Starting phenix.real_space_refine on Thu Jul 25 01:53:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pfg_17646/07_2024/8pfg_17646_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pfg_17646/07_2024/8pfg_17646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pfg_17646/07_2024/8pfg_17646.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pfg_17646/07_2024/8pfg_17646.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pfg_17646/07_2024/8pfg_17646_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pfg_17646/07_2024/8pfg_17646_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 90 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 17149 2.51 5 N 4926 2.21 5 O 5532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 27809 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 8, 'TRANS': 127} Chain breaks: 1 Chain: "I" Number of atoms: 10423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 Chain: "J" Number of atoms: 10240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1317, 10240 Classifications: {'peptide': 1317} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1261} Chain breaks: 3 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "G" Number of atoms: 1807 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Conformer: "B" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} bond proxies already assigned to first conformer: 1812 Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1710 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 9, 'TRANS': 212} Chain breaks: 1 Chain: "R" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 6} Link IDs: {'rna3p': 11} Chain: "B" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 828 Classifications: {'DNA': 40} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 39} Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 808 Classifications: {'DNA': 40} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 39} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17586 SG CYS J 814 57.792 126.733 93.279 1.00 77.22 S ATOM 18151 SG CYS J 888 59.486 123.533 92.598 1.00 97.40 S ATOM 18202 SG CYS J 895 58.648 126.124 89.739 1.00 97.68 S ATOM 18223 SG CYS J 898 61.507 126.684 92.122 1.00 89.95 S Time building chain proxies: 17.18, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.95 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 898 " Number of angles added : 6 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6126 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 46 sheets defined 39.9% alpha, 17.7% beta 41 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 10.67 Creating SS restraints... Processing helix chain 'P' and resid 13 through 24 Processing helix chain 'P' and resid 65 through 71 Processing helix chain 'P' and resid 89 through 99 removed outlier: 3.810A pdb=" N ILE P 93 " --> pdb=" O PRO P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 132 Processing helix chain 'P' and resid 134 through 154 removed outlier: 3.760A pdb=" N MET P 140 " --> pdb=" O GLU P 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 10 removed outlier: 3.626A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 4.226A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE I 35 " --> pdb=" O GLN I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.821A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 212 removed outlier: 3.819A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 294 removed outlier: 4.136A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 294' Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.061A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 480 removed outlier: 3.504A pdb=" N ARG I 478 " --> pdb=" O ALA I 474 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 483 through 487 removed outlier: 3.645A pdb=" N THR I 486 " --> pdb=" O ASP I 483 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.567A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 609 through 613 removed outlier: 3.552A pdb=" N GLY I 612 " --> pdb=" O ILE I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.677A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 3.867A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 863 Processing helix chain 'I' and resid 942 through 983 Processing helix chain 'I' and resid 985 through 992 Processing helix chain 'I' and resid 994 through 998 Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 3.542A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.077A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.526A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1161 through 1164 Processing helix chain 'I' and resid 1165 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.616A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 removed outlier: 3.531A pdb=" N GLY J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 101 removed outlier: 3.706A pdb=" N GLU J 100 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 removed outlier: 3.508A pdb=" N TYR J 140 " --> pdb=" O GLU J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.621A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 291 through 308 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.659A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.776A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.563A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.973A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.684A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1068 through 1074 removed outlier: 4.081A pdb=" N LEU J1074 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.532A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.333A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1296 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.678A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1360 through 1375 removed outlier: 4.251A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.938A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'G' and resid 34 through 48 removed outlier: 3.527A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.655A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 160 removed outlier: 3.736A pdb=" N ILE G 159 " --> pdb=" O SER G 156 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS G 160 " --> pdb=" O THR G 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 156 through 160' Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.381A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.598A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 111 through 115 removed outlier: 3.652A pdb=" N ASP H 114 " --> pdb=" O THR H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 229 removed outlier: 3.564A pdb=" N ALA H 216 " --> pdb=" O ASP H 212 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE H 217 " --> pdb=" O PRO H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 232 No H-bonds generated for 'chain 'H' and resid 230 through 232' Processing sheet with id=AA1, first strand: chain 'P' and resid 27 through 29 removed outlier: 4.729A pdb=" N LEU P 6 " --> pdb=" O VAL P 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 32 through 37 Processing sheet with id=AA3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.423A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.348A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA6, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.341A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.919A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 227 through 231 removed outlier: 3.556A pdb=" N ILE I 333 " --> pdb=" O PHE I 230 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 239 through 240 removed outlier: 3.738A pdb=" N ILE I 285 " --> pdb=" O MET I 239 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.911A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 301 through 303 removed outlier: 3.553A pdb=" N CYS I 311 " --> pdb=" O TYR I 301 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASP I 303 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU I 309 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.528A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB5, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.490A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.785A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AB8, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AB9, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.348A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.956A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 849 through 850 removed outlier: 3.517A pdb=" N GLU I 849 " --> pdb=" O VAL I 887 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.896A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.759A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU J 449 " --> pdb=" O VAL J 354 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N THR J 356 " --> pdb=" O LEU J 449 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC6, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.881A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.800A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.832A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD1, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AD2, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD3, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD4, first strand: chain 'J' and resid 825 through 826 removed outlier: 6.954A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 848 through 849 removed outlier: 7.061A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.169A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.156A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 1024 through 1025 Processing sheet with id=AD9, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE1, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.788A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 1186 through 1190 removed outlier: 4.196A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.644A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.042A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU G 198 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 98 through 105 removed outlier: 7.391A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA G 55 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AE7, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.806A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AE9, first strand: chain 'H' and resid 15 through 20 removed outlier: 3.536A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N THR H 196 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL H 192 " --> pdb=" O THR H 196 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 97 through 105 removed outlier: 7.575A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) 1151 hydrogen bonds defined for protein. 3248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 14.53 Time building geometry restraints manager: 13.60 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: 97.67 - 104.94: 796 104.94 - 112.21: 14722 112.21 - 119.48: 9518 119.48 - 126.75: 13275 126.75 - 134.02: 490 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 2.440 nonbonded pdb=" OG SER I 646 " pdb=" OD1 ASP I 648 " model vdw 2.213 2.440 nonbonded pdb=" O LYS J 964 " pdb=" OG1 THR J 976 " model vdw 2.215 2.440 ... (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 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 4 through 158 or resid 167 through 218 or resid 220 throug \ h 233)) selection = (chain 'H' and (resid 4 through 218 or resid 220 through 233)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.200 Check model and map are aligned: 0.210 Set scattering table: 0.290 Process input model: 95.170 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.100 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.640 ------------------------------------------------------------------------------- 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 28424 Z= 0.178 Angle : 0.450 6.440 38801 Z= 0.243 Chirality : 0.039 0.149 4438 Planarity : 0.003 0.037 4754 Dihedral : 18.936 176.763 11144 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.49 % Allowed : 18.64 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 3288 helix: 1.82 (0.15), residues: 1186 sheet: -0.01 (0.24), residues: 466 loop : -0.28 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 409 HIS 0.003 0.000 HIS J1252 PHE 0.017 0.001 PHE J 461 TYR 0.011 0.001 TYR J 140 ARG 0.002 0.000 ARG I 371 *********************** 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 fitting. rotamer outliers: 155 poor density : 334 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 134 ASP cc_start: 0.8959 (m-30) cc_final: 0.8563 (t0) REVERT: P 143 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8126 (mm) REVERT: I 30 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8961 (tp) REVERT: I 81 ASP cc_start: 0.8217 (t0) cc_final: 0.7591 (t0) REVERT: I 962 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: I 1027 LYS cc_start: 0.9039 (mmtm) cc_final: 0.8807 (mmtm) REVERT: J 29 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7744 (ppp) REVERT: J 196 GLN cc_start: 0.8568 (mp10) cc_final: 0.8325 (mp10) REVERT: J 300 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8097 (tp40) REVERT: J 398 LYS cc_start: 0.9362 (mttt) cc_final: 0.8998 (mtmm) REVERT: J 673 VAL cc_start: 0.8324 (OUTLIER) cc_final: 0.7851 (p) REVERT: J 832 LYS cc_start: 0.9187 (mptt) cc_final: 0.8847 (mmtm) REVERT: J 856 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8277 (mt) REVERT: J 1029 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.7866 (t) REVERT: J 1369 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7685 (ttp-170) REVERT: K 4 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8857 (t) REVERT: K 21 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9070 (mm) REVERT: K 65 ASP cc_start: 0.8266 (p0) cc_final: 0.7981 (p0) REVERT: K 68 GLU cc_start: 0.8640 (pp20) cc_final: 0.8308 (pp20) REVERT: K 71 GLU cc_start: 0.9200 (tp30) cc_final: 0.8738 (tm-30) REVERT: G 58 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7513 (mt-10) REVERT: G 83 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8201 (tt) REVERT: H 186 ASN cc_start: 0.8806 (t0) cc_final: 0.8487 (t0) outliers start: 155 outliers final: 63 residues processed: 483 average time/residue: 0.4339 time to fit residues: 325.0697 Evaluate side-chains 352 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 277 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 677 ASN Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 973 SER Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1164 PHE Chi-restraints excluded: chain I residue 1188 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 655 SER Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1067 ARG Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1116 SER Chi-restraints excluded: chain J residue 1117 SER Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain J residue 1369 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 0.9980 chunk 256 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 161 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 306 optimal weight: 4.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 83 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 28424 Z= 0.442 Angle : 0.609 8.425 38801 Z= 0.321 Chirality : 0.044 0.258 4438 Planarity : 0.004 0.044 4754 Dihedral : 16.976 177.008 4803 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.15 % Allowed : 21.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3288 helix: 1.63 (0.15), residues: 1198 sheet: -0.12 (0.24), residues: 486 loop : -0.44 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J1193 HIS 0.003 0.001 HIS I 526 PHE 0.020 0.002 PHE J 461 TYR 0.015 0.001 TYR J1186 ARG 0.008 0.000 ARG I 637 *********************** 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 fitting. rotamer outliers: 117 poor density : 277 time to evaluate : 3.184 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: 0.8629 (mmm) cc_final: 0.8023 (mmm) REVERT: P 80 ARG cc_start: 0.7885 (ptp-110) cc_final: 0.7614 (ptp-110) REVERT: P 95 GLN cc_start: 0.9296 (tt0) cc_final: 0.8914 (tt0) REVERT: I 30 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9053 (tp) REVERT: I 81 ASP cc_start: 0.8746 (t0) cc_final: 0.8531 (t0) REVERT: I 275 ARG cc_start: 0.8938 (ttp80) cc_final: 0.8704 (ttp80) REVERT: I 681 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8382 (mtm) REVERT: I 1027 LYS cc_start: 0.9038 (mmtm) cc_final: 0.8805 (mmtm) REVERT: I 1047 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8385 (pp) REVERT: J 196 GLN cc_start: 0.8658 (mp10) cc_final: 0.8426 (mp10) REVERT: J 250 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8406 (ptt-90) REVERT: J 398 LYS cc_start: 0.9305 (mttt) cc_final: 0.8984 (mtmm) REVERT: J 497 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8273 (mp0) REVERT: J 667 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8721 (tm130) REVERT: J 832 LYS cc_start: 0.9167 (mptt) cc_final: 0.8788 (mptt) REVERT: J 856 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8444 (mt) REVERT: J 1370 MET cc_start: 0.7866 (ptp) cc_final: 0.7620 (ptp) REVERT: K 21 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8911 (mm) REVERT: K 68 GLU cc_start: 0.8703 (pp20) cc_final: 0.8375 (pp20) REVERT: G 58 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7875 (mt-10) REVERT: G 158 ARG cc_start: 0.8684 (mtm110) cc_final: 0.8463 (ttp-110) REVERT: H 93 GLN cc_start: 0.8425 (mp10) cc_final: 0.8220 (mp10) REVERT: H 95 LYS cc_start: 0.9087 (mtmt) cc_final: 0.8532 (mtmt) REVERT: H 186 ASN cc_start: 0.8974 (t0) cc_final: 0.8538 (t0) outliers start: 117 outliers final: 68 residues processed: 367 average time/residue: 0.4206 time to fit residues: 240.1086 Evaluate side-chains 339 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 263 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 53 ASN 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 70 TYR Chi-restraints excluded: chain I residue 135 THR 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 333 ILE 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 453 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 655 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 1037 THR Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1096 ILE 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 1326 LEU 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 134 ASP Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 250 ARG Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 348 ASP 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 661 VAL Chi-restraints excluded: chain J residue 667 GLN Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 762 ASN 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 1053 LEU Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 32 VAL 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 170 optimal weight: 0.0370 chunk 95 optimal weight: 0.5980 chunk 255 optimal weight: 0.0010 chunk 209 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 307 optimal weight: 0.8980 chunk 332 optimal weight: 4.9990 chunk 273 optimal weight: 0.9980 chunk 304 optimal weight: 1.9990 chunk 104 optimal weight: 0.0770 chunk 246 optimal weight: 20.0000 overall best weight: 0.3222 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 28424 Z= 0.150 Angle : 0.497 6.744 38801 Z= 0.263 Chirality : 0.040 0.150 4438 Planarity : 0.003 0.047 4754 Dihedral : 16.751 173.997 4732 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 3.22 % Allowed : 22.47 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3288 helix: 1.80 (0.15), residues: 1202 sheet: 0.10 (0.25), residues: 463 loop : -0.37 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J1193 HIS 0.003 0.000 HIS I1244 PHE 0.019 0.001 PHE P 126 TYR 0.011 0.001 TYR J 140 ARG 0.003 0.000 ARG J 133 *********************** 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 384 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 293 time to evaluate : 3.241 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: 0.8578 (mmm) cc_final: 0.8252 (mmm) REVERT: P 80 ARG cc_start: 0.7955 (ptp-110) cc_final: 0.7740 (ptp-110) REVERT: P 95 GLN cc_start: 0.9299 (tt0) cc_final: 0.8838 (tt0) REVERT: P 143 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8149 (mm) REVERT: I 30 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9020 (tp) REVERT: I 81 ASP cc_start: 0.8695 (t0) cc_final: 0.8239 (t0) REVERT: I 681 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8518 (mtm) REVERT: I 962 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: I 1027 LYS cc_start: 0.9026 (mmtm) cc_final: 0.8785 (mmtm) REVERT: I 1047 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8398 (pp) REVERT: J 50 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7420 (tmtt) REVERT: J 172 PHE cc_start: 0.8126 (m-80) cc_final: 0.6931 (m-10) REVERT: J 183 GLU cc_start: 0.8608 (pp20) cc_final: 0.8329 (pp20) REVERT: J 196 GLN cc_start: 0.8650 (mp10) cc_final: 0.8433 (mp10) REVERT: J 250 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8472 (ptt-90) REVERT: J 398 LYS cc_start: 0.9304 (mttt) cc_final: 0.8919 (mtpp) REVERT: J 832 LYS cc_start: 0.9174 (mptt) cc_final: 0.8812 (mptt) REVERT: J 856 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8525 (mt) REVERT: J 1029 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.7879 (t) REVERT: J 1143 ASP cc_start: 0.8691 (m-30) cc_final: 0.8349 (m-30) REVERT: J 1370 MET cc_start: 0.7747 (ptp) cc_final: 0.7447 (ptp) REVERT: K 21 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8871 (mm) REVERT: H 13 LEU cc_start: 0.8225 (mp) cc_final: 0.7989 (tt) REVERT: H 25 LYS cc_start: 0.9008 (mtpm) cc_final: 0.8789 (ttmm) REVERT: H 39 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8457 (mt) REVERT: H 95 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8779 (mtmt) REVERT: H 186 ASN cc_start: 0.8906 (t0) cc_final: 0.8508 (t0) outliers start: 91 outliers final: 46 residues processed: 361 average time/residue: 0.4227 time to fit residues: 238.9884 Evaluate side-chains 336 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 279 time to evaluate : 2.891 ------------------------------------------------------------------------------- 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 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 134 ASP 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 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 881 ASP Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1164 PHE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1308 ILE Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 250 ARG Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 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 303 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 146 optimal weight: 0.5980 chunk 206 optimal weight: 3.9990 chunk 308 optimal weight: 8.9990 chunk 326 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 292 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 127 GLN I 173 ASN J 667 GLN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 28424 Z= 0.334 Angle : 0.550 7.547 38801 Z= 0.289 Chirality : 0.042 0.154 4438 Planarity : 0.004 0.049 4754 Dihedral : 16.717 176.634 4707 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 3.79 % Allowed : 22.47 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3288 helix: 1.72 (0.15), residues: 1208 sheet: -0.08 (0.24), residues: 476 loop : -0.45 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J1193 HIS 0.003 0.001 HIS J1252 PHE 0.037 0.001 PHE G 231 TYR 0.038 0.001 TYR H 177 ARG 0.006 0.000 ARG I 275 *********************** 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 383 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 276 time to evaluate : 2.988 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: 0.8574 (mmm) cc_final: 0.8099 (mmm) REVERT: P 143 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8197 (mm) REVERT: I 30 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.9022 (tp) REVERT: I 681 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8451 (mtm) REVERT: I 962 GLU cc_start: 0.8301 (tp30) cc_final: 0.7917 (mt-10) REVERT: I 1027 LYS cc_start: 0.9035 (mmtm) cc_final: 0.8791 (mmtm) REVERT: I 1075 VAL cc_start: 0.9517 (OUTLIER) cc_final: 0.9300 (t) REVERT: J 196 GLN cc_start: 0.8641 (mp10) cc_final: 0.8353 (mp10) REVERT: J 250 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8429 (ptt-90) REVERT: J 300 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8199 (tp40) REVERT: J 398 LYS cc_start: 0.9329 (mttt) cc_final: 0.8988 (mtmm) REVERT: J 832 LYS cc_start: 0.9181 (mptt) cc_final: 0.8809 (mptt) REVERT: J 856 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8527 (mt) REVERT: J 932 MET cc_start: 0.8683 (mtp) cc_final: 0.8479 (mtp) REVERT: J 1029 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.7910 (t) REVERT: J 1370 MET cc_start: 0.7724 (ptp) cc_final: 0.7399 (ptp) REVERT: K 21 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8897 (mm) REVERT: G 158 ARG cc_start: 0.8681 (mtm110) cc_final: 0.8451 (ttp-110) REVERT: H 13 LEU cc_start: 0.8203 (mp) cc_final: 0.7940 (tt) REVERT: H 25 LYS cc_start: 0.9022 (mtpm) cc_final: 0.8799 (ttmm) REVERT: H 186 ASN cc_start: 0.8976 (t0) cc_final: 0.8548 (t0) outliers start: 107 outliers final: 66 residues processed: 357 average time/residue: 0.4315 time to fit residues: 241.8875 Evaluate side-chains 345 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 270 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 CYS Chi-restraints excluded: chain P residue 53 ASN 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 139 CYS Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 23 ASP 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 135 THR 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 445 ILE Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 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 739 ASP Chi-restraints excluded: chain I residue 864 LYS Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 994 ARG 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 1075 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 250 ARG Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 434 ILE 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 825 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1029 THR 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 1209 VAL Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 272 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 243 optimal weight: 20.0000 chunk 134 optimal weight: 0.9990 chunk 278 optimal weight: 0.8980 chunk 225 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28424 Z= 0.246 Angle : 0.523 7.476 38801 Z= 0.276 Chirality : 0.041 0.150 4438 Planarity : 0.003 0.044 4754 Dihedral : 16.715 175.663 4707 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.59 % Rotamer: Outliers : 3.61 % Allowed : 22.22 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 3288 helix: 1.76 (0.15), residues: 1220 sheet: -0.06 (0.24), residues: 483 loop : -0.43 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J1193 HIS 0.010 0.001 HIS P 94 PHE 0.029 0.001 PHE G 231 TYR 0.027 0.001 TYR H 177 ARG 0.007 0.000 ARG I 88 *********************** 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 390 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 288 time to evaluate : 3.512 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: 0.8601 (mmm) cc_final: 0.8157 (mmm) REVERT: P 95 GLN cc_start: 0.9341 (tt0) cc_final: 0.8843 (tt0) REVERT: P 143 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8219 (mm) REVERT: I 30 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.9008 (tp) REVERT: I 681 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8447 (mtm) REVERT: I 1027 LYS cc_start: 0.9021 (mmtm) cc_final: 0.8777 (mmtm) REVERT: I 1047 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8365 (pp) REVERT: J 29 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8448 (ptp) REVERT: J 196 GLN cc_start: 0.8618 (mp10) cc_final: 0.8314 (mp10) REVERT: J 250 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8452 (ptt-90) REVERT: J 300 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8167 (tp40) REVERT: J 398 LYS cc_start: 0.9306 (mttt) cc_final: 0.8975 (mtmm) REVERT: J 462 ASP cc_start: 0.8533 (t0) cc_final: 0.7982 (t0) REVERT: J 832 LYS cc_start: 0.9188 (mptt) cc_final: 0.8954 (mmtm) REVERT: J 856 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8550 (mt) REVERT: J 932 MET cc_start: 0.8672 (mtp) cc_final: 0.8452 (mtp) REVERT: J 1029 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.7924 (t) REVERT: K 21 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8880 (mm) REVERT: G 158 ARG cc_start: 0.8685 (mtm110) cc_final: 0.8471 (ttp-110) REVERT: H 13 LEU cc_start: 0.8176 (mp) cc_final: 0.7905 (tt) REVERT: H 25 LYS cc_start: 0.9017 (mtpm) cc_final: 0.8810 (ttmm) REVERT: H 186 ASN cc_start: 0.8964 (t0) cc_final: 0.8563 (t0) outliers start: 102 outliers final: 74 residues processed: 366 average time/residue: 0.4321 time to fit residues: 247.1147 Evaluate side-chains 356 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 272 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 CYS Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 134 ASP Chi-restraints excluded: chain P residue 139 CYS Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 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 739 ASP Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 864 LYS Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 994 ARG 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 1047 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1308 ILE Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 250 ARG Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 434 ILE 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 825 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1029 THR 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 K residue 18 ASP Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain G residue 33 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 109 optimal weight: 10.0000 chunk 294 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 327 optimal weight: 0.5980 chunk 271 optimal weight: 0.2980 chunk 151 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 127 GLN ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28424 Z= 0.208 Angle : 0.519 7.219 38801 Z= 0.274 Chirality : 0.041 0.165 4438 Planarity : 0.003 0.045 4754 Dihedral : 16.681 175.067 4707 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.59 % Rotamer: Outliers : 3.47 % Allowed : 23.21 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 3288 helix: 1.79 (0.15), residues: 1221 sheet: -0.11 (0.24), residues: 475 loop : -0.42 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J1193 HIS 0.009 0.001 HIS P 94 PHE 0.030 0.001 PHE G 231 TYR 0.023 0.001 TYR H 177 ARG 0.005 0.000 ARG I 275 *********************** 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 382 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 284 time to evaluate : 3.152 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: 0.8541 (mmm) cc_final: 0.8179 (mmm) REVERT: P 94 HIS cc_start: 0.8615 (m90) cc_final: 0.8301 (m90) REVERT: P 95 GLN cc_start: 0.9341 (tt0) cc_final: 0.8841 (tt0) REVERT: P 143 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8184 (mm) REVERT: I 30 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.9005 (tp) REVERT: I 681 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8444 (mtm) REVERT: I 1027 LYS cc_start: 0.9027 (mmtm) cc_final: 0.8805 (mmtm) REVERT: I 1164 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8042 (t80) REVERT: J 29 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8396 (ptp) REVERT: J 50 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7016 (mmtt) REVERT: J 196 GLN cc_start: 0.8612 (mp10) cc_final: 0.8306 (mp10) REVERT: J 250 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8464 (ptt-90) REVERT: J 300 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8201 (tp40) REVERT: J 398 LYS cc_start: 0.9294 (mttt) cc_final: 0.8966 (mtmm) REVERT: J 462 ASP cc_start: 0.8433 (t0) cc_final: 0.8026 (t0) REVERT: J 832 LYS cc_start: 0.9187 (mptt) cc_final: 0.8955 (mmtm) REVERT: J 856 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8556 (mt) REVERT: J 932 MET cc_start: 0.8637 (mtp) cc_final: 0.8401 (mtp) REVERT: J 1029 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.7903 (t) REVERT: J 1370 MET cc_start: 0.7750 (ptp) cc_final: 0.7462 (ptp) REVERT: K 3 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8077 (tpm-80) REVERT: K 21 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8857 (mm) REVERT: G 158 ARG cc_start: 0.8673 (mtm110) cc_final: 0.8458 (ttp-110) REVERT: H 13 LEU cc_start: 0.8169 (mp) cc_final: 0.7900 (tt) REVERT: H 25 LYS cc_start: 0.9011 (mtpm) cc_final: 0.8806 (ttmm) REVERT: H 39 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8436 (mt) REVERT: H 186 ASN cc_start: 0.8947 (t0) cc_final: 0.8531 (t0) outliers start: 98 outliers final: 68 residues processed: 358 average time/residue: 0.4387 time to fit residues: 244.7804 Evaluate side-chains 358 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 277 time to evaluate : 3.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 CYS Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 134 ASP Chi-restraints excluded: chain P residue 139 CYS Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 1037 THR Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 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 26 SER Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 250 ARG Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 434 ILE 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 825 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1029 THR 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 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 33 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 315 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 186 optimal weight: 0.4980 chunk 238 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 275 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 325 optimal weight: 0.0770 chunk 203 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28424 Z= 0.166 Angle : 0.506 7.566 38801 Z= 0.266 Chirality : 0.040 0.175 4438 Planarity : 0.003 0.065 4754 Dihedral : 16.626 174.276 4703 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 3.01 % Allowed : 23.67 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 3288 helix: 1.88 (0.15), residues: 1217 sheet: -0.05 (0.24), residues: 475 loop : -0.39 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J1193 HIS 0.006 0.000 HIS P 94 PHE 0.023 0.001 PHE G 231 TYR 0.028 0.001 TYR G 185 ARG 0.005 0.000 ARG G 191 *********************** 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 382 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 297 time to evaluate : 3.104 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: 0.8576 (mmm) cc_final: 0.8216 (mmm) REVERT: P 95 GLN cc_start: 0.9302 (tt0) cc_final: 0.8826 (tt0) REVERT: P 143 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8128 (mm) REVERT: I 30 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8983 (tp) REVERT: I 681 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8477 (mtm) REVERT: I 1027 LYS cc_start: 0.9030 (mmtm) cc_final: 0.8804 (mmtm) REVERT: I 1164 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8060 (t80) REVERT: J 183 GLU cc_start: 0.8602 (pp20) cc_final: 0.8362 (pp20) REVERT: J 196 GLN cc_start: 0.8612 (mp10) cc_final: 0.8305 (mp10) REVERT: J 250 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8470 (ptt-90) REVERT: J 300 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8173 (tp40) REVERT: J 398 LYS cc_start: 0.9258 (mttt) cc_final: 0.9003 (mtmm) REVERT: J 458 ASN cc_start: 0.9084 (t0) cc_final: 0.8857 (t0) REVERT: J 462 ASP cc_start: 0.8336 (t0) cc_final: 0.8129 (t0) REVERT: J 832 LYS cc_start: 0.9195 (mptt) cc_final: 0.8952 (mmtm) REVERT: J 856 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8582 (mt) REVERT: J 1029 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.7846 (t) REVERT: J 1370 MET cc_start: 0.7718 (ptp) cc_final: 0.7430 (ptp) REVERT: K 3 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8097 (tpm-80) REVERT: K 21 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8828 (mm) REVERT: H 25 LYS cc_start: 0.8997 (mtpm) cc_final: 0.8776 (ttmm) REVERT: H 39 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8389 (mt) REVERT: H 80 GLU cc_start: 0.8827 (mp0) cc_final: 0.8600 (mp0) REVERT: H 186 ASN cc_start: 0.8923 (t0) cc_final: 0.8516 (t0) outliers start: 85 outliers final: 57 residues processed: 363 average time/residue: 0.4243 time to fit residues: 240.5017 Evaluate side-chains 354 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 286 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 CYS Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 134 ASP Chi-restraints excluded: chain P residue 139 CYS Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 1037 THR 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 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 139 LEU Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 250 ARG Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1029 THR 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 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 K residue 56 GLU Chi-restraints excluded: chain G residue 33 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 201 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 221 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 256 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28424 Z= 0.177 Angle : 0.526 15.227 38801 Z= 0.273 Chirality : 0.040 0.195 4438 Planarity : 0.003 0.046 4754 Dihedral : 16.600 174.481 4701 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.13 % Favored : 96.84 % Rotamer: Outliers : 3.05 % Allowed : 24.06 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3288 helix: 1.88 (0.15), residues: 1217 sheet: -0.08 (0.24), residues: 477 loop : -0.40 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP J1193 HIS 0.009 0.001 HIS P 94 PHE 0.026 0.001 PHE G 231 TYR 0.018 0.001 TYR G 185 ARG 0.006 0.000 ARG I 275 *********************** 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 381 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 295 time to evaluate : 3.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 32 MET cc_start: 0.8530 (mmm) cc_final: 0.8217 (mmm) REVERT: P 95 GLN cc_start: 0.9309 (tt0) cc_final: 0.8435 (tt0) REVERT: P 99 TYR cc_start: 0.8724 (m-10) cc_final: 0.8004 (m-10) REVERT: P 143 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8109 (mm) REVERT: I 30 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8963 (tp) REVERT: I 681 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8468 (mtm) REVERT: I 825 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8321 (mt-10) REVERT: I 1027 LYS cc_start: 0.9055 (mmtm) cc_final: 0.8828 (mmtm) REVERT: J 196 GLN cc_start: 0.8654 (mp10) cc_final: 0.8349 (mp10) REVERT: J 250 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8475 (ptt-90) REVERT: J 300 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8151 (tp40) REVERT: J 322 ARG cc_start: 0.8200 (ptp-110) cc_final: 0.7973 (ptp-110) REVERT: J 398 LYS cc_start: 0.9285 (mttt) cc_final: 0.9000 (mtmm) REVERT: J 832 LYS cc_start: 0.9183 (mptt) cc_final: 0.8944 (mmtm) REVERT: J 856 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8569 (mt) REVERT: J 1029 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.7817 (t) REVERT: J 1370 MET cc_start: 0.7714 (ptp) cc_final: 0.7412 (ptp) REVERT: K 3 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8174 (tpm-80) REVERT: K 21 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8826 (mm) REVERT: G 193 GLU cc_start: 0.8779 (mp0) cc_final: 0.8449 (pm20) REVERT: H 25 LYS cc_start: 0.8985 (mtpm) cc_final: 0.8780 (ttmm) REVERT: H 39 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8360 (mt) REVERT: H 80 GLU cc_start: 0.8844 (mp0) cc_final: 0.8611 (mp0) REVERT: H 186 ASN cc_start: 0.8919 (t0) cc_final: 0.8497 (t0) outliers start: 86 outliers final: 67 residues processed: 361 average time/residue: 0.4096 time to fit residues: 231.6566 Evaluate side-chains 362 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 285 time to evaluate : 3.072 ------------------------------------------------------------------------------- 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 134 ASP Chi-restraints excluded: chain P residue 139 CYS Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 152 HIS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 311 CYS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 864 LYS Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 978 VAL 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 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 139 LEU Chi-restraints excluded: chain J residue 142 GLU Chi-restraints excluded: chain J residue 250 ARG Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 434 ILE 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 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 1029 THR 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 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 33 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 296 optimal weight: 4.9990 chunk 312 optimal weight: 9.9990 chunk 284 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 274 optimal weight: 0.7980 chunk 287 optimal weight: 4.9990 chunk 302 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN I 649 GLN ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 28424 Z= 0.432 Angle : 0.634 14.214 38801 Z= 0.330 Chirality : 0.044 0.276 4438 Planarity : 0.004 0.059 4754 Dihedral : 16.778 177.573 4701 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.47 % Rotamer: Outliers : 3.15 % Allowed : 24.13 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3288 helix: 1.61 (0.15), residues: 1216 sheet: -0.30 (0.23), residues: 481 loop : -0.53 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP J1193 HIS 0.008 0.001 HIS P 94 PHE 0.043 0.002 PHE G 231 TYR 0.022 0.002 TYR P 99 ARG 0.006 0.000 ARG I 275 *********************** 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 377 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 288 time to evaluate : 3.132 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: 0.8519 (mmm) cc_final: 0.7922 (mmm) REVERT: P 62 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8714 (mm-30) REVERT: P 123 PHE cc_start: 0.7688 (m-80) cc_final: 0.7294 (m-80) REVERT: P 143 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8242 (mm) REVERT: I 30 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.9006 (tp) REVERT: I 315 MET cc_start: 0.8123 (pmm) cc_final: 0.7847 (pmm) REVERT: I 681 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8423 (mtm) REVERT: I 1027 LYS cc_start: 0.9054 (mmtm) cc_final: 0.8815 (mmtm) REVERT: J 196 GLN cc_start: 0.8650 (mp10) cc_final: 0.8322 (mp10) REVERT: J 250 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8395 (ptt-90) REVERT: J 300 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8231 (tp40) REVERT: J 322 ARG cc_start: 0.8351 (ptp-110) cc_final: 0.8092 (ptp-110) REVERT: J 398 LYS cc_start: 0.9290 (mttt) cc_final: 0.9001 (mtmm) REVERT: J 832 LYS cc_start: 0.9196 (mptt) cc_final: 0.8948 (mmtm) REVERT: J 856 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8513 (mt) REVERT: J 1029 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.7950 (t) REVERT: J 1370 MET cc_start: 0.7794 (ptp) cc_final: 0.7493 (ptp) REVERT: K 3 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8218 (tpm-80) REVERT: K 21 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8901 (mm) REVERT: K 68 GLU cc_start: 0.8786 (pp20) cc_final: 0.8454 (pp20) REVERT: G 158 ARG cc_start: 0.8693 (mtm110) cc_final: 0.8488 (ttp-110) REVERT: H 25 LYS cc_start: 0.9024 (mtpm) cc_final: 0.8819 (ttmm) REVERT: H 186 ASN cc_start: 0.9056 (t0) cc_final: 0.8631 (t0) REVERT: H 194 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6881 (mt0) outliers start: 89 outliers final: 68 residues processed: 356 average time/residue: 0.4178 time to fit residues: 233.1975 Evaluate side-chains 358 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 281 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 CYS Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 95 GLN 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 21 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 30 ILE 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 311 CYS Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 864 LYS Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 1025 PHE 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 1186 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1308 ILE Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 26 SER 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 250 ARG Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1029 THR 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 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 33 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 199 optimal weight: 3.9990 chunk 321 optimal weight: 0.9980 chunk 195 optimal weight: 0.0970 chunk 152 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 336 optimal weight: 4.9990 chunk 309 optimal weight: 3.9990 chunk 268 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28424 Z= 0.260 Angle : 0.584 14.483 38801 Z= 0.304 Chirality : 0.042 0.333 4438 Planarity : 0.004 0.045 4754 Dihedral : 16.749 175.494 4699 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer: Outliers : 2.80 % Allowed : 24.42 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 3288 helix: 1.68 (0.15), residues: 1216 sheet: -0.19 (0.24), residues: 485 loop : -0.50 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J1193 HIS 0.009 0.001 HIS P 94 PHE 0.038 0.001 PHE G 231 TYR 0.026 0.001 TYR P 99 ARG 0.013 0.000 ARG I 996 ********************** 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 368 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 289 time to evaluate : 3.364 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: 0.8477 (mmm) cc_final: 0.7995 (mmm) REVERT: P 62 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8688 (mm-30) REVERT: P 95 GLN cc_start: 0.9315 (OUTLIER) cc_final: 0.9077 (tt0) REVERT: P 99 TYR cc_start: 0.8334 (m-10) cc_final: 0.7901 (m-10) REVERT: P 143 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8227 (mm) REVERT: I 30 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8999 (tp) REVERT: I 315 MET cc_start: 0.8106 (pmm) cc_final: 0.7862 (pmm) REVERT: I 681 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8434 (mtm) REVERT: I 1027 LYS cc_start: 0.9058 (mmtm) cc_final: 0.8830 (mmtm) REVERT: J 196 GLN cc_start: 0.8648 (mp10) cc_final: 0.8344 (mp10) REVERT: J 250 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8457 (ptt-90) REVERT: J 300 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8206 (tp40) REVERT: J 322 ARG cc_start: 0.8344 (ptp-110) cc_final: 0.8124 (ptp-110) REVERT: J 398 LYS cc_start: 0.9290 (mttt) cc_final: 0.8993 (mtmm) REVERT: J 832 LYS cc_start: 0.9199 (mptt) cc_final: 0.8950 (mmtm) REVERT: J 856 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8600 (mt) REVERT: J 1029 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.7941 (t) REVERT: J 1370 MET cc_start: 0.7776 (ptp) cc_final: 0.7467 (ptp) REVERT: K 3 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8210 (tpm-80) REVERT: K 21 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8884 (mm) REVERT: G 158 ARG cc_start: 0.8683 (mtm110) cc_final: 0.8468 (ttp-110) REVERT: G 193 GLU cc_start: 0.8796 (mp0) cc_final: 0.8516 (pm20) REVERT: H 39 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8432 (mt) REVERT: H 186 ASN cc_start: 0.9002 (t0) cc_final: 0.8579 (t0) REVERT: H 194 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6759 (mt0) outliers start: 79 outliers final: 60 residues processed: 350 average time/residue: 0.4319 time to fit residues: 237.3246 Evaluate side-chains 351 residues out of total 2820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 280 time to evaluate : 2.947 ------------------------------------------------------------------------------- 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 95 GLN 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 21 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 132 ASP 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 338 THR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 1025 PHE 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 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 J residue 26 SER Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 134 ASP 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 250 ARG Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1029 THR 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 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 33 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 212 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 74 optimal weight: 0.0000 chunk 268 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 275 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 2 GLN J 458 ASN J 792 ASN ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3624 r_free = 0.3624 target = 0.087015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063343 restraints weight = 82538.953| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.99 r_work: 0.2950 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 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 = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28424 Z= 0.201 Angle : 0.571 14.516 38801 Z= 0.296 Chirality : 0.041 0.314 4438 Planarity : 0.004 0.101 4754 Dihedral : 16.692 174.680 4699 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 2.52 % Allowed : 24.91 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3288 helix: 1.72 (0.15), residues: 1223 sheet: -0.13 (0.24), residues: 483 loop : -0.46 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J1193 HIS 0.020 0.001 HIS P 94 PHE 0.034 0.001 PHE G 231 TYR 0.020 0.001 TYR H 177 ARG 0.012 0.000 ARG I 996 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6612.08 seconds wall clock time: 121 minutes 34.47 seconds (7294.47 seconds total)