Starting phenix.real_space_refine on Mon Jun 23 18:03:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwe_26830/06_2025/7uwe_26830.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwe_26830/06_2025/7uwe_26830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uwe_26830/06_2025/7uwe_26830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwe_26830/06_2025/7uwe_26830.map" model { file = "/net/cci-nas-00/data/ceres_data/7uwe_26830/06_2025/7uwe_26830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwe_26830/06_2025/7uwe_26830.cif" } resolution = 2.9 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 55 5.49 5 Mg 1 5.21 5 S 112 5.16 5 C 16965 2.51 5 N 4844 2.21 5 O 5348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27327 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 19} Chain breaks: 1 Chain: "B" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 520 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "G" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1698 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Chain: "H" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Chain: "I" Number of atoms: 10407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10407 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1263} Chain breaks: 1 Chain: "J" Number of atoms: 10352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 10352 Classifications: {'peptide': 1330} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1274} Chain breaks: 3 Chain: "K" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "C" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1448 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 13, 'TRANS': 175} 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 15391 SG CYS J 70 106.631 75.891 26.167 1.00 58.13 S ATOM 15405 SG CYS J 72 106.235 75.954 22.858 1.00 59.71 S ATOM 21225 SG CYS J 814 108.267 87.899 93.260 1.00 22.17 S ATOM 21790 SG CYS J 888 105.934 87.832 90.203 1.00 15.87 S ATOM 21841 SG CYS J 895 107.042 84.581 91.826 1.00 10.26 S ATOM 21862 SG CYS J 898 104.698 86.683 93.680 1.00 10.05 S Time building chain proxies: 15.66, per 1000 atoms: 0.57 Number of scatterers: 27327 At special positions: 0 Unit cell: (142.284, 165.288, 148.248, 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 112 16.00 P 55 15.00 Mg 1 11.99 O 5348 8.00 N 4844 7.00 C 16965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.86 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 6 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6186 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 50 sheets defined 38.2% alpha, 15.6% beta 11 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 8.95 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 159 removed outlier: 3.979A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 228 Processing helix chain 'G' and resid 229 through 231 No H-bonds generated for 'chain 'G' and resid 229 through 231' Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.787A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 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 226 removed outlier: 3.543A pdb=" N ALA H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.518A 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 213 removed outlier: 3.640A pdb=" N LEU I 213 " --> pdb=" O ILE I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 219 through 224 removed outlier: 4.268A pdb=" N LEU I 223 " --> pdb=" O GLN I 219 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE I 224 " --> pdb=" O ILE I 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 219 through 224' Processing helix chain 'I' and resid 242 through 247 removed outlier: 4.393A 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: 4.230A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 293' Processing helix chain 'I' and resid 318 through 328 removed outlier: 3.952A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 removed outlier: 3.604A pdb=" N ALA I 362 " --> pdb=" O ASP I 358 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 387 Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 480 Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.630A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 544 through 549 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.864A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 607 through 614 removed outlier: 3.901A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 688 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 826 Processing helix chain 'I' and resid 858 through 863 Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 985 through 990 removed outlier: 4.194A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 4.145A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.311A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.936A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1138 through 1151 Processing helix chain 'I' and resid 1165 through 1176 removed outlier: 3.510A pdb=" N LEU I1172 " --> pdb=" O GLU I1168 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA I1173 " --> pdb=" O VAL I1169 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU I1174 " --> pdb=" O MET I1170 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN I1175 " --> pdb=" O ARG I1171 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU I1176 " --> pdb=" O LEU I1172 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1310 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.813A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 96 through 101 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 139 removed outlier: 3.508A pdb=" N ARG J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU J 139 " --> pdb=" O ILE J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 169 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 194 through 204 Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.704A pdb=" N LEU J 223 " --> pdb=" O LYS J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 removed outlier: 4.497A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP J 284 " --> pdb=" O LYS J 280 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU J 285 " --> pdb=" O ARG J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 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 removed outlier: 3.893A pdb=" N ALA J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 417 removed outlier: 4.353A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 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 540 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 589 through 593 removed outlier: 3.557A pdb=" N VAL J 592 " --> pdb=" O TYR J 589 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 640 through 644 Processing helix chain 'J' and resid 649 through 671 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 737 through 742 removed outlier: 3.877A pdb=" N ALA J 741 " --> pdb=" O ILE J 737 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 773 Processing helix chain 'J' and resid 775 through 789 removed outlier: 3.788A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG J 780 " --> pdb=" O THR J 776 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA J 787 " --> pdb=" O LEU J 783 " (cutoff:3.500A) Processing helix chain 'J' and resid 789 through 802 Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.535A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 915 through 925 Processing helix chain 'J' and resid 1068 through 1074 removed outlier: 3.620A pdb=" N LYS J1072 " --> pdb=" O THR J1068 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU J1074 " --> pdb=" O GLY J1070 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1068 through 1074' Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.370A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.561A pdb=" N GLU J1291 " --> pdb=" O ILE J1287 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1319 through 1325 Processing helix chain 'J' and resid 1328 through 1339 Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1362 through 1373 removed outlier: 3.562A pdb=" N HIS J1366 " --> pdb=" O GLY J1362 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 33 removed outlier: 4.150A pdb=" N GLY K 33 " --> pdb=" O GLN K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 74 Processing helix chain 'C' and resid 50 through 65 removed outlier: 3.805A pdb=" N GLU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 97 removed outlier: 7.062A pdb=" N ILE C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N LEU C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N HIS C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 128 Processing helix chain 'C' and resid 129 through 154 removed outlier: 3.543A pdb=" N VAL C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 158 through 163 removed outlier: 3.510A pdb=" N HIS C 162 " --> pdb=" O GLY C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 178 Processing helix chain 'C' and resid 187 through 194 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.720A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.655A pdb=" N VAL G 153 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 104 removed outlier: 6.352A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.587A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 12 through 18 removed outlier: 5.690A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR H 27 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 101 removed outlier: 4.012A pdb=" N VAL H 98 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 removed outlier: 3.524A pdb=" N ARG H 91 " --> pdb=" O GLU H 122 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU H 122 " --> pdb=" O ARG H 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'H' and resid 104 through 105 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: 6.812A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 59 through 60 removed outlier: 4.683A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET I 124 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN I 120 " --> pdb=" O LEU I 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 137 removed outlier: 3.532A pdb=" N VAL I 144 " --> pdb=" O GLN I 513 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN I 513 " --> pdb=" O VAL I 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 451 through 453 removed outlier: 6.241A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.671A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 180 through 181 Processing sheet with id=AB9, first strand: chain 'I' and resid 284 through 285 removed outlier: 3.526A pdb=" N ILE I 285 " --> pdb=" O MET I 239 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 249 through 250 removed outlier: 4.317A 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: 6.869A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.715A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 removed outlier: 6.928A pdb=" N LEU I 587 " --> pdb=" O LEU I 606 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU I 606 " --> pdb=" O LEU I 587 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR I 589 " --> pdb=" O HIS I 604 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N HIS I 604 " --> pdb=" O THR I 589 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR I 591 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU I 602 " --> pdb=" O TYR I 591 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS I 593 " --> pdb=" O THR I 600 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.610A pdb=" N ASP I 654 " --> pdb=" O ALA I 617 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 634 through 637 removed outlier: 3.593A pdb=" N VAL I 634 " --> pdb=" O PHE I 645 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 717 through 718 removed outlier: 3.800A pdb=" N ASP I 781 " --> pdb=" O ALA I 718 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.540A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AD1, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AD2, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AD3, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 4.544A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1066 through 1067 Processing sheet with id=AD5, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.830A pdb=" N GLY I 846 " --> pdb=" O THR I 843 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR I 843 " --> pdb=" O GLY I 846 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.135A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 887 through 888 Processing sheet with id=AD8, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 3.555A pdb=" N SER J 353 " --> pdb=" O MET J 466 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AE1, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AE2, first strand: chain 'I' and resid 1335 through 1338 Processing sheet with id=AE3, first strand: chain 'J' and resid 34 through 37 removed outlier: 5.011A pdb=" N SER J 34 " --> pdb=" O MET J 102 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N HIS J 104 " --> pdb=" O SER J 34 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLY J 36 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N GLU J 106 " --> pdb=" O GLY J 36 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 526 through 527 removed outlier: 3.562A pdb=" N LEU J 527 " --> pdb=" O LYS J 549 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG J 551 " --> pdb=" O LEU J 527 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR J 572 " --> pdb=" O VAL J 548 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL J 550 " --> pdb=" O LYS J 570 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS J 570 " --> pdb=" O VAL J 550 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE J 552 " --> pdb=" O SER J 568 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER J 568 " --> pdb=" O ILE J 552 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE6, first strand: chain 'J' and resid 820 through 822 removed outlier: 3.541A pdb=" N VAL J 880 " --> pdb=" O MET J 822 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 949 through 950 removed outlier: 3.981A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.356A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AF1, first strand: chain 'J' and resid 1098 through 1100 removed outlier: 3.501A pdb=" N GLY J1033 " --> pdb=" O ILE J1115 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 1046 through 1049 removed outlier: 3.900A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 1187 through 1190 removed outlier: 3.510A pdb=" N LEU J1175 " --> pdb=" O GLU J1188 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL J1204 " --> pdb=" O GLY J1161 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.871A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 67 through 73 removed outlier: 6.416A pdb=" N ALA C 13 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASP C 108 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL C 15 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL C 105 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL C 122 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE C 107 " --> pdb=" O VAL C 122 " (cutoff:3.500A) 1051 hydrogen bonds defined for protein. 2952 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 13.19 Time building geometry restraints manager: 8.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9033 1.34 - 1.46: 4380 1.46 - 1.58: 14140 1.58 - 1.70: 107 1.70 - 1.82: 195 Bond restraints: 27855 Sorted by residual: bond pdb=" C GLY C 21 " pdb=" N PRO C 22 " ideal model delta sigma weight residual 1.332 1.391 -0.059 1.33e-02 5.65e+03 2.00e+01 bond pdb=" O3' DC A 4 " pdb=" P DT A 5 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.15e+01 bond pdb=" CA THR I 635 " pdb=" C THR I 635 " ideal model delta sigma weight residual 1.524 1.566 -0.042 1.26e-02 6.30e+03 1.13e+01 bond pdb=" CA ARG J 731 " pdb=" C ARG J 731 " ideal model delta sigma weight residual 1.519 1.555 -0.036 1.14e-02 7.69e+03 9.77e+00 bond pdb=" C ILE I1109 " pdb=" N GLY I1110 " ideal model delta sigma weight residual 1.334 1.372 -0.038 1.27e-02 6.20e+03 8.74e+00 ... (remaining 27850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 36705 1.97 - 3.93: 1007 3.93 - 5.90: 120 5.90 - 7.87: 24 7.87 - 9.83: 7 Bond angle restraints: 37863 Sorted by residual: angle pdb=" N ARG J 156 " pdb=" CA ARG J 156 " pdb=" C ARG J 156 " ideal model delta sigma weight residual 111.07 118.98 -7.91 1.07e+00 8.73e-01 5.46e+01 angle pdb=" N LYS J1170 " pdb=" CA LYS J1170 " pdb=" C LYS J1170 " ideal model delta sigma weight residual 111.24 102.74 8.50 1.29e+00 6.01e-01 4.34e+01 angle pdb=" C ALA J 328 " pdb=" N ASP J 329 " pdb=" CA ASP J 329 " ideal model delta sigma weight residual 120.38 128.72 -8.34 1.37e+00 5.33e-01 3.71e+01 angle pdb=" N THR J1169 " pdb=" CA THR J1169 " pdb=" C THR J1169 " ideal model delta sigma weight residual 112.58 119.64 -7.06 1.22e+00 6.72e-01 3.35e+01 angle pdb=" C ARG J 322 " pdb=" N PRO J 323 " pdb=" CA PRO J 323 " ideal model delta sigma weight residual 119.76 125.64 -5.88 1.03e+00 9.43e-01 3.26e+01 ... (remaining 37858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 15472 17.89 - 35.78: 1130 35.78 - 53.67: 327 53.67 - 71.56: 81 71.56 - 89.45: 15 Dihedral angle restraints: 17025 sinusoidal: 7412 harmonic: 9613 Sorted by residual: dihedral pdb=" CA GLU I1137 " pdb=" C GLU I1137 " pdb=" N VAL I1138 " pdb=" CA VAL I1138 " ideal model delta harmonic sigma weight residual -180.00 -151.25 -28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ALA C 26 " pdb=" C ALA C 26 " pdb=" N VAL C 27 " pdb=" CA VAL C 27 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA LEU C 81 " pdb=" C LEU C 81 " pdb=" N ASN C 82 " pdb=" CA ASN C 82 " ideal model delta harmonic sigma weight residual -180.00 -158.85 -21.15 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 17022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3934 0.084 - 0.168: 368 0.168 - 0.252: 19 0.252 - 0.336: 4 0.336 - 0.420: 2 Chirality restraints: 4327 Sorted by residual: chirality pdb=" CA ILE J1248 " pdb=" N ILE J1248 " pdb=" C ILE J1248 " pdb=" CB ILE J1248 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CG LEU I 468 " pdb=" CB LEU I 468 " pdb=" CD1 LEU I 468 " pdb=" CD2 LEU I 468 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA ASN C 82 " pdb=" N ASN C 82 " pdb=" C ASN C 82 " pdb=" CB ASN C 82 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 4324 not shown) Planarity restraints: 4761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP J 751 " 0.026 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C ASP J 751 " -0.089 2.00e-02 2.50e+03 pdb=" O ASP J 751 " 0.033 2.00e-02 2.50e+03 pdb=" N GLY J 752 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 19 " -0.022 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C GLY C 19 " 0.081 2.00e-02 2.50e+03 pdb=" O GLY C 19 " -0.032 2.00e-02 2.50e+03 pdb=" N ARG C 20 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 45 " -0.015 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" CG ASP C 45 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASP C 45 " -0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP C 45 " -0.019 2.00e-02 2.50e+03 ... (remaining 4758 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 365 2.66 - 3.22: 24302 3.22 - 3.78: 39745 3.78 - 4.34: 54244 4.34 - 4.90: 89628 Nonbonded interactions: 208284 Sorted by model distance: nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.097 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.097 2.170 nonbonded pdb=" OG SER J 119 " pdb=" O PRO J 121 " model vdw 2.201 3.040 nonbonded pdb=" OG SER J 977 " pdb=" OG1 THR J 980 " model vdw 2.208 3.040 nonbonded pdb=" OG SER I 318 " pdb=" OD1 ASP I 320 " model vdw 2.231 3.040 ... (remaining 208279 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 7 through 158 or resid 170 through 232)) selection = (chain 'H' and resid 7 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 individual isotropic 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.140 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 73.280 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.120 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:13.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 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 : 0.004 0.059 27861 Z= 0.233 Angle : 0.746 9.832 37869 Z= 0.477 Chirality : 0.048 0.420 4327 Planarity : 0.005 0.092 4761 Dihedral : 14.004 89.445 10839 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.42 % Favored : 95.46 % Rotamer: Outliers : 0.67 % Allowed : 2.43 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: -0.75 (0.14), residues: 3325 helix: 0.96 (0.16), residues: 1156 sheet: -0.07 (0.25), residues: 414 loop : -1.67 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 68 HIS 0.011 0.001 HIS C 177 PHE 0.018 0.001 PHE J 35 TYR 0.024 0.001 TYR C 157 ARG 0.009 0.000 ARG K 28 Details of bonding type rmsd hydrogen bonds : bond 0.18459 ( 1068) hydrogen bonds : angle 6.88619 ( 3002) metal coordination : bond 0.00483 ( 6) metal coordination : angle 2.73145 ( 6) covalent geometry : bond 0.00384 (27855) covalent geometry : angle 0.74558 (37863) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 538 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 208 THR cc_start: 0.5961 (m) cc_final: 0.5154 (t) REVERT: J 932 MET cc_start: 0.6556 (tpt) cc_final: 0.6342 (tpp) REVERT: C 159 PHE cc_start: 0.6096 (m-80) cc_final: 0.5299 (m-10) outliers start: 19 outliers final: 6 residues processed: 552 average time/residue: 1.5656 time to fit residues: 986.0114 Evaluate side-chains 302 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 296 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 849 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 744 ARG Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain C residue 183 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 0.9990 chunk 255 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 102 optimal weight: 0.4980 chunk 160 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 306 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 HIS I 834 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 GLN J 320 ASN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.138568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.088227 restraints weight = 58231.728| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.09 r_work: 0.3115 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27861 Z= 0.133 Angle : 0.623 9.312 37869 Z= 0.319 Chirality : 0.042 0.209 4327 Planarity : 0.005 0.089 4761 Dihedral : 11.703 73.278 4320 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.97 % Allowed : 12.00 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: -0.45 (0.14), residues: 3325 helix: 1.24 (0.15), residues: 1177 sheet: -0.07 (0.25), residues: 413 loop : -1.50 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J1193 HIS 0.009 0.001 HIS J 651 PHE 0.015 0.001 PHE C 154 TYR 0.012 0.001 TYR J1365 ARG 0.011 0.001 ARG I 371 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 1068) hydrogen bonds : angle 4.86860 ( 3002) metal coordination : bond 0.00383 ( 6) metal coordination : angle 2.67470 ( 6) covalent geometry : bond 0.00294 (27855) covalent geometry : angle 0.62229 (37863) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 337 time to evaluate : 2.936 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: H 102 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8102 (tm) REVERT: H 117 HIS cc_start: 0.7972 (p-80) cc_final: 0.7695 (p-80) REVERT: H 181 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8085 (mp0) REVERT: H 228 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9337 (pp) REVERT: I 6 THR cc_start: 0.8133 (p) cc_final: 0.7889 (t) REVERT: I 7 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7739 (tm-30) REVERT: I 202 ARG cc_start: 0.7899 (ptt180) cc_final: 0.7497 (ptt90) REVERT: I 337 PHE cc_start: 0.7666 (t80) cc_final: 0.7040 (t80) REVERT: I 516 ASP cc_start: 0.8094 (p0) cc_final: 0.7889 (p0) REVERT: I 542 ARG cc_start: 0.6692 (ttt180) cc_final: 0.6249 (ttt180) REVERT: I 635 THR cc_start: 0.7565 (p) cc_final: 0.7355 (p) REVERT: I 951 MET cc_start: 0.8685 (mmm) cc_final: 0.8365 (mmt) REVERT: I 952 GLN cc_start: 0.8755 (tp-100) cc_final: 0.8551 (tp-100) REVERT: I 1232 MET cc_start: 0.9167 (mmm) cc_final: 0.8925 (mmm) REVERT: J 133 ARG cc_start: 0.8792 (tpm-80) cc_final: 0.8571 (tpm-80) REVERT: J 151 MET cc_start: 0.7489 (tpp) cc_final: 0.7165 (tpp) REVERT: J 289 ASP cc_start: 0.8221 (m-30) cc_final: 0.7833 (p0) REVERT: J 932 MET cc_start: 0.8363 (tpt) cc_final: 0.7706 (tpp) REVERT: J 1189 MET cc_start: 0.4143 (tpt) cc_final: 0.3617 (tpt) REVERT: K 54 ILE cc_start: 0.9481 (OUTLIER) cc_final: 0.9235 (mp) REVERT: K 69 ARG cc_start: 0.8737 (ttp80) cc_final: 0.8255 (tmm160) REVERT: C 68 TRP cc_start: 0.8895 (p-90) cc_final: 0.8455 (p90) REVERT: C 147 MET cc_start: 0.9006 (tpp) cc_final: 0.8701 (tpp) REVERT: C 154 PHE cc_start: 0.9016 (m-80) cc_final: 0.8307 (m-80) REVERT: C 159 PHE cc_start: 0.8888 (m-80) cc_final: 0.8010 (m-80) outliers start: 56 outliers final: 26 residues processed: 368 average time/residue: 1.6400 time to fit residues: 702.9702 Evaluate side-chains 308 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 279 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1335 ILE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain C residue 58 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 72 optimal weight: 8.9990 chunk 153 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 109 optimal weight: 0.0670 chunk 8 optimal weight: 0.8980 chunk 290 optimal weight: 9.9990 chunk 124 optimal weight: 0.7980 chunk 279 optimal weight: 40.0000 chunk 254 optimal weight: 3.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN G 132 HIS I 86 GLN I 622 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1218 HIS ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.136756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.086187 restraints weight = 58045.377| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.08 r_work: 0.3075 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27861 Z= 0.123 Angle : 0.591 10.698 37869 Z= 0.302 Chirality : 0.042 0.169 4327 Planarity : 0.004 0.050 4761 Dihedral : 11.502 73.301 4309 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.18 % Allowed : 13.66 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: -0.30 (0.14), residues: 3325 helix: 1.37 (0.15), residues: 1173 sheet: 0.06 (0.26), residues: 416 loop : -1.42 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP I 997 HIS 0.008 0.001 HIS J 651 PHE 0.016 0.001 PHE I 972 TYR 0.012 0.001 TYR C 165 ARG 0.010 0.000 ARG I 407 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 1068) hydrogen bonds : angle 4.48196 ( 3002) metal coordination : bond 0.00395 ( 6) metal coordination : angle 2.31409 ( 6) covalent geometry : bond 0.00262 (27855) covalent geometry : angle 0.59049 (37863) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 317 time to evaluate : 3.078 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: G 197 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.6683 (m-30) REVERT: H 95 LYS cc_start: 0.7416 (tptp) cc_final: 0.6919 (mtmt) REVERT: H 102 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8073 (tm) REVERT: H 117 HIS cc_start: 0.8035 (p-80) cc_final: 0.7723 (p-80) REVERT: H 158 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.5964 (mpp80) REVERT: H 228 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9347 (pp) REVERT: I 7 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7712 (tm-30) REVERT: I 59 ILE cc_start: 0.8827 (pp) cc_final: 0.8008 (pp) REVERT: I 191 LYS cc_start: 0.9414 (mmmt) cc_final: 0.8720 (tmmt) REVERT: I 200 ARG cc_start: 0.7593 (mtm180) cc_final: 0.7294 (mtm180) REVERT: I 337 PHE cc_start: 0.7905 (t80) cc_final: 0.6884 (t80) REVERT: I 407 ARG cc_start: 0.8677 (mmm160) cc_final: 0.8431 (ttm-80) REVERT: I 504 GLU cc_start: 0.8903 (tt0) cc_final: 0.8605 (pp20) REVERT: I 542 ARG cc_start: 0.6821 (ttt180) cc_final: 0.6267 (ttt180) REVERT: I 635 THR cc_start: 0.7878 (p) cc_final: 0.7662 (p) REVERT: I 952 GLN cc_start: 0.8787 (tp-100) cc_final: 0.8556 (tp-100) REVERT: J 151 MET cc_start: 0.8255 (tpp) cc_final: 0.7979 (tpp) REVERT: J 152 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8658 (p) REVERT: J 204 GLU cc_start: 0.9455 (OUTLIER) cc_final: 0.9150 (mm-30) REVERT: J 289 ASP cc_start: 0.8213 (m-30) cc_final: 0.7825 (p0) REVERT: J 591 ILE cc_start: 0.7774 (tp) cc_final: 0.7496 (tp) REVERT: J 599 LYS cc_start: 0.7022 (pmtt) cc_final: 0.6596 (ptpp) REVERT: J 932 MET cc_start: 0.8465 (tpt) cc_final: 0.7611 (tpp) REVERT: J 1189 MET cc_start: 0.3852 (tpt) cc_final: 0.3323 (tpt) REVERT: K 54 ILE cc_start: 0.9384 (mp) cc_final: 0.9113 (mp) REVERT: K 56 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8430 (mm-30) REVERT: K 69 ARG cc_start: 0.8726 (ttp80) cc_final: 0.8518 (ttp80) REVERT: C 68 TRP cc_start: 0.9018 (p-90) cc_final: 0.8492 (p90) REVERT: C 114 LYS cc_start: 0.8349 (pmtt) cc_final: 0.8077 (pmtt) REVERT: C 137 ILE cc_start: 0.9017 (pp) cc_final: 0.8645 (pp) REVERT: C 147 MET cc_start: 0.9096 (tpp) cc_final: 0.8745 (tpp) REVERT: C 154 PHE cc_start: 0.9041 (m-80) cc_final: 0.8516 (m-80) REVERT: C 159 PHE cc_start: 0.8926 (m-80) cc_final: 0.8183 (m-80) outliers start: 62 outliers final: 25 residues processed: 355 average time/residue: 1.4689 time to fit residues: 605.7041 Evaluate side-chains 294 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 263 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain C residue 58 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 192 optimal weight: 20.0000 chunk 166 optimal weight: 0.0470 chunk 321 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 237 optimal weight: 1.9990 chunk 236 optimal weight: 6.9990 chunk 302 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 262 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 overall best weight: 1.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 622 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.131058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.079024 restraints weight = 57509.386| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.04 r_work: 0.2945 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27861 Z= 0.144 Angle : 0.627 12.275 37869 Z= 0.319 Chirality : 0.043 0.164 4327 Planarity : 0.004 0.057 4761 Dihedral : 11.503 73.303 4309 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.43 % Allowed : 15.59 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: -0.30 (0.14), residues: 3325 helix: 1.32 (0.15), residues: 1180 sheet: 0.15 (0.25), residues: 432 loop : -1.44 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 997 HIS 0.009 0.001 HIS C 85 PHE 0.021 0.001 PHE I 972 TYR 0.017 0.001 TYR J 46 ARG 0.013 0.001 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 1068) hydrogen bonds : angle 4.40735 ( 3002) metal coordination : bond 0.00569 ( 6) metal coordination : angle 1.89161 ( 6) covalent geometry : bond 0.00337 (27855) covalent geometry : angle 0.62614 (37863) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 295 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 145 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8289 (tptm) REVERT: H 102 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7956 (tm) REVERT: H 117 HIS cc_start: 0.8122 (p-80) cc_final: 0.7916 (p-80) REVERT: H 127 GLN cc_start: 0.8935 (pm20) cc_final: 0.8691 (pm20) REVERT: H 144 ILE cc_start: 0.9352 (mt) cc_final: 0.9134 (pp) REVERT: H 228 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9353 (pp) REVERT: I 200 ARG cc_start: 0.7738 (mtm180) cc_final: 0.7409 (mtm180) REVERT: I 207 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8183 (p) REVERT: I 337 PHE cc_start: 0.8052 (t80) cc_final: 0.7113 (t80) REVERT: I 370 MET cc_start: 0.8922 (mmm) cc_final: 0.8283 (pp-130) REVERT: I 371 ARG cc_start: 0.9244 (ttm-80) cc_final: 0.8642 (ttm-80) REVERT: I 429 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8578 (mtm) REVERT: I 504 GLU cc_start: 0.8919 (tt0) cc_final: 0.8696 (pp20) REVERT: I 542 ARG cc_start: 0.6736 (ttt180) cc_final: 0.6064 (ttt180) REVERT: I 675 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8610 (t70) REVERT: I 951 MET cc_start: 0.9097 (tpp) cc_final: 0.8832 (ttp) REVERT: I 952 GLN cc_start: 0.8849 (tp-100) cc_final: 0.8589 (tp-100) REVERT: I 1304 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.8146 (tpt) REVERT: J 91 GLU cc_start: 0.8503 (tt0) cc_final: 0.8221 (tp30) REVERT: J 134 ASP cc_start: 0.9382 (m-30) cc_final: 0.9046 (p0) REVERT: J 289 ASP cc_start: 0.8380 (m-30) cc_final: 0.7923 (p0) REVERT: J 304 ASP cc_start: 0.8561 (m-30) cc_final: 0.8264 (p0) REVERT: J 591 ILE cc_start: 0.8814 (tp) cc_final: 0.8517 (tp) REVERT: J 599 LYS cc_start: 0.7863 (pmtt) cc_final: 0.7628 (ptpt) REVERT: J 932 MET cc_start: 0.8857 (tpt) cc_final: 0.7718 (tpp) REVERT: J 1189 MET cc_start: 0.4197 (tpt) cc_final: 0.3533 (tpp) REVERT: C 68 TRP cc_start: 0.9010 (p-90) cc_final: 0.8481 (p90) REVERT: C 147 MET cc_start: 0.8973 (tpp) cc_final: 0.8533 (tpp) REVERT: C 154 PHE cc_start: 0.9004 (m-80) cc_final: 0.8527 (m-80) REVERT: C 159 PHE cc_start: 0.8861 (m-80) cc_final: 0.8125 (m-80) REVERT: C 187 PHE cc_start: 0.9185 (m-80) cc_final: 0.8873 (m-80) outliers start: 69 outliers final: 25 residues processed: 337 average time/residue: 1.4179 time to fit residues: 557.3517 Evaluate side-chains 281 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 675 ASP Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain C residue 58 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 242 optimal weight: 0.0770 chunk 20 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 297 optimal weight: 7.9990 chunk 193 optimal weight: 5.9990 chunk 269 optimal weight: 0.1980 chunk 40 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 304 optimal weight: 0.7980 chunk 208 optimal weight: 3.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 117 HIS ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 GLN I 622 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 200 GLN ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.129356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.077783 restraints weight = 56855.232| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.98 r_work: 0.2940 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27861 Z= 0.134 Angle : 0.606 11.043 37869 Z= 0.307 Chirality : 0.042 0.171 4327 Planarity : 0.004 0.059 4761 Dihedral : 11.323 73.529 4309 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.68 % Allowed : 16.72 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: -0.21 (0.14), residues: 3325 helix: 1.41 (0.15), residues: 1178 sheet: 0.17 (0.25), residues: 435 loop : -1.38 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 997 HIS 0.008 0.001 HIS C 85 PHE 0.014 0.001 PHE I 514 TYR 0.012 0.001 TYR G 177 ARG 0.011 0.001 ARG I 473 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 1068) hydrogen bonds : angle 4.30474 ( 3002) metal coordination : bond 0.00496 ( 6) metal coordination : angle 1.69139 ( 6) covalent geometry : bond 0.00313 (27855) covalent geometry : angle 0.60581 (37863) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 283 time to evaluate : 3.047 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: G 33 ARG cc_start: 0.7736 (mmp80) cc_final: 0.7440 (mmp-170) REVERT: G 168 ILE cc_start: 0.8049 (pt) cc_final: 0.7693 (mt) REVERT: H 28 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8751 (tt) REVERT: H 95 LYS cc_start: 0.7657 (tptp) cc_final: 0.7329 (mtmt) REVERT: H 102 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7896 (tm) REVERT: H 127 GLN cc_start: 0.8929 (pm20) cc_final: 0.8719 (pm20) REVERT: H 144 ILE cc_start: 0.9454 (mt) cc_final: 0.9235 (pp) REVERT: I 191 LYS cc_start: 0.9538 (mmmt) cc_final: 0.8913 (tmmt) REVERT: I 200 ARG cc_start: 0.7824 (mtm180) cc_final: 0.7387 (mtm180) REVERT: I 207 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8279 (p) REVERT: I 337 PHE cc_start: 0.8118 (t80) cc_final: 0.7288 (t80) REVERT: I 370 MET cc_start: 0.9010 (mmm) cc_final: 0.8336 (pp-130) REVERT: I 371 ARG cc_start: 0.9222 (ttm-80) cc_final: 0.8638 (ttm-80) REVERT: I 429 MET cc_start: 0.8855 (mtm) cc_final: 0.8589 (mtm) REVERT: I 542 ARG cc_start: 0.6873 (ttt180) cc_final: 0.6131 (ttt180) REVERT: I 675 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8547 (t70) REVERT: I 951 MET cc_start: 0.9141 (tpp) cc_final: 0.8911 (ttp) REVERT: I 952 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8610 (tp-100) REVERT: I 1304 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.8223 (tpt) REVERT: J 100 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8463 (mp0) REVERT: J 132 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9253 (tm) REVERT: J 137 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8750 (mmm-85) REVERT: J 204 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.9034 (mp0) REVERT: J 220 ARG cc_start: 0.8928 (ttt90) cc_final: 0.8699 (ttt90) REVERT: J 225 GLU cc_start: 0.9143 (tp30) cc_final: 0.8894 (mp0) REVERT: J 289 ASP cc_start: 0.8421 (m-30) cc_final: 0.7945 (p0) REVERT: J 304 ASP cc_start: 0.8506 (m-30) cc_final: 0.8244 (p0) REVERT: J 591 ILE cc_start: 0.9152 (tp) cc_final: 0.8738 (tp) REVERT: J 932 MET cc_start: 0.8834 (tpt) cc_final: 0.7821 (tpp) REVERT: J 1189 MET cc_start: 0.4102 (tpt) cc_final: 0.3445 (tpp) REVERT: K 56 GLU cc_start: 0.8108 (mp0) cc_final: 0.7620 (mp0) REVERT: K 71 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8742 (mm-30) REVERT: C 68 TRP cc_start: 0.9044 (p-90) cc_final: 0.8471 (p90) REVERT: C 154 PHE cc_start: 0.9074 (m-80) cc_final: 0.8643 (m-80) REVERT: C 159 PHE cc_start: 0.8843 (m-80) cc_final: 0.8453 (m-80) REVERT: C 187 PHE cc_start: 0.9121 (m-80) cc_final: 0.8815 (m-80) outliers start: 76 outliers final: 23 residues processed: 343 average time/residue: 1.4092 time to fit residues: 562.3024 Evaluate side-chains 277 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 246 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 675 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 1210 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 58 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 133 optimal weight: 0.3980 chunk 124 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 288 optimal weight: 7.9990 chunk 257 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 300 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 290 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 622 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1126 GLN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 HIS ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.128911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077189 restraints weight = 56910.877| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.98 r_work: 0.2934 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27861 Z= 0.123 Angle : 0.613 13.138 37869 Z= 0.307 Chirality : 0.043 0.349 4327 Planarity : 0.004 0.057 4761 Dihedral : 11.233 75.132 4309 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.29 % Allowed : 18.37 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: -0.16 (0.14), residues: 3325 helix: 1.47 (0.16), residues: 1162 sheet: 0.23 (0.25), residues: 431 loop : -1.35 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 997 HIS 0.005 0.001 HIS C 177 PHE 0.011 0.001 PHE I 972 TYR 0.011 0.001 TYR G 177 ARG 0.013 0.001 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 1068) hydrogen bonds : angle 4.25275 ( 3002) metal coordination : bond 0.00504 ( 6) metal coordination : angle 1.68778 ( 6) covalent geometry : bond 0.00284 (27855) covalent geometry : angle 0.61273 (37863) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 271 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.7694 (mmp80) cc_final: 0.7217 (mmp-170) REVERT: G 168 ILE cc_start: 0.8076 (pt) cc_final: 0.7731 (mt) REVERT: H 28 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8775 (tt) REVERT: H 95 LYS cc_start: 0.7869 (tptp) cc_final: 0.7603 (mtmt) REVERT: H 102 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7858 (tm) REVERT: H 117 HIS cc_start: 0.8026 (p-80) cc_final: 0.7783 (p-80) REVERT: H 144 ILE cc_start: 0.9508 (mt) cc_final: 0.9294 (pp) REVERT: H 158 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7274 (tpp80) REVERT: H 212 ASP cc_start: 0.7815 (t0) cc_final: 0.7585 (t0) REVERT: I 191 LYS cc_start: 0.9514 (mmmt) cc_final: 0.8818 (tmmt) REVERT: I 207 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8158 (p) REVERT: I 337 PHE cc_start: 0.8212 (t80) cc_final: 0.7397 (t80) REVERT: I 429 MET cc_start: 0.8915 (mtm) cc_final: 0.8656 (mtm) REVERT: I 542 ARG cc_start: 0.6916 (ttt180) cc_final: 0.6166 (ttt180) REVERT: I 742 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.7273 (p90) REVERT: I 951 MET cc_start: 0.9180 (tpp) cc_final: 0.8964 (ttp) REVERT: I 952 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8665 (tp-100) REVERT: I 1304 MET cc_start: 0.9478 (OUTLIER) cc_final: 0.8228 (tpt) REVERT: J 100 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8515 (mp0) REVERT: J 137 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8814 (mmm-85) REVERT: J 204 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8847 (mp0) REVERT: J 220 ARG cc_start: 0.8909 (ttt90) cc_final: 0.8689 (ttt90) REVERT: J 289 ASP cc_start: 0.8431 (m-30) cc_final: 0.7965 (p0) REVERT: J 932 MET cc_start: 0.8922 (tpt) cc_final: 0.8081 (tpp) REVERT: J 990 ARG cc_start: 0.8050 (pmm-80) cc_final: 0.7701 (pmm-80) REVERT: J 1189 MET cc_start: 0.4156 (tpt) cc_final: 0.3470 (tpp) REVERT: K 56 GLU cc_start: 0.8040 (mp0) cc_final: 0.7590 (mp0) REVERT: K 73 GLN cc_start: 0.8123 (pp30) cc_final: 0.7862 (pp30) REVERT: C 68 TRP cc_start: 0.9078 (p-90) cc_final: 0.8527 (p90) REVERT: C 154 PHE cc_start: 0.9087 (m-80) cc_final: 0.8835 (m-80) REVERT: C 159 PHE cc_start: 0.9236 (m-80) cc_final: 0.8599 (m-80) REVERT: C 187 PHE cc_start: 0.9101 (m-80) cc_final: 0.8774 (m-80) outliers start: 65 outliers final: 29 residues processed: 320 average time/residue: 1.4273 time to fit residues: 533.7706 Evaluate side-chains 276 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 1042 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 213 LYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1072 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 311 optimal weight: 7.9990 chunk 212 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 276 optimal weight: 30.0000 chunk 80 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 150 HIS I 622 ASN I 628 HIS ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN ** J 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1259 GLN K 31 GLN C 177 HIS ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.124200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.071880 restraints weight = 56680.173| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.90 r_work: 0.2811 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 27861 Z= 0.227 Angle : 0.716 11.076 37869 Z= 0.367 Chirality : 0.046 0.210 4327 Planarity : 0.005 0.080 4761 Dihedral : 11.488 78.335 4309 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.50 % Allowed : 19.32 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.45 (0.14), residues: 3325 helix: 1.03 (0.15), residues: 1175 sheet: 0.22 (0.25), residues: 430 loop : -1.42 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP I 997 HIS 0.008 0.001 HIS C 182 PHE 0.026 0.002 PHE I 514 TYR 0.017 0.001 TYR J 631 ARG 0.018 0.001 ARG I 371 Details of bonding type rmsd hydrogen bonds : bond 0.05465 ( 1068) hydrogen bonds : angle 4.62541 ( 3002) metal coordination : bond 0.00875 ( 6) metal coordination : angle 1.95156 ( 6) covalent geometry : bond 0.00542 (27855) covalent geometry : angle 0.71562 (37863) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 246 time to evaluate : 3.054 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: H 28 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8871 (tt) REVERT: H 137 ASN cc_start: 0.9436 (p0) cc_final: 0.9222 (p0) REVERT: H 158 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7615 (mpp80) REVERT: I 59 ILE cc_start: 0.9172 (pp) cc_final: 0.8933 (pp) REVERT: I 230 PHE cc_start: 0.6664 (OUTLIER) cc_final: 0.5975 (t80) REVERT: I 337 PHE cc_start: 0.8216 (t80) cc_final: 0.7830 (t80) REVERT: I 340 ASP cc_start: 0.8811 (m-30) cc_final: 0.8570 (p0) REVERT: I 488 MET cc_start: 0.8785 (mmp) cc_final: 0.8457 (tpt) REVERT: I 542 ARG cc_start: 0.6995 (ttt180) cc_final: 0.6213 (ttt180) REVERT: I 952 GLN cc_start: 0.8956 (tp-100) cc_final: 0.8702 (tp-100) REVERT: I 1304 MET cc_start: 0.9483 (OUTLIER) cc_final: 0.8270 (tpt) REVERT: J 100 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8526 (mp0) REVERT: J 137 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.9000 (mmm-85) REVERT: J 204 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8815 (mm-30) REVERT: J 289 ASP cc_start: 0.8615 (m-30) cc_final: 0.8206 (p0) REVERT: J 1189 MET cc_start: 0.4582 (tpt) cc_final: 0.4159 (tmm) REVERT: J 1343 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7869 (mm-30) REVERT: K 42 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8123 (mp0) REVERT: K 56 GLU cc_start: 0.8258 (mp0) cc_final: 0.7764 (mp0) REVERT: C 151 ASP cc_start: 0.9286 (t70) cc_final: 0.8559 (m-30) REVERT: C 159 PHE cc_start: 0.9271 (m-80) cc_final: 0.9034 (m-10) REVERT: C 187 PHE cc_start: 0.9099 (m-80) cc_final: 0.8788 (m-80) outliers start: 71 outliers final: 31 residues processed: 304 average time/residue: 1.5535 time to fit residues: 549.4642 Evaluate side-chains 258 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 1042 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 213 LYS Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 356 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1072 LYS Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 80 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 280 optimal weight: 0.0370 chunk 298 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 311 optimal weight: 1.9990 overall best weight: 0.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 622 ASN I 628 HIS ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN ** J 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.127266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.075874 restraints weight = 56475.399| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.92 r_work: 0.2902 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27861 Z= 0.121 Angle : 0.651 13.619 37869 Z= 0.325 Chirality : 0.043 0.193 4327 Planarity : 0.004 0.059 4761 Dihedral : 11.254 80.310 4309 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.62 % Allowed : 21.05 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: -0.24 (0.14), residues: 3325 helix: 1.31 (0.16), residues: 1158 sheet: 0.37 (0.27), residues: 392 loop : -1.34 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP I 997 HIS 0.007 0.001 HIS H 117 PHE 0.015 0.001 PHE I 195 TYR 0.013 0.001 TYR C 58 ARG 0.014 0.001 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 1068) hydrogen bonds : angle 4.35742 ( 3002) metal coordination : bond 0.00343 ( 6) metal coordination : angle 1.77405 ( 6) covalent geometry : bond 0.00281 (27855) covalent geometry : angle 0.65055 (37863) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 7.038 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 168 ILE cc_start: 0.8225 (pt) cc_final: 0.7904 (mt) REVERT: H 137 ASN cc_start: 0.9460 (p0) cc_final: 0.9201 (p0) REVERT: I 59 ILE cc_start: 0.9097 (pp) cc_final: 0.8831 (pp) REVERT: I 191 LYS cc_start: 0.9589 (mmmt) cc_final: 0.8972 (tmmt) REVERT: I 200 ARG cc_start: 0.7890 (mtm180) cc_final: 0.7393 (mtm180) REVERT: I 230 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5714 (t80) REVERT: I 337 PHE cc_start: 0.8274 (t80) cc_final: 0.7757 (t80) REVERT: I 340 ASP cc_start: 0.8822 (m-30) cc_final: 0.8558 (p0) REVERT: I 488 MET cc_start: 0.8723 (mmp) cc_final: 0.8496 (tpt) REVERT: I 542 ARG cc_start: 0.7088 (ttt180) cc_final: 0.6233 (ttt180) REVERT: I 952 GLN cc_start: 0.8910 (tp-100) cc_final: 0.8694 (tp-100) REVERT: J 136 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8150 (pm20) REVERT: J 289 ASP cc_start: 0.8572 (m-30) cc_final: 0.8181 (p0) REVERT: J 802 ASP cc_start: 0.8717 (t70) cc_final: 0.8399 (t0) REVERT: J 1343 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7727 (mm-30) REVERT: K 42 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8049 (mp0) REVERT: K 55 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8033 (mm-30) REVERT: K 56 GLU cc_start: 0.8115 (mp0) cc_final: 0.7710 (mp0) REVERT: K 67 ARG cc_start: 0.8831 (mmm160) cc_final: 0.8413 (tpp80) REVERT: K 69 ARG cc_start: 0.8537 (ttp80) cc_final: 0.8263 (tmm160) REVERT: K 73 GLN cc_start: 0.8003 (pp30) cc_final: 0.7590 (pp30) REVERT: C 144 ASP cc_start: 0.9554 (p0) cc_final: 0.9292 (p0) REVERT: C 151 ASP cc_start: 0.9224 (t70) cc_final: 0.8493 (m-30) REVERT: C 159 PHE cc_start: 0.9241 (m-80) cc_final: 0.8910 (m-80) REVERT: C 187 PHE cc_start: 0.9099 (m-80) cc_final: 0.8777 (m-80) outliers start: 46 outliers final: 28 residues processed: 287 average time/residue: 2.2121 time to fit residues: 746.7145 Evaluate side-chains 251 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 6.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 1042 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain J residue 35 PHE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 213 LYS Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1072 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 67 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 212 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 307 optimal weight: 0.9990 chunk 321 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 125 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.127685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.076417 restraints weight = 56662.047| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.93 r_work: 0.2915 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27861 Z= 0.118 Angle : 0.661 17.481 37869 Z= 0.328 Chirality : 0.043 0.220 4327 Planarity : 0.004 0.066 4761 Dihedral : 11.120 81.967 4309 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.58 % Allowed : 21.96 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: -0.18 (0.14), residues: 3325 helix: 1.30 (0.16), residues: 1165 sheet: 0.32 (0.26), residues: 432 loop : -1.28 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.002 TRP I 997 HIS 0.005 0.001 HIS H 117 PHE 0.030 0.001 PHE I 972 TYR 0.014 0.001 TYR C 58 ARG 0.014 0.001 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 1068) hydrogen bonds : angle 4.30826 ( 3002) metal coordination : bond 0.00331 ( 6) metal coordination : angle 1.67232 ( 6) covalent geometry : bond 0.00275 (27855) covalent geometry : angle 0.66094 (37863) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 168 ILE cc_start: 0.8238 (pt) cc_final: 0.7921 (mt) REVERT: H 137 ASN cc_start: 0.9474 (p0) cc_final: 0.9195 (p0) REVERT: H 158 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7737 (mpp80) REVERT: H 228 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9377 (pp) REVERT: I 59 ILE cc_start: 0.9087 (pp) cc_final: 0.8846 (pp) REVERT: I 191 LYS cc_start: 0.9586 (mmmt) cc_final: 0.8970 (tmmt) REVERT: I 337 PHE cc_start: 0.8288 (t80) cc_final: 0.7789 (t80) REVERT: I 340 ASP cc_start: 0.8832 (m-30) cc_final: 0.8582 (p0) REVERT: I 542 ARG cc_start: 0.7059 (ttt180) cc_final: 0.6244 (ttt180) REVERT: I 952 GLN cc_start: 0.8900 (tp-100) cc_final: 0.8678 (tp-100) REVERT: J 136 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: J 156 ARG cc_start: 0.9220 (tpp80) cc_final: 0.9001 (tpp80) REVERT: J 289 ASP cc_start: 0.8586 (m-30) cc_final: 0.8153 (p0) REVERT: J 802 ASP cc_start: 0.8738 (t70) cc_final: 0.8409 (t0) REVERT: J 1189 MET cc_start: 0.4212 (tpp) cc_final: 0.3425 (tpp) REVERT: J 1343 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7614 (mm-30) REVERT: K 42 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7937 (mp0) REVERT: K 55 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8050 (mm-30) REVERT: K 56 GLU cc_start: 0.8127 (mp0) cc_final: 0.7725 (mp0) REVERT: K 67 ARG cc_start: 0.8826 (mmm160) cc_final: 0.8409 (tpp80) REVERT: K 73 GLN cc_start: 0.8012 (pp30) cc_final: 0.7782 (pp30) REVERT: C 159 PHE cc_start: 0.9371 (m-80) cc_final: 0.8972 (m-80) REVERT: C 187 PHE cc_start: 0.9110 (m-80) cc_final: 0.8769 (m-80) outliers start: 45 outliers final: 29 residues processed: 267 average time/residue: 1.4246 time to fit residues: 441.6837 Evaluate side-chains 253 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 221 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain J residue 35 PHE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 213 LYS Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1072 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 12 optimal weight: 2.9990 chunk 144 optimal weight: 40.0000 chunk 9 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 161 optimal weight: 0.0010 chunk 18 optimal weight: 0.2980 chunk 297 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 120 GLN I1129 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.126568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.075292 restraints weight = 56470.990| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.90 r_work: 0.2885 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27861 Z= 0.137 Angle : 0.679 16.065 37869 Z= 0.341 Chirality : 0.043 0.272 4327 Planarity : 0.005 0.060 4761 Dihedral : 11.115 83.980 4309 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.58 % Allowed : 22.00 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: -0.17 (0.14), residues: 3325 helix: 1.24 (0.16), residues: 1167 sheet: 0.38 (0.26), residues: 431 loop : -1.23 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP I 997 HIS 0.005 0.001 HIS C 182 PHE 0.019 0.001 PHE I 972 TYR 0.015 0.001 TYR C 58 ARG 0.023 0.001 ARG K 69 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 1068) hydrogen bonds : angle 4.37896 ( 3002) metal coordination : bond 0.00461 ( 6) metal coordination : angle 1.63717 ( 6) covalent geometry : bond 0.00328 (27855) covalent geometry : angle 0.67891 (37863) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 2.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 145 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8326 (tptm) REVERT: G 168 ILE cc_start: 0.8278 (pt) cc_final: 0.7946 (mt) REVERT: H 137 ASN cc_start: 0.9478 (p0) cc_final: 0.9174 (p0) REVERT: H 158 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7666 (mpp80) REVERT: H 228 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9355 (pp) REVERT: I 59 ILE cc_start: 0.9068 (pp) cc_final: 0.8840 (pp) REVERT: I 191 LYS cc_start: 0.9586 (mmmt) cc_final: 0.8984 (tmtt) REVERT: I 200 ARG cc_start: 0.7959 (mtm180) cc_final: 0.7403 (mtm180) REVERT: I 319 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8297 (OUTLIER) REVERT: I 337 PHE cc_start: 0.8337 (t80) cc_final: 0.7779 (t80) REVERT: I 340 ASP cc_start: 0.8886 (m-30) cc_final: 0.8621 (p0) REVERT: I 542 ARG cc_start: 0.7035 (ttt180) cc_final: 0.6171 (ttt180) REVERT: I 856 ASN cc_start: 0.8721 (m-40) cc_final: 0.8068 (t0) REVERT: I 1304 MET cc_start: 0.9472 (OUTLIER) cc_final: 0.8395 (tpt) REVERT: J 156 ARG cc_start: 0.9237 (tpp80) cc_final: 0.9026 (tpp80) REVERT: J 289 ASP cc_start: 0.8624 (m-30) cc_final: 0.8168 (p0) REVERT: J 802 ASP cc_start: 0.8765 (t70) cc_final: 0.8442 (t0) REVERT: J 1189 MET cc_start: 0.4228 (tpp) cc_final: 0.3407 (tpp) REVERT: J 1343 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7636 (mm-30) REVERT: K 42 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8175 (mp0) REVERT: K 55 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8132 (mm-30) REVERT: K 56 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: K 69 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8357 (tmm160) REVERT: C 68 TRP cc_start: 0.9051 (p-90) cc_final: 0.8565 (p90) REVERT: C 151 ASP cc_start: 0.9063 (p0) cc_final: 0.8681 (m-30) REVERT: C 154 PHE cc_start: 0.9085 (m-80) cc_final: 0.8677 (m-80) REVERT: C 187 PHE cc_start: 0.9064 (m-80) cc_final: 0.8722 (m-80) outliers start: 45 outliers final: 31 residues processed: 262 average time/residue: 1.4738 time to fit residues: 449.9435 Evaluate side-chains 254 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 35 PHE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 213 LYS Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1072 LYS Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 130 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 271 optimal weight: 8.9990 chunk 153 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 214 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.126586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.075337 restraints weight = 56613.808| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.90 r_work: 0.2890 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.5872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27861 Z= 0.133 Angle : 0.689 15.665 37869 Z= 0.345 Chirality : 0.043 0.269 4327 Planarity : 0.004 0.060 4761 Dihedral : 11.084 85.817 4309 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.65 % Allowed : 22.07 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: -0.13 (0.14), residues: 3325 helix: 1.28 (0.16), residues: 1162 sheet: 0.48 (0.26), residues: 426 loop : -1.24 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP I 997 HIS 0.006 0.001 HIS C 182 PHE 0.018 0.001 PHE C 169 TYR 0.014 0.001 TYR C 157 ARG 0.016 0.001 ARG K 69 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 1068) hydrogen bonds : angle 4.35326 ( 3002) metal coordination : bond 0.00431 ( 6) metal coordination : angle 1.60898 ( 6) covalent geometry : bond 0.00315 (27855) covalent geometry : angle 0.68844 (37863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22840.17 seconds wall clock time: 393 minutes 37.39 seconds (23617.39 seconds total)