Starting phenix.real_space_refine on Mon Aug 25 12:02:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pfg_17646/08_2025/8pfg_17646.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pfg_17646/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8pfg_17646/08_2025/8pfg_17646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pfg_17646/08_2025/8pfg_17646.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pfg_17646/08_2025/8pfg_17646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pfg_17646/08_2025/8pfg_17646.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.66, per 1000 atoms: 0.20 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: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 3.27 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: 5.46 Time building geometry restraints manager: 3.14 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: 4.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.150 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.240 ------------------------------------------------------------------------------- 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 : 8.90 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG I 371 TYR 0.011 0.001 TYR J 140 PHE 0.017 0.001 PHE J 461 TRP 0.008 0.001 TRP J 409 HIS 0.003 0.000 HIS J1252 Details of bonding type rmsd covalent geometry : bond 0.00273 (28424) covalent geometry : angle 0.44985 (38801) SS BOND : bond 0.00314 ( 1) SS BOND : angle 2.09342 ( 2) hydrogen bonds : bond 0.13147 ( 1254) hydrogen bonds : angle 5.23223 ( 3454) metal coordination : bond 0.00719 ( 4) metal coordination : angle 4.17674 ( 6) *********************** 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 : 0.806 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: 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: 0.8999 (mtmm) REVERT: J 673 VAL cc_start: 0.8324 (OUTLIER) cc_final: 0.7852 (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: 0.7982 (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: 0.1701 time to fit residues: 128.2024 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 : 0.994 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.0040 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.0156 ------------------------------------------------------------------------------- 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.086078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.062392 restraints weight = 75156.737| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.85 r_work: 0.2931 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 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 = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1144 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= 0.205 Angle : 0.567 8.013 38809 Z= 0.300 Chirality : 0.042 0.183 4438 Planarity : 0.004 0.044 4754 Dihedral : 16.878 175.271 4803 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.69 % Allowed : 20.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.15), residues: 3288 helix: 1.71 (0.15), residues: 1207 sheet: 0.01 (0.24), residues: 475 loop : -0.34 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 637 TYR 0.012 0.001 TYR J1186 PHE 0.022 0.001 PHE P 126 TRP 0.018 0.001 TRP J1193 HIS 0.003 0.001 HIS J1252 Details of bonding type rmsd covalent geometry : bond 0.00470 (28424) covalent geometry : angle 0.56602 (38801) SS BOND : bond 0.00395 ( 1) SS BOND : angle 2.61525 ( 2) hydrogen bonds : bond 0.04173 ( 1254) hydrogen bonds : angle 4.44511 ( 3454) metal coordination : bond 0.01012 ( 4) metal coordination : angle 2.33504 ( 6) *********************** 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 394 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 290 time to evaluate : 0.795 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 80 ARG cc_start: 0.7914 (ptp-110) cc_final: 0.7642 (ptp-110) REVERT: P 95 GLN cc_start: 0.9367 (tt0) cc_final: 0.8964 (tt0) REVERT: I 30 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.9052 (tp) REVERT: I 275 ARG cc_start: 0.8981 (ttp80) cc_final: 0.8751 (ttp80) REVERT: I 681 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8575 (mtm) REVERT: I 741 MET cc_start: 0.8793 (tpp) cc_final: 0.8240 (mmt) REVERT: I 1027 LYS cc_start: 0.9061 (mmtm) cc_final: 0.8841 (mmtm) REVERT: I 1164 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8100 (t80) REVERT: I 1219 GLU cc_start: 0.8750 (mp0) cc_final: 0.8238 (mp0) REVERT: J 183 GLU cc_start: 0.8777 (pp20) cc_final: 0.8460 (pp20) REVERT: J 398 LYS cc_start: 0.9336 (mttt) cc_final: 0.8984 (mtpp) REVERT: J 497 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8421 (mp0) REVERT: J 541 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9333 (mp) REVERT: J 667 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8780 (tm130) REVERT: J 832 LYS cc_start: 0.9254 (mptt) cc_final: 0.8823 (mptt) REVERT: J 856 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8407 (mt) REVERT: J 932 MET cc_start: 0.8523 (mtp) cc_final: 0.8234 (mtp) REVERT: J 1370 MET cc_start: 0.7826 (ptp) cc_final: 0.7579 (ptp) REVERT: K 21 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8716 (mm) REVERT: K 68 GLU cc_start: 0.8676 (pp20) cc_final: 0.8340 (pp20) REVERT: K 71 GLU cc_start: 0.9229 (tp30) cc_final: 0.8779 (tm-30) REVERT: H 80 GLU cc_start: 0.8764 (mp0) cc_final: 0.8533 (mp0) REVERT: H 95 LYS cc_start: 0.9132 (mtmt) cc_final: 0.8892 (mtmt) REVERT: H 186 ASN cc_start: 0.8930 (t0) cc_final: 0.8497 (t0) outliers start: 104 outliers final: 54 residues processed: 365 average time/residue: 0.1844 time to fit residues: 104.1545 Evaluate side-chains 335 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 273 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 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 347 ILE 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 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 142 GLU 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 541 LEU Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 667 GLN Chi-restraints excluded: chain J residue 762 ASN 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 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 282 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 240 optimal weight: 20.0000 chunk 103 optimal weight: 0.4980 chunk 214 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 272 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 256 optimal weight: 0.0370 overall best weight: 1.1064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 127 GLN J 667 GLN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** 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 = 0.3622 r_free = 0.3622 target = 0.086974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063546 restraints weight = 70681.217| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.76 r_work: 0.2957 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 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 = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1260 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= 0.138 Angle : 0.520 7.498 38809 Z= 0.275 Chirality : 0.041 0.198 4438 Planarity : 0.004 0.046 4754 Dihedral : 16.755 175.143 4732 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.47 % Allowed : 21.12 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.15), residues: 3288 helix: 1.75 (0.15), residues: 1201 sheet: -0.06 (0.24), residues: 490 loop : -0.31 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 996 TYR 0.011 0.001 TYR J 140 PHE 0.020 0.001 PHE P 126 TRP 0.018 0.001 TRP J1193 HIS 0.002 0.001 HIS I1244 Details of bonding type rmsd covalent geometry : bond 0.00315 (28424) covalent geometry : angle 0.51941 (38801) SS BOND : bond 0.00258 ( 1) SS BOND : angle 2.43534 ( 2) hydrogen bonds : bond 0.03827 ( 1254) hydrogen bonds : angle 4.30863 ( 3454) metal coordination : bond 0.00569 ( 4) metal coordination : angle 2.11125 ( 6) *********************** 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 392 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 294 time to evaluate : 0.826 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: 0.8580 (mmm) cc_final: 0.8084 (mmm) REVERT: I 30 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.9029 (tp) REVERT: I 135 THR cc_start: 0.9113 (p) cc_final: 0.8868 (t) REVERT: I 142 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7898 (mm-30) REVERT: I 653 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8375 (ttt) REVERT: I 681 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8627 (mtm) REVERT: I 962 GLU cc_start: 0.8218 (tp30) cc_final: 0.7832 (mt-10) REVERT: I 1027 LYS cc_start: 0.9042 (mmtm) cc_final: 0.8816 (mmtm) REVERT: I 1164 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8196 (t80) REVERT: J 50 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7423 (tmtt) REVERT: J 183 GLU cc_start: 0.8764 (pp20) cc_final: 0.8460 (pp20) REVERT: J 398 LYS cc_start: 0.9321 (mttt) cc_final: 0.8966 (mtpp) REVERT: J 404 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8116 (mm-30) REVERT: J 497 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8650 (mm-30) REVERT: J 832 LYS cc_start: 0.9272 (mptt) cc_final: 0.8864 (mptt) REVERT: J 856 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8518 (mt) REVERT: J 1370 MET cc_start: 0.7731 (ptp) cc_final: 0.7458 (ptp) REVERT: K 3 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8320 (tpm-80) REVERT: K 21 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8719 (mm) REVERT: K 65 ASP cc_start: 0.7946 (p0) cc_final: 0.7660 (p0) REVERT: K 68 GLU cc_start: 0.8679 (pp20) cc_final: 0.8353 (pp20) REVERT: H 25 LYS cc_start: 0.9085 (mtpm) cc_final: 0.8877 (ttmm) REVERT: H 39 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8414 (mt) REVERT: H 80 GLU cc_start: 0.8729 (mp0) cc_final: 0.8447 (mp0) REVERT: H 186 ASN cc_start: 0.8899 (t0) cc_final: 0.8478 (t0) outliers start: 98 outliers final: 53 residues processed: 369 average time/residue: 0.1720 time to fit residues: 98.8766 Evaluate side-chains 332 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 269 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 134 ASP 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 132 ASP 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 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 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 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 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 408 VAL 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 693 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 885 VAL 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 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 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 107 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 260 optimal weight: 0.5980 chunk 284 optimal weight: 0.0870 chunk 110 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 337 optimal weight: 6.9990 chunk 148 optimal weight: 0.0470 chunk 281 optimal weight: 2.9990 chunk 333 optimal weight: 10.0000 overall best weight: 1.1460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 72 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 = 0.3623 r_free = 0.3623 target = 0.087037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.062909 restraints weight = 87313.602| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.11 r_work: 0.2936 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1397 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= 0.140 Angle : 0.526 13.712 38809 Z= 0.276 Chirality : 0.040 0.148 4438 Planarity : 0.004 0.050 4754 Dihedral : 16.696 175.086 4718 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.76 % Allowed : 20.80 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.15), residues: 3288 helix: 1.78 (0.15), residues: 1202 sheet: -0.07 (0.24), residues: 488 loop : -0.31 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 191 TYR 0.010 0.001 TYR J 140 PHE 0.017 0.001 PHE P 126 TRP 0.018 0.001 TRP J1193 HIS 0.014 0.001 HIS P 94 Details of bonding type rmsd covalent geometry : bond 0.00319 (28424) covalent geometry : angle 0.52466 (38801) SS BOND : bond 0.00197 ( 1) SS BOND : angle 2.41143 ( 2) hydrogen bonds : bond 0.03685 ( 1254) hydrogen bonds : angle 4.24045 ( 3454) metal coordination : bond 0.00608 ( 4) metal coordination : angle 2.25883 ( 6) *********************** 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 390 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 284 time to evaluate : 0.834 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: 0.8653 (mmm) cc_final: 0.7923 (mmm) REVERT: P 143 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8046 (mm) REVERT: I 30 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.9029 (tp) REVERT: I 135 THR cc_start: 0.9207 (p) cc_final: 0.8854 (t) REVERT: I 142 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7930 (mm-30) REVERT: I 275 ARG cc_start: 0.9101 (ttp80) cc_final: 0.8678 (ttp80) REVERT: I 681 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8555 (mtm) REVERT: I 1027 LYS cc_start: 0.9077 (mmtm) cc_final: 0.8871 (mmtm) REVERT: I 1164 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8197 (t80) REVERT: J 50 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7396 (tmtt) REVERT: J 183 GLU cc_start: 0.8827 (pp20) cc_final: 0.8524 (pp20) REVERT: J 398 LYS cc_start: 0.9333 (mttt) cc_final: 0.8961 (mtpp) REVERT: J 497 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8683 (mm-30) REVERT: J 832 LYS cc_start: 0.9273 (mptt) cc_final: 0.8821 (mptt) REVERT: J 856 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8531 (mt) REVERT: K 3 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8182 (tpm-80) REVERT: K 4 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8793 (t) REVERT: K 21 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8692 (mm) REVERT: K 65 ASP cc_start: 0.7956 (p0) cc_final: 0.7629 (p0) REVERT: K 68 GLU cc_start: 0.8701 (pp20) cc_final: 0.8368 (pp20) REVERT: H 25 LYS cc_start: 0.9088 (mtpm) cc_final: 0.8884 (ttmm) REVERT: H 39 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8418 (mt) REVERT: H 80 GLU cc_start: 0.8846 (mp0) cc_final: 0.8529 (mp0) REVERT: H 95 LYS cc_start: 0.9102 (mtmt) cc_final: 0.8713 (mtmm) REVERT: H 186 ASN cc_start: 0.8956 (t0) cc_final: 0.8490 (t0) outliers start: 106 outliers final: 64 residues processed: 369 average time/residue: 0.1779 time to fit residues: 103.0561 Evaluate side-chains 345 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 270 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 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 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 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 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 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 408 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 497 GLU Chi-restraints excluded: chain J residue 541 LEU 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 693 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 825 VAL 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 1059 LEU Chi-restraints excluded: chain J residue 1067 ARG Chi-restraints excluded: chain J residue 1072 LYS 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 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 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 50 optimal weight: 0.6980 chunk 248 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 253 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 331 optimal weight: 4.9990 chunk 149 optimal weight: 0.4980 chunk 7 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 207 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** I 173 ASN J 875 ASN J1259 GLN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.088790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064772 restraints weight = 84790.632| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.98 r_work: 0.3016 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28429 Z= 0.116 Angle : 0.519 14.019 38809 Z= 0.271 Chirality : 0.040 0.162 4438 Planarity : 0.003 0.052 4754 Dihedral : 16.628 174.398 4713 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.12 % Allowed : 22.15 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.15), residues: 3288 helix: 1.83 (0.15), residues: 1214 sheet: -0.02 (0.24), residues: 492 loop : -0.26 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 3 TYR 0.017 0.001 TYR G 185 PHE 0.017 0.001 PHE P 126 TRP 0.020 0.001 TRP J1193 HIS 0.004 0.000 HIS P 94 Details of bonding type rmsd covalent geometry : bond 0.00263 (28424) covalent geometry : angle 0.51784 (38801) SS BOND : bond 0.00199 ( 1) SS BOND : angle 2.33930 ( 2) hydrogen bonds : bond 0.03468 ( 1254) hydrogen bonds : angle 4.15997 ( 3454) metal coordination : bond 0.00452 ( 4) metal coordination : angle 2.22200 ( 6) *********************** 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 384 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 296 time to evaluate : 0.691 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: 0.8662 (mmm) cc_final: 0.7921 (mmm) REVERT: P 94 HIS cc_start: 0.8428 (m90) cc_final: 0.8123 (m90) REVERT: P 95 GLN cc_start: 0.9425 (tt0) cc_final: 0.8920 (tt0) REVERT: P 143 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8045 (mm) REVERT: I 30 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8958 (tp) REVERT: I 135 THR cc_start: 0.9183 (p) cc_final: 0.8860 (t) REVERT: I 142 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7817 (mm-30) REVERT: I 275 ARG cc_start: 0.9046 (ttp80) cc_final: 0.8635 (ttp80) REVERT: I 653 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8533 (ttt) REVERT: I 681 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8668 (mtm) REVERT: I 741 MET cc_start: 0.8618 (tpp) cc_final: 0.8155 (mmt) REVERT: I 1164 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8311 (t80) REVERT: J 37 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: J 50 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7536 (tmtt) REVERT: J 183 GLU cc_start: 0.8701 (pp20) cc_final: 0.8446 (pp20) REVERT: J 300 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8137 (tp40) REVERT: J 398 LYS cc_start: 0.9329 (mttt) cc_final: 0.8995 (mtpp) REVERT: J 458 ASN cc_start: 0.9111 (t0) cc_final: 0.8857 (t0) REVERT: J 462 ASP cc_start: 0.8564 (t0) cc_final: 0.7957 (t0) REVERT: J 497 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8663 (mm-30) REVERT: J 832 LYS cc_start: 0.9279 (mptt) cc_final: 0.8906 (mptt) REVERT: K 3 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8170 (tpm-80) REVERT: K 4 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8808 (t) REVERT: K 21 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8790 (mm) REVERT: K 65 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7655 (p0) REVERT: K 68 GLU cc_start: 0.8718 (pp20) cc_final: 0.8368 (pp20) REVERT: H 39 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8376 (mt) REVERT: H 76 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: H 186 ASN cc_start: 0.8772 (t0) cc_final: 0.8399 (t0) outliers start: 88 outliers final: 52 residues processed: 364 average time/residue: 0.1722 time to fit residues: 97.9818 Evaluate side-chains 346 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 279 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 132 ASP Chi-restraints excluded: chain I residue 237 LEU 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 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 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 139 LEU Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 497 GLU Chi-restraints excluded: chain J residue 541 LEU 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 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 1067 ARG Chi-restraints excluded: chain J residue 1101 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 322 optimal weight: 9.9990 chunk 321 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 259 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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** ** 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 = 0.3631 r_free = 0.3631 target = 0.086258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.062406 restraints weight = 71370.754| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.71 r_work: 0.2966 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 28429 Z= 0.242 Angle : 0.585 13.757 38809 Z= 0.306 Chirality : 0.042 0.195 4438 Planarity : 0.004 0.051 4754 Dihedral : 16.727 176.893 4706 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.47 % Allowed : 22.01 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.15), residues: 3288 helix: 1.67 (0.15), residues: 1220 sheet: -0.22 (0.24), residues: 479 loop : -0.36 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 3 TYR 0.044 0.001 TYR H 177 PHE 0.016 0.001 PHE P 126 TRP 0.019 0.001 TRP J1193 HIS 0.004 0.001 HIS P 94 Details of bonding type rmsd covalent geometry : bond 0.00560 (28424) covalent geometry : angle 0.58347 (38801) SS BOND : bond 0.00202 ( 1) SS BOND : angle 2.65888 ( 2) hydrogen bonds : bond 0.04202 ( 1254) hydrogen bonds : angle 4.33927 ( 3454) metal coordination : bond 0.01311 ( 4) metal coordination : angle 2.52914 ( 6) *********************** 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 374 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 276 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 32 MET cc_start: 0.8608 (mmm) cc_final: 0.7787 (mmm) REVERT: P 95 GLN cc_start: 0.9419 (tt0) cc_final: 0.8983 (tt0) REVERT: P 143 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8125 (mm) REVERT: I 30 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8994 (tp) REVERT: I 681 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8595 (mtm) REVERT: I 741 MET cc_start: 0.8636 (tpp) cc_final: 0.8138 (mmt) REVERT: I 1164 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8173 (t80) REVERT: J 37 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: J 50 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7495 (tmtt) REVERT: J 300 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8126 (tp40) REVERT: J 398 LYS cc_start: 0.9317 (mttt) cc_final: 0.8970 (mtpp) REVERT: J 462 ASP cc_start: 0.8535 (t0) cc_final: 0.8066 (t0) REVERT: J 497 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8629 (mm-30) REVERT: J 832 LYS cc_start: 0.9269 (mptt) cc_final: 0.8908 (mptt) REVERT: K 3 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8174 (tpm-80) REVERT: K 4 VAL cc_start: 0.9076 (OUTLIER) cc_final: 0.8842 (t) REVERT: K 21 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8844 (mm) REVERT: K 65 ASP cc_start: 0.8074 (p0) cc_final: 0.7741 (p0) REVERT: K 68 GLU cc_start: 0.8732 (pp20) cc_final: 0.8393 (pp20) REVERT: H 76 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: H 186 ASN cc_start: 0.8872 (t0) cc_final: 0.8497 (t0) outliers start: 98 outliers final: 68 residues processed: 352 average time/residue: 0.1732 time to fit residues: 96.9102 Evaluate side-chains 346 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 266 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 124 MET Chi-restraints excluded: chain I residue 132 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 569 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 994 ARG 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 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 142 GLU 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 693 VAL Chi-restraints excluded: chain J residue 762 ASN 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 1053 LEU Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1067 ARG Chi-restraints excluded: chain J residue 1101 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 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 325 optimal weight: 0.9990 chunk 321 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 224 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 317 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 97 optimal weight: 0.0670 chunk 269 optimal weight: 1.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- 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** ** 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 = 0.3668 r_free = 0.3668 target = 0.088106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.064176 restraints weight = 80617.084| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.90 r_work: 0.3005 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 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 = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1662 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= 0.130 Angle : 0.546 13.557 38809 Z= 0.284 Chirality : 0.041 0.179 4438 Planarity : 0.004 0.053 4754 Dihedral : 16.667 174.365 4706 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.62 % Allowed : 22.61 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.15), residues: 3288 helix: 1.78 (0.15), residues: 1216 sheet: -0.14 (0.24), residues: 483 loop : -0.32 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 275 TYR 0.032 0.001 TYR H 177 PHE 0.015 0.001 PHE P 126 TRP 0.017 0.001 TRP J1193 HIS 0.008 0.001 HIS P 94 Details of bonding type rmsd covalent geometry : bond 0.00299 (28424) covalent geometry : angle 0.54487 (38801) SS BOND : bond 0.00178 ( 1) SS BOND : angle 2.54248 ( 2) hydrogen bonds : bond 0.03572 ( 1254) hydrogen bonds : angle 4.21049 ( 3454) metal coordination : bond 0.00554 ( 4) metal coordination : angle 2.30626 ( 6) *********************** 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 361 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 287 time to evaluate : 0.953 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: 0.8559 (mmm) cc_final: 0.7830 (mmm) REVERT: P 95 GLN cc_start: 0.9394 (tt0) cc_final: 0.8577 (tt0) REVERT: P 99 TYR cc_start: 0.8577 (m-10) cc_final: 0.7674 (m-10) REVERT: P 143 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8107 (mm) REVERT: I 30 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8989 (tp) REVERT: I 653 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8536 (ttt) REVERT: I 681 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8655 (mtm) REVERT: I 741 MET cc_start: 0.8698 (tpp) cc_final: 0.8249 (mmt) REVERT: I 1164 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8349 (t80) REVERT: J 37 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7262 (tm-30) REVERT: J 50 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7551 (tmtt) REVERT: J 300 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8126 (tp40) REVERT: J 398 LYS cc_start: 0.9327 (mttt) cc_final: 0.9026 (mtmm) REVERT: J 462 ASP cc_start: 0.8380 (t0) cc_final: 0.8112 (t0) REVERT: J 832 LYS cc_start: 0.9281 (mptt) cc_final: 0.8929 (mptt) REVERT: K 3 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8124 (tpm-80) REVERT: K 4 VAL cc_start: 0.9038 (OUTLIER) cc_final: 0.8818 (t) REVERT: K 21 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8815 (mm) REVERT: K 65 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7742 (p0) REVERT: K 68 GLU cc_start: 0.8717 (pp20) cc_final: 0.8366 (pp20) REVERT: H 39 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8397 (mt) REVERT: H 76 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: H 186 ASN cc_start: 0.8818 (t0) cc_final: 0.8430 (t0) outliers start: 74 outliers final: 50 residues processed: 344 average time/residue: 0.1756 time to fit residues: 94.8473 Evaluate side-chains 336 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 272 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 CYS 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 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 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 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 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 290 ILE Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 541 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 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 1101 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 65 ASP Chi-restraints excluded: chain G residue 146 VAL 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 170 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 269 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 315 optimal weight: 1.9990 chunk 329 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 101 optimal weight: 0.0870 chunk 243 optimal weight: 20.0000 overall best weight: 1.4162 ------------------------------------------------------------------------------- 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** ** 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 = 0.3616 r_free = 0.3616 target = 0.086634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.063010 restraints weight = 71486.719| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.78 r_work: 0.2949 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1706 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= 0.158 Angle : 0.562 13.576 38809 Z= 0.293 Chirality : 0.041 0.167 4438 Planarity : 0.004 0.053 4754 Dihedral : 16.658 175.347 4699 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 2.98 % Allowed : 22.64 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.15), residues: 3288 helix: 1.77 (0.15), residues: 1216 sheet: -0.16 (0.24), residues: 480 loop : -0.35 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 275 TYR 0.029 0.001 TYR H 177 PHE 0.016 0.001 PHE P 126 TRP 0.024 0.001 TRP J1193 HIS 0.007 0.001 HIS P 94 Details of bonding type rmsd covalent geometry : bond 0.00365 (28424) covalent geometry : angle 0.56136 (38801) SS BOND : bond 0.00178 ( 1) SS BOND : angle 2.60605 ( 2) hydrogen bonds : bond 0.03708 ( 1254) hydrogen bonds : angle 4.21952 ( 3454) metal coordination : bond 0.00787 ( 4) metal coordination : angle 2.39480 ( 6) *********************** 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 362 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 278 time to evaluate : 1.127 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: 0.8536 (mmm) cc_final: 0.7739 (mmm) REVERT: P 95 GLN cc_start: 0.9211 (tt0) cc_final: 0.8883 (tt0) REVERT: P 138 ARG cc_start: 0.9291 (mtt180) cc_final: 0.9079 (ptt-90) REVERT: P 143 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8098 (mm) REVERT: I 30 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.9028 (tp) REVERT: I 291 TYR cc_start: 0.8500 (t80) cc_final: 0.8294 (t80) REVERT: I 653 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8676 (ttt) REVERT: I 681 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8511 (mtm) REVERT: I 741 MET cc_start: 0.8781 (tpp) cc_final: 0.8271 (mmt) REVERT: I 1164 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8250 (t80) REVERT: J 37 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: J 50 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7505 (tmtt) REVERT: J 300 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8043 (tp40) REVERT: J 398 LYS cc_start: 0.9316 (mttt) cc_final: 0.8974 (mtpp) REVERT: J 462 ASP cc_start: 0.8330 (t0) cc_final: 0.8104 (t0) REVERT: J 832 LYS cc_start: 0.9290 (mptt) cc_final: 0.8838 (mptt) REVERT: J 977 SER cc_start: 0.6782 (OUTLIER) cc_final: 0.6129 (t) REVERT: K 3 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8104 (tpm-80) REVERT: K 4 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8795 (t) REVERT: K 21 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8681 (mm) REVERT: K 55 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7395 (mt-10) REVERT: K 65 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7642 (p0) REVERT: K 68 GLU cc_start: 0.8724 (pp20) cc_final: 0.8381 (pp20) REVERT: H 39 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8350 (mt) REVERT: H 76 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: H 186 ASN cc_start: 0.8980 (t0) cc_final: 0.8495 (t0) outliers start: 84 outliers final: 55 residues processed: 344 average time/residue: 0.1888 time to fit residues: 102.3275 Evaluate side-chains 343 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 273 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 CYS 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 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 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 1101 LEU 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 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 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 317 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 639 VAL 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 821 MET 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 1059 LEU Chi-restraints excluded: chain J residue 1101 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 146 VAL 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 131 optimal weight: 0.0670 chunk 164 optimal weight: 0.0770 chunk 183 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- 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** ** 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 = 0.3683 r_free = 0.3683 target = 0.089057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.065231 restraints weight = 76174.569| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.83 r_work: 0.3026 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 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 = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28429 Z= 0.113 Angle : 0.554 13.463 38809 Z= 0.289 Chirality : 0.041 0.296 4438 Planarity : 0.003 0.054 4754 Dihedral : 16.594 173.786 4699 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 2.41 % Allowed : 23.25 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.15), residues: 3288 helix: 1.77 (0.15), residues: 1224 sheet: -0.01 (0.24), residues: 473 loop : -0.29 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 47 TYR 0.026 0.001 TYR H 177 PHE 0.014 0.001 PHE P 126 TRP 0.028 0.001 TRP J1193 HIS 0.007 0.001 HIS P 94 Details of bonding type rmsd covalent geometry : bond 0.00259 (28424) covalent geometry : angle 0.55338 (38801) SS BOND : bond 0.00101 ( 1) SS BOND : angle 2.34550 ( 2) hydrogen bonds : bond 0.03367 ( 1254) hydrogen bonds : angle 4.14441 ( 3454) metal coordination : bond 0.00351 ( 4) metal coordination : angle 2.34375 ( 6) *********************** 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 361 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 293 time to evaluate : 1.035 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: 0.8529 (mmm) cc_final: 0.7840 (mmm) REVERT: P 95 GLN cc_start: 0.9135 (tt0) cc_final: 0.8843 (tt0) REVERT: P 123 PHE cc_start: 0.7349 (m-80) cc_final: 0.6851 (m-80) REVERT: P 143 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8053 (mm) REVERT: I 30 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8967 (tp) REVERT: I 291 TYR cc_start: 0.8432 (t80) cc_final: 0.8224 (t80) REVERT: I 653 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8411 (ttt) REVERT: I 681 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8561 (mtm) REVERT: I 727 VAL cc_start: 0.8778 (t) cc_final: 0.8364 (p) REVERT: I 1164 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8344 (t80) REVERT: J 37 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: J 50 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7669 (tmtt) REVERT: J 275 ARG cc_start: 0.8487 (mmp80) cc_final: 0.8179 (mmp80) REVERT: J 300 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8069 (tp40) REVERT: J 398 LYS cc_start: 0.9325 (mttt) cc_final: 0.9029 (mtmm) REVERT: J 458 ASN cc_start: 0.9120 (t0) cc_final: 0.8871 (t0) REVERT: J 832 LYS cc_start: 0.9288 (mptt) cc_final: 0.8894 (mptt) REVERT: J 977 SER cc_start: 0.6831 (OUTLIER) cc_final: 0.6123 (t) REVERT: J 1067 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.5628 (ptp90) REVERT: K 3 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8231 (tpm-80) REVERT: K 4 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8804 (t) REVERT: K 21 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8756 (mm) REVERT: K 65 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7715 (p0) REVERT: K 68 GLU cc_start: 0.8730 (pp20) cc_final: 0.8373 (pp20) REVERT: H 39 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8344 (mt) REVERT: H 76 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: H 186 ASN cc_start: 0.8820 (t0) cc_final: 0.8446 (t0) outliers start: 68 outliers final: 46 residues processed: 349 average time/residue: 0.1828 time to fit residues: 100.2142 Evaluate side-chains 338 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 276 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 CYS 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 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 764 CYS 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 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 300 GLN Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 541 LEU 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 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 1067 ARG 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 65 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 193 GLU 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 69 optimal weight: 0.0570 chunk 294 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 74 optimal weight: 0.0870 chunk 221 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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** ** 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 = 0.3691 r_free = 0.3691 target = 0.089500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.065208 restraints weight = 88910.554| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.10 r_work: 0.3019 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1845 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= 0.113 Angle : 0.564 12.698 38809 Z= 0.294 Chirality : 0.040 0.193 4438 Planarity : 0.004 0.054 4754 Dihedral : 16.554 174.049 4698 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 2.34 % Allowed : 23.64 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.15), residues: 3288 helix: 1.76 (0.15), residues: 1233 sheet: -0.07 (0.24), residues: 482 loop : -0.24 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 47 TYR 0.037 0.001 TYR P 99 PHE 0.015 0.001 PHE P 126 TRP 0.028 0.001 TRP J1193 HIS 0.006 0.001 HIS P 94 Details of bonding type rmsd covalent geometry : bond 0.00258 (28424) covalent geometry : angle 0.56289 (38801) SS BOND : bond 0.00166 ( 1) SS BOND : angle 2.52417 ( 2) hydrogen bonds : bond 0.03358 ( 1254) hydrogen bonds : angle 4.11663 ( 3454) metal coordination : bond 0.00349 ( 4) metal coordination : angle 2.33339 ( 6) ********************** 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 356 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 290 time to evaluate : 1.046 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: 0.8510 (mmm) cc_final: 0.7732 (mmm) REVERT: P 143 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8017 (mm) REVERT: I 30 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8922 (tp) REVERT: I 291 TYR cc_start: 0.8422 (t80) cc_final: 0.8209 (t80) REVERT: I 315 MET cc_start: 0.8117 (pmm) cc_final: 0.7854 (pmm) REVERT: I 653 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8439 (ttt) REVERT: I 681 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8588 (mtm) REVERT: I 727 VAL cc_start: 0.8727 (t) cc_final: 0.8314 (p) REVERT: I 968 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8171 (pp20) REVERT: I 1164 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8366 (t80) REVERT: I 1329 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7785 (mm-30) REVERT: J 37 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7202 (tm-30) REVERT: J 50 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7681 (tmtt) REVERT: J 275 ARG cc_start: 0.8496 (mmp80) cc_final: 0.8242 (mmp80) REVERT: J 300 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8109 (tp40) REVERT: J 398 LYS cc_start: 0.9308 (mttt) cc_final: 0.9034 (mtmm) REVERT: J 832 LYS cc_start: 0.9284 (mptt) cc_final: 0.8900 (mptt) REVERT: J 977 SER cc_start: 0.6828 (OUTLIER) cc_final: 0.6100 (t) REVERT: J 1067 ARG cc_start: 0.6145 (OUTLIER) cc_final: 0.5698 (ptp90) REVERT: K 3 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8193 (tpm-80) REVERT: K 4 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8813 (t) REVERT: K 65 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7723 (p0) REVERT: K 68 GLU cc_start: 0.8741 (pp20) cc_final: 0.8383 (pp20) REVERT: H 39 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8323 (mt) REVERT: H 76 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: H 186 ASN cc_start: 0.8801 (t0) cc_final: 0.8426 (t0) outliers start: 66 outliers final: 48 residues processed: 346 average time/residue: 0.1826 time to fit residues: 98.5001 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 : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 CYS 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 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 764 CYS Chi-restraints excluded: chain I residue 864 LYS Chi-restraints excluded: chain I residue 968 GLU 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 1101 LEU Chi-restraints excluded: chain I residue 1164 PHE 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 300 GLN Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 541 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 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 1067 ARG 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 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 146 VAL Chi-restraints excluded: chain G residue 193 GLU 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 100 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 165 optimal weight: 0.3980 chunk 226 optimal weight: 0.0040 chunk 46 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 311 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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** K 15 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 = 0.3692 r_free = 0.3692 target = 0.089617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.065336 restraints weight = 88744.080| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.09 r_work: 0.3020 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1903 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= 0.116 Angle : 0.572 12.554 38809 Z= 0.296 Chirality : 0.040 0.202 4438 Planarity : 0.004 0.084 4754 Dihedral : 16.532 174.030 4695 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 2.30 % Allowed : 23.85 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.15), residues: 3288 helix: 1.76 (0.15), residues: 1232 sheet: -0.07 (0.24), residues: 482 loop : -0.24 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 47 TYR 0.038 0.001 TYR P 99 PHE 0.018 0.001 PHE P 126 TRP 0.025 0.001 TRP J1193 HIS 0.006 0.000 HIS P 94 Details of bonding type rmsd covalent geometry : bond 0.00267 (28424) covalent geometry : angle 0.57150 (38801) SS BOND : bond 0.00171 ( 1) SS BOND : angle 2.54389 ( 2) hydrogen bonds : bond 0.03336 ( 1254) hydrogen bonds : angle 4.10270 ( 3454) metal coordination : bond 0.00382 ( 4) metal coordination : angle 2.24020 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7252.60 seconds wall clock time: 124 minutes 37.77 seconds (7477.77 seconds total)