Starting phenix.real_space_refine on Tue Jun 24 00:21:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pfg_17646/06_2025/8pfg_17646.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pfg_17646/06_2025/8pfg_17646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pfg_17646/06_2025/8pfg_17646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pfg_17646/06_2025/8pfg_17646.map" model { file = "/net/cci-nas-00/data/ceres_data/8pfg_17646/06_2025/8pfg_17646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pfg_17646/06_2025/8pfg_17646.cif" } resolution = 3.1 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= 0.006 sd= 0.048 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 1 6.06 5 P 90 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 17149 2.51 5 N 4926 2.21 5 O 5532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 27809 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 8, 'TRANS': 127} Chain breaks: 1 Chain: "I" Number of atoms: 10423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 Chain: "J" Number of atoms: 10240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1317, 10240 Classifications: {'peptide': 1317} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1261} Chain breaks: 3 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "G" Number of atoms: 1807 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Conformer: "B" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} bond proxies already assigned to first conformer: 1812 Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1710 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 9, 'TRANS': 212} Chain breaks: 1 Chain: "R" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 6} Link IDs: {'rna3p': 11} Chain: "B" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 828 Classifications: {'DNA': 40} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 39} Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 808 Classifications: {'DNA': 40} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 39} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17586 SG CYS J 814 57.792 126.733 93.279 1.00 77.22 S ATOM 18151 SG CYS J 888 59.486 123.533 92.598 1.00 97.40 S ATOM 18202 SG CYS J 895 58.648 126.124 89.739 1.00 97.68 S ATOM 18223 SG CYS J 898 61.507 126.684 92.122 1.00 89.95 S Time building chain proxies: 17.06, per 1000 atoms: 0.61 Number of scatterers: 27809 At special positions: 0 Unit cell: (138.944, 171.392, 158.08, 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 1 29.99 S 110 16.00 P 90 15.00 Mg 1 11.99 O 5532 8.00 N 4926 7.00 C 17149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS P 51 " - pdb=" SG CYS P 139 " distance=2.03 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: 6.64 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 898 " Number of angles added : 6 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6126 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 46 sheets defined 39.9% alpha, 17.7% beta 41 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 10.53 Creating SS restraints... Processing helix chain 'P' and resid 13 through 24 Processing helix chain 'P' and resid 65 through 71 Processing helix chain 'P' and resid 89 through 99 removed outlier: 3.810A pdb=" N ILE P 93 " --> pdb=" O PRO P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 132 Processing helix chain 'P' and resid 134 through 154 removed outlier: 3.760A pdb=" N MET P 140 " --> pdb=" O GLU P 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 10 removed outlier: 3.626A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 4.226A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE I 35 " --> pdb=" O GLN I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.821A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 212 removed outlier: 3.819A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 294 removed outlier: 4.136A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 294' Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.061A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 480 removed outlier: 3.504A pdb=" N ARG I 478 " --> pdb=" O ALA I 474 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 483 through 487 removed outlier: 3.645A pdb=" N THR I 486 " --> pdb=" O ASP I 483 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.567A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 609 through 613 removed outlier: 3.552A pdb=" N GLY I 612 " --> pdb=" O ILE I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.677A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 3.867A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 863 Processing helix chain 'I' and resid 942 through 983 Processing helix chain 'I' and resid 985 through 992 Processing helix chain 'I' and resid 994 through 998 Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 3.542A 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: 4.077A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.526A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1161 through 1164 Processing helix chain 'I' and resid 1165 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.616A 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 58 through 63 removed outlier: 3.531A pdb=" N GLY J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 101 removed outlier: 3.706A pdb=" N GLU J 100 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 removed outlier: 3.508A pdb=" N TYR J 140 " --> pdb=" O GLU J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.621A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 291 through 308 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.659A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 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 removed outlier: 3.776A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.563A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.973A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.684A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1068 through 1074 removed outlier: 4.081A pdb=" N LEU J1074 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.532A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.333A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1296 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.678A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1360 through 1375 removed outlier: 4.251A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.938A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'G' and resid 34 through 48 removed outlier: 3.527A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.655A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 160 removed outlier: 3.736A pdb=" N ILE G 159 " --> pdb=" O SER G 156 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS G 160 " --> pdb=" O THR G 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 156 through 160' Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.381A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.598A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 111 through 115 removed outlier: 3.652A pdb=" N ASP H 114 " --> pdb=" O THR H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 229 removed outlier: 3.564A pdb=" N ALA H 216 " --> pdb=" O ASP H 212 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE H 217 " --> pdb=" O PRO H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 232 No H-bonds generated for 'chain 'H' and resid 230 through 232' Processing sheet with id=AA1, first strand: chain 'P' and resid 27 through 29 removed outlier: 4.729A pdb=" N LEU P 6 " --> pdb=" O VAL P 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 32 through 37 Processing sheet with id=AA3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.423A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.348A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA6, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.341A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.919A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 227 through 231 removed outlier: 3.556A pdb=" N ILE I 333 " --> pdb=" O PHE I 230 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 239 through 240 removed outlier: 3.738A pdb=" N ILE I 285 " --> pdb=" O MET I 239 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.911A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 301 through 303 removed outlier: 3.553A pdb=" N CYS I 311 " --> pdb=" O TYR I 301 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASP I 303 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU I 309 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.528A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB5, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.490A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.785A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AB8, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AB9, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.348A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.956A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 849 through 850 removed outlier: 3.517A pdb=" N GLU I 849 " --> pdb=" O VAL I 887 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.896A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.759A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU J 449 " --> pdb=" O VAL J 354 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N THR J 356 " --> pdb=" O LEU J 449 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC6, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.881A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.800A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.832A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD1, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AD2, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD3, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD4, first strand: chain 'J' and resid 825 through 826 removed outlier: 6.954A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 848 through 849 removed outlier: 7.061A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.169A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.156A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 1024 through 1025 Processing sheet with id=AD9, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE1, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.788A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 1186 through 1190 removed outlier: 4.196A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.644A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.042A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU G 198 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 98 through 105 removed outlier: 7.391A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA G 55 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AE7, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.806A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AE9, first strand: chain 'H' and resid 15 through 20 removed outlier: 3.536A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N THR H 196 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL H 192 " --> pdb=" O THR H 196 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 97 through 105 removed outlier: 7.575A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) 1151 hydrogen bonds defined for protein. 3248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 14.51 Time building geometry restraints manager: 7.92 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: 9008 1.34 - 1.46: 3991 1.46 - 1.58: 15054 1.58 - 1.70: 179 1.70 - 1.81: 192 Bond restraints: 28424 Sorted by residual: bond pdb=" C3' DA A 2 " pdb=" O3' DA A 2 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.26e+00 bond pdb=" C GLY H 108 " pdb=" N PRO H 109 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.51e+00 bond pdb=" N THR J1169 " pdb=" CA THR J1169 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.15e+00 bond pdb=" C3' DC A 11 " pdb=" O3' DC A 11 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.13e+00 bond pdb=" CB ASP J 256 " pdb=" CG ASP J 256 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.50e-01 ... (remaining 28419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 37999 1.29 - 2.58: 633 2.58 - 3.86: 142 3.86 - 5.15: 15 5.15 - 6.44: 12 Bond angle restraints: 38801 Sorted by residual: angle pdb=" N GLY H 108 " pdb=" CA GLY H 108 " pdb=" C GLY H 108 " ideal model delta sigma weight residual 112.34 118.12 -5.78 2.04e+00 2.40e-01 8.04e+00 angle pdb=" C3' DC A 36 " pdb=" C2' DC A 36 " pdb=" C1' DC A 36 " ideal model delta sigma weight residual 101.60 97.67 3.93 1.50e+00 4.44e-01 6.86e+00 angle pdb=" C THR J1169 " pdb=" CA THR J1169 " pdb=" CB THR J1169 " ideal model delta sigma weight residual 110.42 115.42 -5.00 1.99e+00 2.53e-01 6.32e+00 angle pdb=" C ASN K 15 " pdb=" N ARG K 16 " pdb=" CA ARG K 16 " ideal model delta sigma weight residual 121.54 126.33 -4.79 1.91e+00 2.74e-01 6.29e+00 angle pdb=" C LEU J 255 " pdb=" N ASP J 256 " pdb=" CA ASP J 256 " ideal model delta sigma weight residual 122.08 125.35 -3.27 1.47e+00 4.63e-01 4.94e+00 ... (remaining 38796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 16327 35.35 - 70.71: 901 70.71 - 106.06: 40 106.06 - 141.41: 3 141.41 - 176.76: 2 Dihedral angle restraints: 17273 sinusoidal: 7759 harmonic: 9514 Sorted by residual: dihedral pdb=" CB CYS P 51 " pdb=" SG CYS P 51 " pdb=" SG CYS P 139 " pdb=" CB CYS P 139 " ideal model delta sinusoidal sigma weight residual 93.00 9.67 83.33 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CA ASN I 314 " pdb=" C ASN I 314 " pdb=" N MET I 315 " pdb=" CA MET I 315 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" C4' DC A 11 " pdb=" C3' DC A 11 " pdb=" O3' DC A 11 " pdb=" P DG A 12 " ideal model delta sinusoidal sigma weight residual -140.00 36.76 -176.76 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 17270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2881 0.030 - 0.059: 1029 0.059 - 0.089: 287 0.089 - 0.119: 209 0.119 - 0.149: 32 Chirality restraints: 4438 Sorted by residual: chirality pdb=" CA ILE J1090 " pdb=" N ILE J1090 " pdb=" C ILE J1090 " pdb=" CB ILE J1090 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA ASP J 256 " pdb=" N ASP J 256 " pdb=" C ASP J 256 " pdb=" CB ASP J 256 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE I 668 " pdb=" N ILE I 668 " pdb=" C ILE I 668 " pdb=" CB ILE I 668 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 4435 not shown) Planarity restraints: 4754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL J 858 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO J 859 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO J 859 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 859 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN I 519 " -0.023 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO I 520 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO I 520 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 520 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 245 " -0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO J 246 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO J 246 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO J 246 " -0.020 5.00e-02 4.00e+02 ... (remaining 4751 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 263 2.58 - 3.16: 22086 3.16 - 3.74: 45563 3.74 - 4.32: 60425 4.32 - 4.90: 100935 Nonbonded interactions: 229272 Sorted by model distance: nonbonded pdb=" OP1 U R 17 " pdb="MG MG J1502 " model vdw 1.999 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1502 " model vdw 2.152 2.170 nonbonded pdb=" O TRP J 115 " pdb=" OG SER J 119 " model vdw 2.206 3.040 nonbonded pdb=" OG SER I 646 " pdb=" OD1 ASP I 648 " model vdw 2.213 3.040 nonbonded pdb=" O LYS J 964 " pdb=" OG1 THR J 976 " model vdw 2.215 3.040 ... (remaining 229267 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 4 through 158 or resid 167 through 218 or resid 220 throug \ h 233)) selection = (chain 'H' and (resid 4 through 218 or resid 220 through 233)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.230 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 78.260 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 : 0.003 0.045 28429 Z= 0.123 Angle : 0.453 6.783 38809 Z= 0.244 Chirality : 0.039 0.149 4438 Planarity : 0.003 0.037 4754 Dihedral : 18.936 176.763 11144 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.49 % Allowed : 18.64 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 3288 helix: 1.82 (0.15), residues: 1186 sheet: -0.01 (0.24), residues: 466 loop : -0.28 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 409 HIS 0.003 0.000 HIS J1252 PHE 0.017 0.001 PHE J 461 TYR 0.011 0.001 TYR J 140 ARG 0.002 0.000 ARG I 371 Details of bonding type rmsd hydrogen bonds : bond 0.13147 ( 1254) hydrogen bonds : angle 5.23223 ( 3454) metal coordination : bond 0.00719 ( 4) metal coordination : angle 4.17674 ( 6) SS BOND : bond 0.00314 ( 1) SS BOND : angle 2.09342 ( 2) covalent geometry : bond 0.00273 (28424) covalent geometry : angle 0.44985 (38801) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 334 time to evaluate : 3.303 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: P 134 ASP cc_start: 0.8959 (m-30) cc_final: 0.8563 (t0) REVERT: P 143 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8126 (mm) REVERT: I 30 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8961 (tp) REVERT: I 81 ASP cc_start: 0.8217 (t0) cc_final: 0.7591 (t0) REVERT: I 962 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: I 1027 LYS cc_start: 0.9039 (mmtm) cc_final: 0.8807 (mmtm) REVERT: J 29 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7744 (ppp) REVERT: J 196 GLN cc_start: 0.8568 (mp10) cc_final: 0.8325 (mp10) REVERT: J 300 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8097 (tp40) REVERT: J 398 LYS cc_start: 0.9362 (mttt) cc_final: 0.8998 (mtmm) REVERT: J 673 VAL cc_start: 0.8324 (OUTLIER) cc_final: 0.7851 (p) REVERT: J 832 LYS cc_start: 0.9187 (mptt) cc_final: 0.8847 (mmtm) REVERT: J 856 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8277 (mt) REVERT: J 1029 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.7866 (t) REVERT: J 1369 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7685 (ttp-170) REVERT: K 4 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8857 (t) REVERT: K 21 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9070 (mm) REVERT: K 65 ASP cc_start: 0.8266 (p0) cc_final: 0.7981 (p0) REVERT: K 68 GLU cc_start: 0.8640 (pp20) cc_final: 0.8308 (pp20) REVERT: K 71 GLU cc_start: 0.9200 (tp30) cc_final: 0.8738 (tm-30) REVERT: G 58 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7513 (mt-10) REVERT: G 83 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8201 (tt) REVERT: H 186 ASN cc_start: 0.8806 (t0) cc_final: 0.8487 (t0) outliers start: 155 outliers final: 63 residues processed: 483 average time/residue: 0.4281 time to fit residues: 322.1075 Evaluate side-chains 352 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 277 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 677 ASN Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1164 PHE Chi-restraints excluded: chain I residue 1188 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 655 SER Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1067 ARG Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1116 SER Chi-restraints excluded: chain J residue 1117 SER Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain J residue 1369 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 0.7980 chunk 256 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 chunk 102 optimal weight: 0.0050 chunk 161 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 83 GLN I 649 GLN I1038 GLN ** J 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** 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 = 0.3637 r_free = 0.3637 target = 0.086690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.062257 restraints weight = 92466.230| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.13 r_work: 0.2948 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 28429 Z= 0.228 Angle : 0.567 7.779 38809 Z= 0.301 Chirality : 0.042 0.186 4438 Planarity : 0.004 0.043 4754 Dihedral : 16.894 176.006 4803 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.65 % Allowed : 20.66 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.69 (0.15), residues: 3288 helix: 1.75 (0.15), residues: 1200 sheet: -0.02 (0.24), residues: 475 loop : -0.34 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J1193 HIS 0.003 0.001 HIS J1252 PHE 0.020 0.001 PHE P 126 TYR 0.012 0.001 TYR J1186 ARG 0.011 0.000 ARG P 138 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 1254) hydrogen bonds : angle 4.50764 ( 3454) metal coordination : bond 0.00920 ( 4) metal coordination : angle 2.48264 ( 6) SS BOND : bond 0.00204 ( 1) SS BOND : angle 2.45170 ( 2) covalent geometry : bond 0.00523 (28424) covalent geometry : angle 0.56621 (38801) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 283 time to evaluate : 3.303 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: P 95 GLN cc_start: 0.9370 (tt0) cc_final: 0.8984 (tt0) REVERT: I 30 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9008 (tp) REVERT: I 275 ARG cc_start: 0.8931 (ttp80) cc_final: 0.8713 (ttp80) REVERT: I 681 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8580 (mtm) REVERT: I 741 MET cc_start: 0.8662 (tpp) cc_final: 0.8149 (mmt) REVERT: I 1027 LYS cc_start: 0.9001 (mmtm) cc_final: 0.8791 (mmtm) REVERT: I 1164 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8129 (t80) REVERT: J 398 LYS cc_start: 0.9325 (mttt) cc_final: 0.9011 (mtpp) REVERT: J 497 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8451 (mp0) REVERT: J 832 LYS cc_start: 0.9260 (mptt) cc_final: 0.8913 (mptt) REVERT: J 856 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8471 (mt) REVERT: K 3 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8143 (tpt90) REVERT: K 21 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.8865 (mm) REVERT: K 55 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7392 (mt-10) REVERT: K 65 ASP cc_start: 0.8005 (p0) cc_final: 0.7698 (p0) REVERT: K 68 GLU cc_start: 0.8691 (pp20) cc_final: 0.8362 (pp20) REVERT: K 71 GLU cc_start: 0.9233 (tp30) cc_final: 0.8829 (tm-30) REVERT: H 95 LYS cc_start: 0.9035 (mtmt) cc_final: 0.8797 (mtmt) REVERT: H 186 ASN cc_start: 0.8825 (t0) cc_final: 0.8507 (t0) outliers start: 103 outliers final: 57 residues processed: 360 average time/residue: 0.4408 time to fit residues: 245.4168 Evaluate side-chains 329 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 265 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 139 CYS Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 864 LYS Chi-restraints excluded: chain I residue 881 ASP Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 1036 ILE Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1164 PHE Chi-restraints excluded: chain I residue 1188 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 497 GLU Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain J residue 1067 ARG Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 305 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 254 optimal weight: 0.0470 chunk 217 optimal weight: 0.0970 chunk 335 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 chunk 326 optimal weight: 0.9990 chunk 288 optimal weight: 0.9980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 127 GLN I 173 ASN J 667 GLN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** 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 = 0.3633 r_free = 0.3633 target = 0.087514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.063578 restraints weight = 88374.912| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.13 r_work: 0.2943 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28429 Z= 0.121 Angle : 0.513 7.261 38809 Z= 0.271 Chirality : 0.040 0.169 4438 Planarity : 0.004 0.047 4754 Dihedral : 16.716 174.346 4736 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.30 % Allowed : 21.01 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3288 helix: 1.75 (0.15), residues: 1203 sheet: -0.05 (0.24), residues: 490 loop : -0.28 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J1193 HIS 0.003 0.000 HIS I1244 PHE 0.020 0.001 PHE P 126 TYR 0.011 0.001 TYR J 140 ARG 0.005 0.000 ARG K 3 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 1254) hydrogen bonds : angle 4.29292 ( 3454) metal coordination : bond 0.00456 ( 4) metal coordination : angle 2.34521 ( 6) SS BOND : bond 0.00251 ( 1) SS BOND : angle 2.42892 ( 2) covalent geometry : bond 0.00274 (28424) covalent geometry : angle 0.51176 (38801) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 304 time to evaluate : 3.069 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: P 32 MET cc_start: 0.8554 (mmm) cc_final: 0.8047 (mmm) REVERT: P 143 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8038 (mm) REVERT: I 30 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9030 (tp) REVERT: I 142 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7972 (mm-30) REVERT: I 653 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8306 (ttt) REVERT: I 681 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8622 (mtm) REVERT: I 741 MET cc_start: 0.8775 (tpp) cc_final: 0.8559 (mmm) REVERT: I 962 GLU cc_start: 0.8304 (tp30) cc_final: 0.7903 (mt-10) REVERT: I 1027 LYS cc_start: 0.9066 (mmtm) cc_final: 0.8838 (mmtm) REVERT: I 1164 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8217 (t80) REVERT: J 50 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7383 (tmtt) REVERT: J 183 GLU cc_start: 0.8800 (pp20) cc_final: 0.8482 (pp20) REVERT: J 398 LYS cc_start: 0.9330 (mttt) cc_final: 0.8925 (mtpp) REVERT: J 404 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8003 (mm-30) REVERT: J 405 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6732 (tp30) REVERT: J 497 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8685 (mm-30) REVERT: J 832 LYS cc_start: 0.9269 (mptt) cc_final: 0.8837 (mptt) REVERT: J 856 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8497 (mt) REVERT: J 1143 ASP cc_start: 0.8722 (m-30) cc_final: 0.8399 (m-30) REVERT: J 1370 MET cc_start: 0.7491 (ptp) cc_final: 0.7274 (ptp) REVERT: K 3 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8384 (tpm-80) REVERT: K 4 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8776 (t) REVERT: K 21 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8667 (mm) REVERT: K 65 ASP cc_start: 0.7875 (p0) cc_final: 0.7549 (p0) REVERT: K 68 GLU cc_start: 0.8690 (pp20) cc_final: 0.8373 (pp20) REVERT: K 71 GLU cc_start: 0.9210 (tp30) cc_final: 0.8807 (tm-30) REVERT: H 25 LYS cc_start: 0.9096 (mtpm) cc_final: 0.8882 (ttmm) REVERT: H 39 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8414 (mt) REVERT: H 80 GLU cc_start: 0.8773 (mp0) cc_final: 0.8450 (pm20) REVERT: H 186 ASN cc_start: 0.8945 (t0) cc_final: 0.8521 (t0) outliers start: 93 outliers final: 49 residues processed: 374 average time/residue: 0.4343 time to fit residues: 252.4632 Evaluate side-chains 342 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 280 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 51 CYS Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 134 ASP Chi-restraints excluded: chain P residue 139 CYS Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 881 ASP Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1164 PHE Chi-restraints excluded: chain I residue 1188 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1308 ILE Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 405 GLU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 497 GLU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain J residue 1067 ARG Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 44 optimal weight: 5.9990 chunk 314 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 328 optimal weight: 0.8980 chunk 255 optimal weight: 2.9990 chunk 324 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 319 optimal weight: 0.0870 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 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 = 0.3619 r_free = 0.3619 target = 0.086794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.062887 restraints weight = 80170.852| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.94 r_work: 0.2938 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28429 Z= 0.156 Angle : 0.532 13.988 38809 Z= 0.279 Chirality : 0.041 0.145 4438 Planarity : 0.004 0.050 4754 Dihedral : 16.681 175.511 4719 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.79 % Allowed : 20.91 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.71 (0.15), residues: 3288 helix: 1.77 (0.15), residues: 1201 sheet: -0.12 (0.24), residues: 486 loop : -0.29 (0.16), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J1193 HIS 0.003 0.001 HIS J1252 PHE 0.025 0.001 PHE I 80 TYR 0.037 0.001 TYR H 177 ARG 0.008 0.000 ARG G 191 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 1254) hydrogen bonds : angle 4.25671 ( 3454) metal coordination : bond 0.00756 ( 4) metal coordination : angle 2.51230 ( 6) SS BOND : bond 0.00205 ( 1) SS BOND : angle 2.48756 ( 2) covalent geometry : bond 0.00358 (28424) covalent geometry : angle 0.53133 (38801) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 285 time to evaluate : 3.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 32 MET cc_start: 0.8660 (mmm) cc_final: 0.7931 (mmm) REVERT: P 95 GLN cc_start: 0.9338 (tt0) cc_final: 0.9018 (tt0) REVERT: P 143 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8047 (mm) REVERT: I 30 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.9013 (tp) REVERT: I 142 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8129 (mm-30) REVERT: I 275 ARG cc_start: 0.9110 (ttp80) cc_final: 0.8716 (ttp80) REVERT: I 653 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8388 (ttt) REVERT: I 681 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8555 (mtm) REVERT: I 741 MET cc_start: 0.8757 (tpp) cc_final: 0.8538 (mmm) REVERT: I 1027 LYS cc_start: 0.9070 (mmtm) cc_final: 0.8842 (mmtm) REVERT: I 1164 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8177 (t80) REVERT: J 50 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7398 (tmtt) REVERT: J 183 GLU cc_start: 0.8813 (pp20) cc_final: 0.8503 (pp20) REVERT: J 300 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8040 (tp40) REVERT: J 398 LYS cc_start: 0.9330 (mttt) cc_final: 0.9013 (mtmm) REVERT: J 404 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8145 (mm-30) REVERT: J 497 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8684 (mm-30) REVERT: J 832 LYS cc_start: 0.9275 (mptt) cc_final: 0.8828 (mptt) REVERT: J 856 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8525 (mt) REVERT: J 1143 ASP cc_start: 0.8718 (m-30) cc_final: 0.8402 (m-30) REVERT: J 1370 MET cc_start: 0.7418 (ptp) cc_final: 0.7206 (ptp) REVERT: K 3 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8289 (tpm-80) REVERT: K 4 VAL cc_start: 0.9046 (OUTLIER) cc_final: 0.8787 (t) REVERT: K 21 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8714 (mm) REVERT: K 65 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7610 (p0) REVERT: K 68 GLU cc_start: 0.8709 (pp20) cc_final: 0.8371 (pp20) REVERT: H 25 LYS cc_start: 0.9090 (mtpm) cc_final: 0.8885 (ttmm) REVERT: H 80 GLU cc_start: 0.8794 (mp0) cc_final: 0.8535 (mp0) REVERT: H 95 LYS cc_start: 0.9129 (mtmt) cc_final: 0.8783 (mtmm) REVERT: H 186 ASN cc_start: 0.8948 (t0) cc_final: 0.8491 (t0) outliers start: 107 outliers final: 60 residues processed: 369 average time/residue: 0.4338 time to fit residues: 249.0139 Evaluate side-chains 342 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 269 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 51 CYS Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 139 CYS Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 864 LYS Chi-restraints excluded: chain I residue 881 ASP Chi-restraints excluded: chain I residue 1036 ILE Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1164 PHE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1188 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 497 GLU Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1067 ARG Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 325 optimal weight: 2.9990 chunk 263 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 91 optimal weight: 0.0970 chunk 8 optimal weight: 0.0980 chunk 22 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 312 optimal weight: 10.0000 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 875 ASN J1259 GLN ** G 41 ASN ** 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 = 0.3695 r_free = 0.3695 target = 0.093491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.068770 restraints weight = 90942.288| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.02 r_work: 0.3017 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28429 Z= 0.105 Angle : 0.513 14.111 38809 Z= 0.268 Chirality : 0.040 0.174 4438 Planarity : 0.003 0.051 4754 Dihedral : 16.628 173.751 4714 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.87 % Allowed : 22.18 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.80 (0.15), residues: 3288 helix: 1.81 (0.15), residues: 1228 sheet: -0.01 (0.24), residues: 480 loop : -0.27 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J1193 HIS 0.004 0.000 HIS P 94 PHE 0.018 0.001 PHE P 126 TYR 0.025 0.001 TYR H 177 ARG 0.006 0.000 ARG I 996 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 1254) hydrogen bonds : angle 4.13899 ( 3454) metal coordination : bond 0.00308 ( 4) metal coordination : angle 2.36695 ( 6) SS BOND : bond 0.00183 ( 1) SS BOND : angle 2.33692 ( 2) covalent geometry : bond 0.00233 (28424) covalent geometry : angle 0.51235 (38801) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 298 time to evaluate : 5.189 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: P 32 MET cc_start: 0.8645 (mmm) cc_final: 0.7917 (mmm) REVERT: P 143 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8015 (mm) REVERT: I 30 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8924 (tp) REVERT: I 681 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8726 (mtm) REVERT: I 968 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8253 (pp20) REVERT: I 1027 LYS cc_start: 0.9009 (mmtm) cc_final: 0.8809 (mmtm) REVERT: I 1164 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8347 (t80) REVERT: J 37 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7231 (tm-30) REVERT: J 50 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7549 (tmtt) REVERT: J 172 PHE cc_start: 0.8107 (m-80) cc_final: 0.7017 (m-10) REVERT: J 183 GLU cc_start: 0.8686 (pp20) cc_final: 0.8427 (pp20) REVERT: J 300 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8107 (tp40) REVERT: J 398 LYS cc_start: 0.9337 (mttt) cc_final: 0.9066 (mtmm) REVERT: J 458 ASN cc_start: 0.9097 (t0) cc_final: 0.8883 (t0) REVERT: J 462 ASP cc_start: 0.8567 (t0) cc_final: 0.7970 (t0) REVERT: J 832 LYS cc_start: 0.9291 (mptt) cc_final: 0.8933 (mptt) REVERT: J 1040 MET cc_start: 0.5184 (pmm) cc_final: 0.4840 (pmm) REVERT: J 1143 ASP cc_start: 0.8743 (m-30) cc_final: 0.8451 (m-30) REVERT: K 3 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8207 (tpm-80) REVERT: K 4 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8799 (t) REVERT: K 21 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8980 (mt) REVERT: K 65 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7649 (p0) REVERT: K 68 GLU cc_start: 0.8724 (pp20) cc_final: 0.8374 (pp20) REVERT: H 39 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8367 (mt) REVERT: H 76 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: H 80 GLU cc_start: 0.8702 (mp0) cc_final: 0.8501 (mp0) REVERT: H 186 ASN cc_start: 0.8741 (t0) cc_final: 0.8385 (t0) outliers start: 81 outliers final: 44 residues processed: 360 average time/residue: 0.6056 time to fit residues: 345.8810 Evaluate side-chains 331 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 273 time to evaluate : 5.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 51 CYS Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 139 CYS Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 864 LYS Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1164 PHE Chi-restraints excluded: chain I residue 1188 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1308 ILE Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1067 ARG Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 162 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 282 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 284 optimal weight: 0.5980 chunk 207 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 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 = 0.3638 r_free = 0.3638 target = 0.087820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.064127 restraints weight = 74530.315| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.85 r_work: 0.2973 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28429 Z= 0.129 Angle : 0.524 13.978 38809 Z= 0.275 Chirality : 0.040 0.161 4438 Planarity : 0.004 0.052 4754 Dihedral : 16.584 174.869 4704 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 2.83 % Allowed : 22.68 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.80 (0.15), residues: 3288 helix: 1.84 (0.15), residues: 1221 sheet: -0.06 (0.24), residues: 487 loop : -0.26 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J1193 HIS 0.029 0.001 HIS P 94 PHE 0.014 0.001 PHE I 80 TYR 0.041 0.001 TYR H 177 ARG 0.007 0.000 ARG I 275 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 1254) hydrogen bonds : angle 4.11452 ( 3454) metal coordination : bond 0.00569 ( 4) metal coordination : angle 2.39029 ( 6) SS BOND : bond 0.00154 ( 1) SS BOND : angle 2.48022 ( 2) covalent geometry : bond 0.00296 (28424) covalent geometry : angle 0.52308 (38801) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 287 time to evaluate : 3.181 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: P 32 MET cc_start: 0.8526 (mmm) cc_final: 0.7830 (mmm) REVERT: P 94 HIS cc_start: 0.8463 (m-70) cc_final: 0.8201 (m90) REVERT: P 95 GLN cc_start: 0.9421 (tt0) cc_final: 0.8983 (tt0) REVERT: P 143 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7994 (mm) REVERT: I 30 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8965 (tp) REVERT: I 142 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7979 (mm-30) REVERT: I 515 MET cc_start: 0.8920 (ttm) cc_final: 0.8624 (ttt) REVERT: I 653 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8406 (ttt) REVERT: I 681 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8509 (mtm) REVERT: I 1164 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8278 (t80) REVERT: J 37 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7112 (tm-30) REVERT: J 50 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7468 (tmtt) REVERT: J 172 PHE cc_start: 0.7862 (m-80) cc_final: 0.6983 (m-80) REVERT: J 183 GLU cc_start: 0.8798 (pp20) cc_final: 0.8501 (pp20) REVERT: J 300 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7983 (tp40) REVERT: J 398 LYS cc_start: 0.9299 (mttt) cc_final: 0.8955 (mtmm) REVERT: J 458 ASN cc_start: 0.9073 (t0) cc_final: 0.8869 (t0) REVERT: J 462 ASP cc_start: 0.8449 (t0) cc_final: 0.7953 (t0) REVERT: J 832 LYS cc_start: 0.9286 (mptt) cc_final: 0.8860 (mptt) REVERT: J 1040 MET cc_start: 0.5324 (pmm) cc_final: 0.4890 (pmm) REVERT: J 1143 ASP cc_start: 0.8666 (m-30) cc_final: 0.8343 (m-30) REVERT: J 1370 MET cc_start: 0.7727 (ptp) cc_final: 0.7386 (ptp) REVERT: K 3 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8178 (tpm-80) REVERT: K 4 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8795 (t) REVERT: K 21 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8647 (mm) REVERT: K 65 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7533 (p0) REVERT: K 68 GLU cc_start: 0.8710 (pp20) cc_final: 0.8370 (pp20) REVERT: H 39 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8348 (mt) REVERT: H 76 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: H 80 GLU cc_start: 0.8832 (mp0) cc_final: 0.8548 (mp0) REVERT: H 186 ASN cc_start: 0.8924 (t0) cc_final: 0.8451 (t0) outliers start: 80 outliers final: 49 residues processed: 350 average time/residue: 0.4399 time to fit residues: 241.9416 Evaluate side-chains 344 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 281 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 CYS Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 139 CYS Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 864 LYS Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1164 PHE Chi-restraints excluded: chain I residue 1188 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1308 ILE Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 208 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 252 optimal weight: 9.9990 chunk 311 optimal weight: 0.9980 chunk 310 optimal weight: 0.9990 chunk 246 optimal weight: 40.0000 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 30.0000 chunk 167 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 792 ASN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.087716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.063238 restraints weight = 93603.037| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.16 r_work: 0.2976 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28429 Z= 0.168 Angle : 0.550 13.176 38809 Z= 0.287 Chirality : 0.041 0.178 4438 Planarity : 0.004 0.053 4754 Dihedral : 16.633 175.716 4699 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.13 % Favored : 96.84 % Rotamer: Outliers : 2.94 % Allowed : 22.40 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.73 (0.15), residues: 3288 helix: 1.80 (0.15), residues: 1221 sheet: -0.10 (0.24), residues: 484 loop : -0.32 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J1193 HIS 0.023 0.001 HIS P 94 PHE 0.030 0.001 PHE J 172 TYR 0.033 0.001 TYR H 177 ARG 0.005 0.000 ARG K 3 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 1254) hydrogen bonds : angle 4.17545 ( 3454) metal coordination : bond 0.00878 ( 4) metal coordination : angle 2.48912 ( 6) SS BOND : bond 0.00188 ( 1) SS BOND : angle 2.55065 ( 2) covalent geometry : bond 0.00389 (28424) covalent geometry : angle 0.54888 (38801) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 283 time to evaluate : 3.278 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: P 2 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7826 (tp40) REVERT: P 32 MET cc_start: 0.8554 (mmm) cc_final: 0.7748 (mmm) REVERT: P 62 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8651 (mm-30) REVERT: P 95 GLN cc_start: 0.9410 (tt0) cc_final: 0.8972 (tt0) REVERT: P 143 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8088 (mm) REVERT: I 30 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8958 (tp) REVERT: I 653 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8445 (ttt) REVERT: I 681 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8692 (mtm) REVERT: I 949 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8354 (mm-30) REVERT: I 1164 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8323 (t80) REVERT: J 37 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: J 50 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7498 (tmtt) REVERT: J 300 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8124 (tp40) REVERT: J 398 LYS cc_start: 0.9287 (mttt) cc_final: 0.9075 (mtmm) REVERT: J 462 ASP cc_start: 0.8397 (t0) cc_final: 0.8079 (t0) REVERT: J 1040 MET cc_start: 0.5533 (pmm) cc_final: 0.5004 (pmm) REVERT: J 1370 MET cc_start: 0.7705 (ptp) cc_final: 0.7490 (ptp) REVERT: K 3 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8253 (tpm-80) REVERT: K 4 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8823 (t) REVERT: K 21 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8818 (mm) REVERT: K 65 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7658 (p0) REVERT: K 68 GLU cc_start: 0.8788 (pp20) cc_final: 0.8447 (pp20) REVERT: H 39 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8387 (mt) REVERT: H 76 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: H 186 ASN cc_start: 0.8837 (t0) cc_final: 0.8447 (t0) outliers start: 83 outliers final: 56 residues processed: 349 average time/residue: 0.4747 time to fit residues: 259.9124 Evaluate side-chains 340 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 270 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 CYS Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 139 CYS Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 864 LYS Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1164 PHE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1308 ILE Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 58 optimal weight: 0.8980 chunk 246 optimal weight: 30.0000 chunk 179 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 272 optimal weight: 0.9990 chunk 308 optimal weight: 5.9990 chunk 306 optimal weight: 0.0670 chunk 255 optimal weight: 9.9990 chunk 292 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 792 ASN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.087965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.063967 restraints weight = 79676.303| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.90 r_work: 0.3000 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28429 Z= 0.152 Angle : 0.555 13.973 38809 Z= 0.290 Chirality : 0.041 0.170 4438 Planarity : 0.004 0.053 4754 Dihedral : 16.627 175.255 4697 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 3.08 % Allowed : 22.36 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.71 (0.15), residues: 3288 helix: 1.78 (0.15), residues: 1221 sheet: -0.10 (0.24), residues: 484 loop : -0.33 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP J1193 HIS 0.007 0.001 HIS P 94 PHE 0.020 0.001 PHE J 172 TYR 0.030 0.001 TYR H 177 ARG 0.007 0.000 ARG J 47 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 1254) hydrogen bonds : angle 4.17752 ( 3454) metal coordination : bond 0.00750 ( 4) metal coordination : angle 2.42253 ( 6) SS BOND : bond 0.00171 ( 1) SS BOND : angle 2.57993 ( 2) covalent geometry : bond 0.00352 (28424) covalent geometry : angle 0.55435 (38801) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 282 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 32 MET cc_start: 0.8512 (mmm) cc_final: 0.7783 (mmm) REVERT: P 62 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8595 (mm-30) REVERT: P 138 ARG cc_start: 0.9222 (mtt180) cc_final: 0.9006 (ptt-90) REVERT: P 143 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8112 (mm) REVERT: I 30 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8942 (tp) REVERT: I 291 TYR cc_start: 0.8378 (t80) cc_final: 0.8166 (t80) REVERT: I 653 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8377 (ttt) REVERT: I 681 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8667 (mtm) REVERT: I 1164 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8318 (t80) REVERT: J 37 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7214 (tm-30) REVERT: J 50 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7549 (tmtt) REVERT: J 300 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8096 (tp40) REVERT: J 398 LYS cc_start: 0.9319 (mttt) cc_final: 0.9059 (mtmm) REVERT: J 505 ASP cc_start: 0.8555 (m-30) cc_final: 0.8080 (m-30) REVERT: J 977 SER cc_start: 0.6866 (OUTLIER) cc_final: 0.6140 (t) REVERT: J 1040 MET cc_start: 0.5506 (pmm) cc_final: 0.4951 (pmm) REVERT: J 1370 MET cc_start: 0.7726 (ptp) cc_final: 0.7515 (ptp) REVERT: K 3 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8219 (tpm-80) REVERT: K 4 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8803 (t) REVERT: K 21 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8786 (mm) REVERT: K 65 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7683 (p0) REVERT: K 68 GLU cc_start: 0.8745 (pp20) cc_final: 0.8398 (pp20) REVERT: H 39 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8406 (mt) REVERT: H 76 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: H 186 ASN cc_start: 0.8821 (t0) cc_final: 0.8434 (t0) outliers start: 87 outliers final: 60 residues processed: 348 average time/residue: 0.4524 time to fit residues: 248.7636 Evaluate side-chains 348 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 273 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 CYS Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 139 CYS Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 864 LYS Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1164 PHE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1308 ILE Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1053 LEU Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 257 optimal weight: 0.0870 chunk 302 optimal weight: 3.9990 chunk 324 optimal weight: 0.9990 chunk 301 optimal weight: 0.5980 chunk 186 optimal weight: 0.2980 chunk 155 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 271 optimal weight: 0.8980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.089352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.065386 restraints weight = 81787.041| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.95 r_work: 0.3033 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28429 Z= 0.113 Angle : 0.548 13.538 38809 Z= 0.287 Chirality : 0.040 0.274 4438 Planarity : 0.003 0.054 4754 Dihedral : 16.575 173.993 4697 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 2.52 % Allowed : 23.25 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.78 (0.15), residues: 3288 helix: 1.80 (0.15), residues: 1222 sheet: 0.01 (0.24), residues: 472 loop : -0.28 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP J1193 HIS 0.007 0.001 HIS P 94 PHE 0.018 0.001 PHE J 172 TYR 0.028 0.001 TYR H 177 ARG 0.007 0.000 ARG I 275 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 1254) hydrogen bonds : angle 4.09992 ( 3454) metal coordination : bond 0.00374 ( 4) metal coordination : angle 2.41174 ( 6) SS BOND : bond 0.00147 ( 1) SS BOND : angle 2.45612 ( 2) covalent geometry : bond 0.00261 (28424) covalent geometry : angle 0.54724 (38801) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 292 time to evaluate : 3.061 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: P 32 MET cc_start: 0.8520 (mmm) cc_final: 0.7829 (mmm) REVERT: P 62 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8592 (mm-30) REVERT: P 143 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8052 (mm) REVERT: I 30 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8899 (tp) REVERT: I 291 TYR cc_start: 0.8339 (t80) cc_final: 0.8120 (t80) REVERT: I 653 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8288 (ttt) REVERT: I 681 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8655 (mtm) REVERT: I 949 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8286 (mm-30) REVERT: I 968 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8196 (pp20) REVERT: I 1164 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8393 (t80) REVERT: J 37 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: J 50 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7661 (tmtt) REVERT: J 300 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8108 (tp40) REVERT: J 398 LYS cc_start: 0.9305 (mttt) cc_final: 0.9052 (mtmm) REVERT: J 932 MET cc_start: 0.8096 (mtp) cc_final: 0.7893 (mtt) REVERT: J 977 SER cc_start: 0.6828 (OUTLIER) cc_final: 0.6104 (t) REVERT: J 1040 MET cc_start: 0.5551 (pmm) cc_final: 0.4970 (pmm) REVERT: K 3 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8150 (tpm-80) REVERT: K 4 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8800 (t) REVERT: K 21 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8761 (mm) REVERT: K 65 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7708 (p0) REVERT: K 68 GLU cc_start: 0.8749 (pp20) cc_final: 0.8395 (pp20) REVERT: H 39 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8345 (mt) REVERT: H 76 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: H 186 ASN cc_start: 0.8775 (t0) cc_final: 0.8395 (t0) outliers start: 71 outliers final: 50 residues processed: 350 average time/residue: 0.4323 time to fit residues: 235.1321 Evaluate side-chains 345 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 279 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 CYS Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 864 LYS Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1164 PHE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1308 ILE Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 104 optimal weight: 0.1980 chunk 201 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 236 optimal weight: 8.9990 chunk 308 optimal weight: 0.4980 chunk 273 optimal weight: 0.7980 chunk 257 optimal weight: 5.9990 chunk 281 optimal weight: 0.9990 chunk 272 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 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 = 0.3692 r_free = 0.3692 target = 0.089516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.065545 restraints weight = 80662.478| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.92 r_work: 0.3037 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28429 Z= 0.117 Angle : 0.565 13.884 38809 Z= 0.293 Chirality : 0.040 0.200 4438 Planarity : 0.004 0.057 4754 Dihedral : 16.558 174.346 4697 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 2.37 % Allowed : 23.39 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.78 (0.15), residues: 3288 helix: 1.78 (0.15), residues: 1230 sheet: -0.02 (0.24), residues: 470 loop : -0.27 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J1193 HIS 0.007 0.001 HIS P 94 PHE 0.019 0.001 PHE J 172 TYR 0.027 0.001 TYR H 177 ARG 0.019 0.000 ARG J 47 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 1254) hydrogen bonds : angle 4.08966 ( 3454) metal coordination : bond 0.00420 ( 4) metal coordination : angle 2.38057 ( 6) SS BOND : bond 0.00141 ( 1) SS BOND : angle 2.36424 ( 2) covalent geometry : bond 0.00272 (28424) covalent geometry : angle 0.56383 (38801) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 282 time to evaluate : 3.275 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: P 32 MET cc_start: 0.8512 (mmm) cc_final: 0.7827 (mmm) REVERT: P 62 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8595 (mm-30) REVERT: P 95 GLN cc_start: 0.9396 (tt0) cc_final: 0.8977 (tt0) REVERT: P 138 ARG cc_start: 0.9238 (mtt180) cc_final: 0.9027 (ptt-90) REVERT: P 143 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8020 (mm) REVERT: I 30 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8882 (tp) REVERT: I 291 TYR cc_start: 0.8375 (t80) cc_final: 0.8153 (t80) REVERT: I 315 MET cc_start: 0.8074 (pmm) cc_final: 0.7862 (pmm) REVERT: I 653 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8298 (ttt) REVERT: I 681 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8650 (mtm) REVERT: I 949 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8293 (mm-30) REVERT: I 968 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8166 (pp20) REVERT: I 1164 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8377 (t80) REVERT: I 1329 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7758 (mm-30) REVERT: J 37 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7185 (tm-30) REVERT: J 50 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7687 (tmtt) REVERT: J 300 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8067 (tp40) REVERT: J 398 LYS cc_start: 0.9297 (mttt) cc_final: 0.9048 (mtmm) REVERT: J 505 ASP cc_start: 0.8515 (m-30) cc_final: 0.8017 (m-30) REVERT: J 932 MET cc_start: 0.8106 (mtp) cc_final: 0.7647 (mtt) REVERT: J 977 SER cc_start: 0.6815 (OUTLIER) cc_final: 0.6088 (t) REVERT: J 1040 MET cc_start: 0.5576 (pmm) cc_final: 0.5053 (pmm) REVERT: K 3 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8144 (tpm-80) REVERT: K 4 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8804 (t) REVERT: K 65 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7689 (p0) REVERT: K 68 GLU cc_start: 0.8786 (pp20) cc_final: 0.8434 (pp20) REVERT: H 39 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8313 (mt) REVERT: H 76 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: H 186 ASN cc_start: 0.8770 (t0) cc_final: 0.8395 (t0) outliers start: 67 outliers final: 49 residues processed: 335 average time/residue: 0.4359 time to fit residues: 228.1405 Evaluate side-chains 339 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 274 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 CYS Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 864 LYS Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1164 PHE Chi-restraints excluded: chain I residue 1308 ILE Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 242 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 314 optimal weight: 0.9990 chunk 204 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 2 GLN ** P 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.086955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.062918 restraints weight = 76369.452| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.82 r_work: 0.2977 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28429 Z= 0.215 Angle : 0.622 14.110 38809 Z= 0.322 Chirality : 0.042 0.175 4438 Planarity : 0.004 0.097 4754 Dihedral : 16.674 176.700 4694 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 2.48 % Allowed : 23.56 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.63 (0.15), residues: 3288 helix: 1.74 (0.15), residues: 1214 sheet: -0.18 (0.24), residues: 484 loop : -0.37 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J1193 HIS 0.006 0.001 HIS P 94 PHE 0.017 0.001 PHE J 172 TYR 0.030 0.001 TYR H 177 ARG 0.017 0.001 ARG J 47 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 1254) hydrogen bonds : angle 4.29400 ( 3454) metal coordination : bond 0.01179 ( 4) metal coordination : angle 2.74660 ( 6) SS BOND : bond 0.00186 ( 1) SS BOND : angle 2.71867 ( 2) covalent geometry : bond 0.00495 (28424) covalent geometry : angle 0.62085 (38801) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17523.29 seconds wall clock time: 302 minutes 24.48 seconds (18144.48 seconds total)