153.540 10391 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.91 % Favored : 91.02 % Rotamer: Outliers : 0.11 % Allowed : 0.45 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.14), residues: 3152 helix: -0.14 (0.15), residues: 1077 sheet: -1.95 (0.23), residues: 413 loop : -2.28 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J1193 HIS 0.009 0.002 HIS J 80 PHE 0.027 0.003 PHE J 17 TYR 0.040 0.003 TYR I1018 ARG 0.023 0.001 ARG I1033 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 473 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 347 ILE cc_start: 0.8271 (mm) cc_final: 0.8032 (mm) REVERT: I 369 MET cc_start: 0.8088 (tmm) cc_final: 0.7869 (tmm) REVERT: I 371 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7913 (mtm-85) REVERT: I 514 PHE cc_start: 0.8741 (t80) cc_final: 0.8374 (t80) REVERT: I 524 ILE cc_start: 0.9190 (tp) cc_final: 0.8963 (tp) REVERT: I 588 GLU cc_start: 0.7930 (mp0) cc_final: 0.7720 (mp0) REVERT: I 628 HIS cc_start: 0.7380 (m-70) cc_final: 0.7133 (m-70) REVERT: I 1171 ARG cc_start: 0.7696 (ttp-170) cc_final: 0.7453 (ttp-170) REVERT: I 1188 ASP cc_start: 0.8836 (p0) cc_final: 0.8574 (p0) REVERT: J 81 ARG cc_start: 0.8172 (ttp80) cc_final: 0.7964 (ptm-80) REVERT: J 136 GLU cc_start: 0.8231 (pp20) cc_final: 0.7979 (pp20) REVERT: J 298 MET cc_start: 0.7176 (ttt) cc_final: 0.6939 (ttm) REVERT: J 679 TYR cc_start: 0.7463 (t80) cc_final: 0.7160 (t80) REVERT: J 788 LEU cc_start: 0.8878 (mt) cc_final: 0.8288 (tt) REVERT: J 811 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7199 (mt-10) REVERT: J 862 THR cc_start: 0.8489 (p) cc_final: 0.8276 (p) REVERT: J 983 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8118 (mptt) REVERT: K 56 GLU cc_start: 0.7830 (pt0) cc_final: 0.7534 (pt0) outliers start: 3 outliers final: 0 residues processed: 475 average time/residue: 0.4243 time to fit residues: 305.6157 Evaluate side-chains 395 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 0.6980 chunk 242 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 163 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 250 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 152 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 chunk 290 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS H 137 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1268 GLN J 232 ASN J 489 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26534 Z= 0.216 Angle : 0.640 9.619 36091 Z= 0.333 Chirality : 0.044 0.230 4129 Planarity : 0.005 0.060 4519 Dihedral : 13.365 151.541 4202 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.71 % Favored : 94.26 % Rotamer: Outliers : 1.11 % Allowed : 8.72 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3152 helix: 0.72 (0.16), residues: 1078 sheet: -1.39 (0.25), residues: 409 loop : -2.07 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J1020 HIS 0.007 0.001 HIS G 23 PHE 0.016 0.001 PHE I 337 TYR 0.025 0.001 TYR I1018 ARG 0.008 0.000 ARG G 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 457 time to evaluate : 3.369 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: G 10 LYS cc_start: 0.8868 (mtmm) cc_final: 0.8603 (mppt) REVERT: H 51 MET cc_start: 0.8063 (tpp) cc_final: 0.7776 (ttm) REVERT: H 75 GLN cc_start: 0.7941 (tt0) cc_final: 0.7572 (tt0) REVERT: I 14 ASP cc_start: 0.8565 (t0) cc_final: 0.8321 (t0) REVERT: I 299 LYS cc_start: 0.7568 (tptp) cc_final: 0.7304 (tptp) REVERT: I 369 MET cc_start: 0.8105 (tmm) cc_final: 0.7805 (tmm) REVERT: I 510 GLN cc_start: 0.8092 (mt0) cc_final: 0.7844 (tt0) REVERT: I 628 HIS cc_start: 0.7209 (m-70) cc_final: 0.6892 (m-70) REVERT: I 1211 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7373 (ttm110) REVERT: I 1304 MET cc_start: 0.8707 (tpp) cc_final: 0.8447 (tpp) REVERT: J 136 GLU cc_start: 0.8106 (pp20) cc_final: 0.7899 (pp20) REVERT: J 140 TYR cc_start: 0.7582 (m-80) cc_final: 0.6835 (m-80) REVERT: J 602 SER cc_start: 0.8769 (t) cc_final: 0.8305 (p) REVERT: J 625 MET cc_start: 0.8265 (ttp) cc_final: 0.8035 (ttp) REVERT: J 788 LEU cc_start: 0.8639 (mt) cc_final: 0.7952 (tt) REVERT: J 918 ILE cc_start: 0.8916 (pt) cc_final: 0.8486 (mt) REVERT: J 1241 TYR cc_start: 0.8345 (m-80) cc_final: 0.8115 (m-80) REVERT: J 1289 ASN cc_start: 0.7038 (p0) cc_final: 0.6463 (m110) REVERT: J 1290 ARG cc_start: 0.7620 (ttp-110) cc_final: 0.7107 (ttp-110) REVERT: K 11 GLU cc_start: 0.7800 (pp20) cc_final: 0.7589 (pp20) REVERT: K 72 GLN cc_start: 0.7817 (tp40) cc_final: 0.7589 (tp-100) outliers start: 30 outliers final: 21 residues processed: 465 average time/residue: 0.3934 time to fit residues: 283.7212 Evaluate side-chains 410 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 389 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 197 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 291 optimal weight: 0.7980 chunk 314 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 288 optimal weight: 0.0040 chunk 99 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN I 955 GLN J 702 GLN J 792 ASN ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26534 Z= 0.225 Angle : 0.606 8.651 36091 Z= 0.314 Chirality : 0.043 0.212 4129 Planarity : 0.004 0.051 4519 Dihedral : 13.272 151.370 4202 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.00 % Favored : 93.97 % Rotamer: Outliers : 1.97 % Allowed : 12.02 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 3152 helix: 1.03 (0.16), residues: 1078 sheet: -1.25 (0.24), residues: 421 loop : -1.93 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J1020 HIS 0.007 0.001 HIS I 628 PHE 0.024 0.001 PHE I 337 TYR 0.019 0.001 TYR I1018 ARG 0.010 0.000 ARG G 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 419 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.8858 (mtmm) cc_final: 0.8601 (mppt) REVERT: G 77 ASP cc_start: 0.7808 (m-30) cc_final: 0.7309 (m-30) REVERT: G 200 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8240 (ttpt) REVERT: H 51 MET cc_start: 0.8097 (tpp) cc_final: 0.7803 (ttm) REVERT: I 369 MET cc_start: 0.8123 (tmm) cc_final: 0.7756 (tmm) REVERT: I 370 MET cc_start: 0.8062 (mmm) cc_final: 0.7825 (mtm) REVERT: I 490 GLN cc_start: 0.8320 (pp30) cc_final: 0.7870 (pp30) REVERT: I 628 HIS cc_start: 0.7150 (m-70) cc_final: 0.6752 (m-70) REVERT: I 696 ASP cc_start: 0.7275 (t70) cc_final: 0.7053 (t70) REVERT: I 768 MET cc_start: 0.6987 (mmm) cc_final: 0.6677 (mmm) REVERT: I 1033 ARG cc_start: 0.8183 (tpp80) cc_final: 0.7979 (tpp80) REVERT: I 1095 ASP cc_start: 0.8822 (t0) cc_final: 0.8601 (t0) REVERT: I 1211 ARG cc_start: 0.7654 (ttm-80) cc_final: 0.7293 (ttm110) REVERT: I 1304 MET cc_start: 0.8752 (tpp) cc_final: 0.8532 (tpp) REVERT: J 68 TYR cc_start: 0.7587 (m-80) cc_final: 0.6964 (m-80) REVERT: J 136 GLU cc_start: 0.8067 (pp20) cc_final: 0.7843 (pp20) REVERT: J 788 LEU cc_start: 0.8422 (mt) cc_final: 0.7811 (tt) REVERT: J 811 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6630 (mt-10) REVERT: J 1289 ASN cc_start: 0.6779 (p0) cc_final: 0.6269 (m-40) REVERT: J 1290 ARG cc_start: 0.7497 (ttp-110) cc_final: 0.7144 (ttp-110) REVERT: K 11 GLU cc_start: 0.7877 (pp20) cc_final: 0.7671 (pp20) REVERT: K 75 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8126 (tm-30) outliers start: 53 outliers final: 38 residues processed: 450 average time/residue: 0.4014 time to fit residues: 282.1587 Evaluate side-chains 422 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 384 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 366 ILE Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 287 optimal weight: 30.0000 chunk 218 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 138 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 chunk 292 optimal weight: 20.0000 chunk 309 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 276 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 702 GLN ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN K 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 26534 Z= 0.315 Angle : 0.628 9.135 36091 Z= 0.324 Chirality : 0.044 0.269 4129 Planarity : 0.005 0.067 4519 Dihedral : 13.284 151.651 4202 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.35 % Favored : 93.62 % Rotamer: Outliers : 2.67 % Allowed : 13.87 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.15), residues: 3152 helix: 1.04 (0.16), residues: 1083 sheet: -1.25 (0.24), residues: 434 loop : -1.89 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J1020 HIS 0.008 0.001 HIS H 132 PHE 0.016 0.001 PHE I 385 TYR 0.026 0.001 TYR I 5 ARG 0.006 0.000 ARG K 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 403 time to evaluate : 2.811 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 10 LYS cc_start: 0.8848 (mtmm) cc_final: 0.8609 (mppt) REVERT: H 51 MET cc_start: 0.8134 (tpp) cc_final: 0.7843 (ttm) REVERT: H 104 LYS cc_start: 0.8457 (tptp) cc_final: 0.8255 (tptp) REVERT: H 226 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7338 (tm-30) REVERT: I 202 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7863 (ttp-110) REVERT: I 369 MET cc_start: 0.8147 (tmm) cc_final: 0.7861 (tmm) REVERT: I 490 GLN cc_start: 0.8528 (pp30) cc_final: 0.7919 (pp30) REVERT: I 1095 ASP cc_start: 0.8863 (t0) cc_final: 0.8597 (t0) REVERT: I 1211 ARG cc_start: 0.7626 (ttm-80) cc_final: 0.7247 (ttm110) REVERT: J 698 MET cc_start: 0.8765 (tpp) cc_final: 0.8564 (mmm) REVERT: J 788 LEU cc_start: 0.8481 (mt) cc_final: 0.7813 (tt) REVERT: J 811 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6629 (mt-10) REVERT: J 1279 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: K 72 GLN cc_start: 0.8103 (tp40) cc_final: 0.7401 (tp-100) REVERT: K 75 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8155 (tm-30) outliers start: 72 outliers final: 50 residues processed: 440 average time/residue: 0.4030 time to fit residues: 276.3884 Evaluate side-chains 433 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 382 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 777 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 411 ILE Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1279 GLN Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 257 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 230 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 chunk 213 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 277 optimal weight: 0.0030 chunk 78 optimal weight: 8.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 702 GLN ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26534 Z= 0.227 Angle : 0.597 9.271 36091 Z= 0.306 Chirality : 0.042 0.172 4129 Planarity : 0.004 0.050 4519 Dihedral : 13.245 151.482 4202 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.93 % Favored : 94.04 % Rotamer: Outliers : 2.63 % Allowed : 16.14 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3152 helix: 1.20 (0.16), residues: 1082 sheet: -1.04 (0.25), residues: 433 loop : -1.81 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J1020 HIS 0.005 0.001 HIS J 104 PHE 0.016 0.001 PHE I 80 TYR 0.017 0.001 TYR G 185 ARG 0.014 0.000 ARG J 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 408 time to evaluate : 2.684 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 76 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: H 18 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7560 (mm-40) REVERT: H 51 MET cc_start: 0.8135 (tpp) cc_final: 0.7811 (ttm) REVERT: H 104 LYS cc_start: 0.8493 (tptp) cc_final: 0.8104 (tptm) REVERT: H 226 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7364 (tm-30) REVERT: I 202 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7862 (ttp-110) REVERT: I 369 MET cc_start: 0.8150 (tmm) cc_final: 0.7901 (tmm) REVERT: I 371 ARG cc_start: 0.7820 (mtm-85) cc_final: 0.7589 (mtm-85) REVERT: I 490 GLN cc_start: 0.8502 (pp30) cc_final: 0.7734 (tm-30) REVERT: I 741 MET cc_start: 0.6760 (ptm) cc_final: 0.6556 (ptp) REVERT: I 1095 ASP cc_start: 0.8830 (t0) cc_final: 0.8566 (t0) REVERT: I 1211 ARG cc_start: 0.7675 (ttm-80) cc_final: 0.7267 (ttm110) REVERT: J 136 GLU cc_start: 0.8005 (pp20) cc_final: 0.7787 (pp20) REVERT: J 235 GLU cc_start: 0.6987 (pm20) cc_final: 0.6706 (pm20) REVERT: J 788 LEU cc_start: 0.8380 (mt) cc_final: 0.7746 (tt) REVERT: J 811 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6681 (mt-10) REVERT: J 1279 GLN cc_start: 0.8158 (tt0) cc_final: 0.7844 (tm-30) REVERT: J 1289 ASN cc_start: 0.6971 (p0) cc_final: 0.6335 (m110) REVERT: J 1290 ARG cc_start: 0.7513 (ttp-110) cc_final: 0.7260 (ttp-110) REVERT: K 62 GLN cc_start: 0.7763 (tp40) cc_final: 0.7451 (mm-40) REVERT: K 75 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8149 (tm-30) outliers start: 71 outliers final: 60 residues processed: 449 average time/residue: 0.4025 time to fit residues: 281.6759 Evaluate side-chains 448 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 387 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1128 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 0.4980 chunk 278 optimal weight: 0.0270 chunk 61 optimal weight: 0.7980 chunk 181 optimal weight: 0.6980 chunk 76 optimal weight: 20.0000 chunk 309 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 102 optimal weight: 0.3980 chunk 162 optimal weight: 2.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN J 702 GLN ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26534 Z= 0.163 Angle : 0.575 10.349 36091 Z= 0.295 Chirality : 0.042 0.199 4129 Planarity : 0.004 0.048 4519 Dihedral : 13.174 151.393 4202 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.11 % Favored : 94.86 % Rotamer: Outliers : 2.23 % Allowed : 17.32 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.15), residues: 3152 helix: 1.37 (0.16), residues: 1074 sheet: -0.90 (0.26), residues: 405 loop : -1.69 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J1193 HIS 0.004 0.001 HIS H 66 PHE 0.013 0.001 PHE J1199 TYR 0.017 0.001 TYR G 185 ARG 0.006 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 430 time to evaluate : 3.012 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: G 76 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: H 18 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7567 (mm-40) REVERT: H 226 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7385 (tm-30) REVERT: I 202 ARG cc_start: 0.8147 (ttp80) cc_final: 0.7924 (ttp80) REVERT: I 369 MET cc_start: 0.8088 (tmm) cc_final: 0.7832 (tmm) REVERT: I 371 ARG cc_start: 0.7738 (mtm-85) cc_final: 0.7478 (mtm-85) REVERT: I 490 GLN cc_start: 0.8465 (pp30) cc_final: 0.7736 (tm-30) REVERT: I 524 ILE cc_start: 0.8813 (tp) cc_final: 0.8569 (tp) REVERT: I 1095 ASP cc_start: 0.8798 (t0) cc_final: 0.8565 (t0) REVERT: I 1211 ARG cc_start: 0.7678 (ttm-80) cc_final: 0.7218 (ttm110) REVERT: I 1304 MET cc_start: 0.8750 (tpp) cc_final: 0.8530 (tpp) REVERT: J 136 GLU cc_start: 0.7983 (pp20) cc_final: 0.7763 (pp20) REVERT: J 172 PHE cc_start: 0.6616 (m-80) cc_final: 0.5850 (m-80) REVERT: J 235 GLU cc_start: 0.6957 (pm20) cc_final: 0.6651 (pm20) REVERT: J 327 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8197 (mm) REVERT: J 602 SER cc_start: 0.8793 (t) cc_final: 0.8288 (p) REVERT: J 698 MET cc_start: 0.8508 (tpt) cc_final: 0.8301 (tpp) REVERT: J 788 LEU cc_start: 0.8234 (mt) cc_final: 0.7608 (tt) REVERT: J 1279 GLN cc_start: 0.8005 (tt0) cc_final: 0.7787 (tm-30) REVERT: J 1289 ASN cc_start: 0.6763 (p0) cc_final: 0.6363 (m110) REVERT: J 1290 ARG cc_start: 0.7497 (ttp-110) cc_final: 0.7214 (ttp-110) REVERT: K 62 GLN cc_start: 0.7776 (tp40) cc_final: 0.7568 (mm-40) outliers start: 60 outliers final: 45 residues processed: 465 average time/residue: 0.3885 time to fit residues: 280.3619 Evaluate side-chains 442 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 395 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 260 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 308 optimal weight: 0.3980 chunk 193 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 702 GLN ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26534 Z= 0.272 Angle : 0.616 10.993 36091 Z= 0.315 Chirality : 0.043 0.274 4129 Planarity : 0.004 0.046 4519 Dihedral : 13.190 151.394 4202 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.19 % Favored : 93.78 % Rotamer: Outliers : 2.93 % Allowed : 17.51 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.15), residues: 3152 helix: 1.28 (0.16), residues: 1087 sheet: -0.98 (0.25), residues: 426 loop : -1.67 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP J1193 HIS 0.006 0.001 HIS J 777 PHE 0.015 0.001 PHE I 385 TYR 0.018 0.001 TYR H 177 ARG 0.010 0.000 ARG I 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 406 time to evaluate : 2.778 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 76 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: H 18 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7604 (mm-40) REVERT: H 51 MET cc_start: 0.7881 (tpp) cc_final: 0.7656 (ttm) REVERT: H 226 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7401 (tm-30) REVERT: I 510 GLN cc_start: 0.8107 (mt0) cc_final: 0.7826 (tt0) REVERT: I 1095 ASP cc_start: 0.8849 (t0) cc_final: 0.8567 (t0) REVERT: I 1211 ARG cc_start: 0.7668 (ttm-80) cc_final: 0.7288 (ttm110) REVERT: J 136 GLU cc_start: 0.7997 (pp20) cc_final: 0.7794 (pp20) REVERT: J 172 PHE cc_start: 0.6612 (m-80) cc_final: 0.5844 (m-80) REVERT: J 235 GLU cc_start: 0.6983 (pm20) cc_final: 0.6680 (pm20) REVERT: J 327 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8229 (mm) REVERT: J 698 MET cc_start: 0.8538 (tpt) cc_final: 0.8337 (tpp) REVERT: J 788 LEU cc_start: 0.8389 (mt) cc_final: 0.7679 (tt) REVERT: J 1279 GLN cc_start: 0.8045 (tt0) cc_final: 0.7828 (tm-30) REVERT: J 1289 ASN cc_start: 0.7008 (p0) cc_final: 0.6498 (m110) REVERT: J 1290 ARG cc_start: 0.7516 (ttp-110) cc_final: 0.7279 (ttp-110) REVERT: K 69 ARG cc_start: 0.6973 (ttp80) cc_final: 0.6467 (ttp80) REVERT: K 72 GLN cc_start: 0.7908 (tp40) cc_final: 0.7601 (tp40) outliers start: 79 outliers final: 64 residues processed: 451 average time/residue: 0.4165 time to fit residues: 295.5778 Evaluate side-chains 457 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 391 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1128 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 190 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 210 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 242 optimal weight: 0.5980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 702 GLN ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26534 Z= 0.296 Angle : 0.642 11.623 36091 Z= 0.327 Chirality : 0.043 0.252 4129 Planarity : 0.004 0.046 4519 Dihedral : 13.226 151.036 4202 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.04 % Allowed : 17.99 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3152 helix: 1.20 (0.16), residues: 1085 sheet: -1.02 (0.25), residues: 431 loop : -1.66 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J1193 HIS 0.006 0.001 HIS J 777 PHE 0.013 0.001 PHE I 405 TYR 0.028 0.001 TYR I 70 ARG 0.010 0.000 ARG I 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 398 time to evaluate : 2.918 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 76 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: H 18 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7614 (mm-40) REVERT: H 51 MET cc_start: 0.7941 (tpp) cc_final: 0.7730 (ttm) REVERT: H 226 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7428 (tm-30) REVERT: I 70 TYR cc_start: 0.8321 (t80) cc_final: 0.7988 (t80) REVERT: I 490 GLN cc_start: 0.8470 (pp30) cc_final: 0.7920 (pp30) REVERT: I 542 ARG cc_start: 0.7249 (ttt180) cc_final: 0.6873 (ttt180) REVERT: I 1095 ASP cc_start: 0.8857 (t0) cc_final: 0.8543 (t0) REVERT: I 1211 ARG cc_start: 0.7667 (ttm-80) cc_final: 0.7317 (ttm110) REVERT: J 136 GLU cc_start: 0.8086 (pp20) cc_final: 0.7843 (pp20) REVERT: J 140 TYR cc_start: 0.7543 (m-80) cc_final: 0.7258 (m-80) REVERT: J 172 PHE cc_start: 0.6611 (m-80) cc_final: 0.5847 (m-80) REVERT: J 235 GLU cc_start: 0.7016 (pm20) cc_final: 0.6700 (pm20) REVERT: J 327 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8244 (mm) REVERT: J 788 LEU cc_start: 0.8483 (mt) cc_final: 0.7793 (tt) REVERT: J 1279 GLN cc_start: 0.8030 (tt0) cc_final: 0.7783 (tm-30) REVERT: J 1289 ASN cc_start: 0.6917 (p0) cc_final: 0.6339 (m110) outliers start: 82 outliers final: 71 residues processed: 446 average time/residue: 0.3922 time to fit residues: 271.3703 Evaluate side-chains 454 residues out of total 2699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 381 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 123 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1128 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1160 ASP Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 411 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.3471 > 50: distance: 82 - 138: 17.936 distance: 104 - 108: 11.403 distance: 108 - 109: 6.356 distance: 109 - 110: 12.234 distance: 109 - 112: 9.505 distance: 110 - 111: 14.592 distance: 110 - 117: 25.227 distance: 112 - 113: 8.533 distance: 113 - 114: 8.278 distance: 114 - 115: 5.399 distance: 114 - 116: 4.887 distance: 117 - 118: 14.437 distance: 118 - 119: 11.416 distance: 118 - 121: 20.710 distance: 119 - 120: 16.258 distance: 119 - 125: 15.355 distance: 121 - 122: 8.523 distance: 122 - 123: 8.192 distance: 122 - 124: 16.518 distance: 125 - 126: 8.478 distance: 126 - 127: 14.689 distance: 126 - 129: 22.368 distance: 127 - 128: 11.057 distance: 127 - 132: 6.049 distance: 129 - 130: 19.260 distance: 129 - 131: 16.538 distance: 132 - 133: 10.469 distance: 133 - 134: 13.774 distance: 133 - 136: 33.008 distance: 134 - 135: 24.992 distance: 134 - 138: 17.791 distance: 136 - 137: 7.183 distance: 138 - 139: 17.064 distance: 139 - 140: 14.264 distance: 139 - 142: 14.209 distance: 140 - 141: 13.969 distance: 140 - 146: 15.147 distance: 142 - 143: 16.863 distance: 142 - 144: 16.657 distance: 143 - 145: 23.633 distance: 146 - 147: 9.425 distance: 147 - 148: 10.020 distance: 147 - 150: 16.054 distance: 148 - 149: 20.342 distance: 148 - 154: 37.967 distance: 150 - 151: 28.184 distance: 151 - 152: 16.485 distance: 151 - 153: 15.174 distance: 154 - 155: 10.929 distance: 155 - 156: 20.947 distance: 155 - 158: 25.533 distance: 156 - 157: 18.391 distance: 156 - 163: 34.782 distance: 158 - 159: 17.312 distance: 159 - 160: 34.114 distance: 160 - 161: 13.452 distance: 160 - 162: 23.425 distance: 163 - 164: 33.231 distance: 164 - 165: 17.168 distance: 164 - 167: 31.905 distance: 165 - 166: 20.238 distance: 165 - 171: 16.620 distance: 166 - 204: 21.131 distance: 167 - 168: 6.292 distance: 168 - 169: 22.364 distance: 169 - 170: 41.372 distance: 171 - 172: 25.925 distance: 171 - 177: 9.819 distance: 172 - 173: 20.621 distance: 172 - 175: 8.355 distance: 173 - 174: 15.096 distance: 173 - 178: 26.066 distance: 175 - 176: 34.398 distance: 176 - 177: 30.079 distance: 178 - 179: 43.761 distance: 179 - 180: 27.626 distance: 180 - 181: 25.478 distance: 180 - 184: 20.653 distance: 182 - 183: 20.294