Starting phenix.real_space_refine on Tue Sep 15 06:25:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x4w_22043/09_2026/6x4w_22043.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x4w_22043/09_2026/6x4w_22043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x4w_22043/09_2026/6x4w_22043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x4w_22043/09_2026/6x4w_22043.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x4w_22043/09_2026/6x4w_22043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x4w_22043/09_2026/6x4w_22043.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6x4w_22043/09_2026/6x4w_22043.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x4w_22043/09_2026/6x4w_22043.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 1.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 113 5.49 5 Mg 1 5.21 5 S 142 5.16 5 C 22279 2.51 5 N 6391 2.21 5 O 7093 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.23s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36021 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 8955 Classifications: {'peptide': 1144} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 55, 'TRANS': 1088} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 11, 'GLU:plan': 10, 'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 131 Chain: "G" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1717 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1667 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 10348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10348 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "J" Number of atoms: 10373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10373 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 201 Classifications: {'RNAv2': 9} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna3p': 8} Chain: "P" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1112 Classifications: {'DNA': 55} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 54} Chain: "Q" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 991 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23132 SG CYS J 70 20.856 92.418 99.987 1.00183.37 S ATOM 23146 SG CYS J 72 19.869 95.903 98.848 1.00177.89 S ATOM 23254 SG CYS J 85 18.184 92.799 97.433 1.00203.51 S ATOM 23278 SG CYS J 88 21.735 93.305 96.550 1.00199.09 S ATOM 28948 SG CYS J 814 53.426 35.649 101.612 1.00 96.96 S ATOM 29513 SG CYS J 888 53.987 38.864 100.479 1.00 78.85 S ATOM 29585 SG CYS J 898 55.902 35.910 103.171 1.00 85.60 S Time building chain proxies: 7.82, per 1000 atoms: 0.22 Number of scatterers: 36021 At special positions: 0 Unit cell: (140.4, 193.7, 191.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 142 16.00 P 113 15.00 Mg 1 11.99 O 7093 8.00 N 6391 7.00 C 22279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 6 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8012 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 53 sheets defined 38.1% alpha, 15.5% beta 53 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 5.12 Creating SS restraints... Processing helix chain 'A' and resid 25 through 38 removed outlier: 3.995A pdb=" N THR A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 63 removed outlier: 4.525A pdb=" N SER A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 98 removed outlier: 3.504A pdb=" N ILE A 88 " --> pdb=" O HIS A 84 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.576A pdb=" N GLN A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 220 through 235 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 255 through 260 removed outlier: 4.686A pdb=" N GLU A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 287 through 306 removed outlier: 4.332A pdb=" N SER A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 321 removed outlier: 4.109A pdb=" N LEU A 320 " --> pdb=" O PRO A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 371 through 378 Processing helix chain 'A' and resid 391 through 404 removed outlier: 3.649A pdb=" N GLU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.665A pdb=" N ALA A 418 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.874A pdb=" N LEU A 450 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 564 through 578 Processing helix chain 'A' and resid 586 through 597 removed outlier: 3.677A pdb=" N PHE A 597 " --> pdb=" O PHE A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 617 Processing helix chain 'A' and resid 634 through 648 removed outlier: 3.579A pdb=" N ALA A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 673 removed outlier: 3.529A pdb=" N ALA A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 667 " --> pdb=" O GLN A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 702 removed outlier: 3.765A pdb=" N GLN A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.698A pdb=" N GLN A 715 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 742 removed outlier: 4.424A pdb=" N ILE A 742 " --> pdb=" O HIS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 768 Processing helix chain 'A' and resid 794 through 807 Processing helix chain 'A' and resid 821 through 831 removed outlier: 3.724A pdb=" N GLU A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 859 Processing helix chain 'A' and resid 869 through 874 Processing helix chain 'A' and resid 892 through 901 Processing helix chain 'A' and resid 923 through 936 Processing helix chain 'A' and resid 941 through 950 Processing helix chain 'A' and resid 971 through 987 Processing helix chain 'A' and resid 993 through 1000 removed outlier: 3.695A pdb=" N LEU A 997 " --> pdb=" O SER A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1032 Processing helix chain 'A' and resid 1035 through 1051 Processing helix chain 'A' and resid 1054 through 1074 Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1127 through 1145 Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.676A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 154 through 158 removed outlier: 4.197A pdb=" N ARG G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 229 removed outlier: 3.651A pdb=" N ALA G 221 " --> pdb=" O ILE G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 4.070A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG H 44 " --> pdb=" O GLY H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 111 through 115 Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'I' and resid 28 through 38 removed outlier: 3.609A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 212 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.562A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 288 through 293 removed outlier: 3.565A pdb=" N ILE I 292 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA I 293 " --> pdb=" O GLU I 290 " (cutoff:3.500A) 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: 3.786A pdb=" N ALA I 381 " --> pdb=" O THR I 377 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 481 Processing helix chain 'I' and resid 483 through 487 removed outlier: 3.665A pdb=" N THR I 486 " --> pdb=" O ASP I 483 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 608 through 613 Processing helix chain 'I' and resid 663 through 667 removed outlier: 3.507A pdb=" N SER I 666 " --> pdb=" O VAL I 663 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 663 through 667' Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.712A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1099 through 1103 removed outlier: 3.680A pdb=" N GLY I1102 " --> pdb=" O ASN I1099 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.665A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU I1143 " --> pdb=" O ALA I1139 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 4.124A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 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 removed outlier: 3.542A pdb=" N TYR I1281 " --> pdb=" O ALA I1277 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1310 Processing helix chain 'I' and resid 1320 through 1332 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 removed outlier: 3.562A pdb=" N PHE J 62 " --> pdb=" O CYS J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 193 through 207 removed outlier: 4.046A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 230 Processing helix chain 'J' and resid 233 through 236 removed outlier: 3.835A pdb=" N TRP J 236 " --> pdb=" O LYS J 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 233 through 236' Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 removed outlier: 4.007A pdb=" N VAL J 292 " --> pdb=" O PRO J 288 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN J 294 " --> pdb=" O ILE J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 332 through 336 removed outlier: 4.313A pdb=" N GLN J 335 " --> pdb=" O LYS J 332 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY J 336 " --> pdb=" O GLY J 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 332 through 336' Processing helix chain 'J' and resid 338 through 343 removed outlier: 4.107A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.545A pdb=" N PHE J 377 " --> pdb=" O ALA J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 403 Processing helix chain 'J' and resid 406 through 416 removed outlier: 4.226A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 505 through 514 Processing helix chain 'J' and resid 529 through 540 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 597 through 612 removed outlier: 3.565A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.788A 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 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.686A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 787 removed outlier: 4.261A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY J 782 " --> pdb=" O GLY J 778 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU J 783 " --> pdb=" O ALA J 779 " (cutoff:3.500A) Processing helix chain 'J' and resid 791 through 804 Processing helix chain 'J' and resid 834 through 839 removed outlier: 3.539A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 930 removed outlier: 3.643A pdb=" N LEU J 930 " --> pdb=" O GLY J 927 " (cutoff:3.500A) Processing helix chain 'J' and resid 1068 through 1072 removed outlier: 3.750A pdb=" N LYS J1072 " --> pdb=" O ALA J1069 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 removed outlier: 3.574A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.769A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 removed outlier: 3.867A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1293 removed outlier: 3.646A pdb=" N GLU J1291 " --> pdb=" O ILE J1287 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1315 removed outlier: 3.792A pdb=" N LEU J1314 " --> pdb=" O THR J1310 " (cutoff:3.500A) Processing helix chain 'J' and resid 1318 through 1323 Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 4.000A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) Processing helix chain 'J' and resid 1348 through 1354 Processing helix chain 'J' and resid 1360 through 1373 Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 removed outlier: 4.014A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 77 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 69 removed outlier: 3.816A pdb=" N THR A 285 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 282 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU A 339 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASN A 284 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG A 17 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N ALA A 351 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU A 18 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 152 removed outlier: 5.745A pdb=" N ARG A 151 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR A 164 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL A 194 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 356 through 357 removed outlier: 6.371A pdb=" N VAL A 385 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLN A 410 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 529 through 531 removed outlier: 5.757A pdb=" N TYR A 493 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR A 512 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 495 " --> pdb=" O MET A 510 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE I 117 " --> pdb=" O TYR A 520 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU I 100 " --> pdb=" O GLN I 120 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 679 through 683 removed outlier: 6.635A pdb=" N ARG A 679 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ARG A 624 " --> pdb=" O THR A 753 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP A 623 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 788 through 792 removed outlier: 6.378A pdb=" N PHE A 789 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR A 916 " --> pdb=" O PHE A 789 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ARG A 791 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASN A 881 " --> pdb=" O TYR A 911 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N TRP A 913 " --> pdb=" O ASN A 881 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE A 883 " --> pdb=" O TRP A 913 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU A 915 " --> pdb=" O ILE A 883 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 885 " --> pdb=" O LEU A 915 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN A 811 " --> pdb=" O ALA A 880 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR A 882 " --> pdb=" O GLN A 811 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 812 " --> pdb=" O LEU A 865 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N CYS A 867 " --> pdb=" O VAL A 812 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR A 814 " --> pdb=" O CYS A 867 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1075 through 1080 Processing sheet with id=AA9, first strand: chain 'G' and resid 16 through 17 removed outlier: 6.574A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.390A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N GLY G 151 " --> pdb=" O PRO G 52 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.390A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL G 153 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AB4, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.720A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.477A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.709A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY H 149 " --> pdb=" O GLY H 53 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB8, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB9, first strand: chain 'H' and resid 108 through 109 Processing sheet with id=AC1, first strand: chain 'H' and resid 152 through 153 removed outlier: 3.643A pdb=" N VAL H 153 " --> pdb=" O ALA H 175 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.420A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AC4, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AC5, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.669A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN I 193 " --> pdb=" O ASP I 189 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 284 through 286 removed outlier: 4.552A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.732A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.799A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.760A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.377A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AD3, first strand: chain 'I' and resid 616 through 617 Processing sheet with id=AD4, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.507A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.304A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AD7, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 4.666A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 1066 through 1067 Processing sheet with id=AD9, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.526A pdb=" N THR I 843 " --> pdb=" O GLY I 846 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASP I 842 " --> pdb=" O VAL I1046 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL I1046 " --> pdb=" O ASP I 842 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AE2, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AE3, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.517A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 1269 through 1270 removed outlier: 3.832A pdb=" N LYS J 345 " --> pdb=" O PHE I1270 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.581A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.220A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AE8, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE9, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AF1, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AF2, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.219A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA J1001 " --> pdb=" O ILE J 975 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 991 through 996 removed outlier: 6.535A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 1025 through 1028 removed outlier: 3.651A pdb=" N VAL J1027 " --> pdb=" O ALA J1122 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA J1122 " --> pdb=" O VAL J1027 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id=AF6, first strand: chain 'J' and resid 1046 through 1048 Processing sheet with id=AF7, first strand: chain 'J' and resid 1187 through 1190 Processing sheet with id=AF8, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.446A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1401 hydrogen bonds defined for protein. 3888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 136 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 11.60 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10124 1.33 - 1.45: 6905 1.45 - 1.57: 19337 1.57 - 1.70: 222 1.70 - 1.82: 249 Bond restraints: 36837 Sorted by residual: bond pdb=" C1' DC P 13 " pdb=" N1 DC P 13 " ideal model delta sigma weight residual 1.468 1.550 -0.082 1.40e-02 5.10e+03 3.41e+01 bond pdb=" O3' DT P 24 " pdb=" P DA P 25 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.20e-02 6.94e+03 2.53e+01 bond pdb=" N PRO A 467 " pdb=" CD PRO A 467 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.89e+01 bond pdb=" CA LYS I1234 " pdb=" CB LYS I1234 " ideal model delta sigma weight residual 1.527 1.475 0.052 1.30e-02 5.92e+03 1.62e+01 bond pdb=" C5' DA Q 10 " pdb=" C4' DA Q 10 " ideal model delta sigma weight residual 1.512 1.540 -0.028 7.00e-03 2.04e+04 1.58e+01 ... (remaining 36832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 48414 2.79 - 5.59: 1630 5.59 - 8.38: 207 8.38 - 11.17: 44 11.17 - 13.97: 10 Bond angle restraints: 50305 Sorted by residual: angle pdb=" O4' DG P 34 " pdb=" C4' DG P 34 " pdb=" C3' DG P 34 " ideal model delta sigma weight residual 106.00 102.32 3.68 6.00e-01 2.78e+00 3.76e+01 angle pdb=" CA ILE A 877 " pdb=" CB ILE A 877 " pdb=" CG2 ILE A 877 " ideal model delta sigma weight residual 110.50 120.31 -9.81 1.70e+00 3.46e-01 3.33e+01 angle pdb=" C ILE I1079 " pdb=" N ASN I1080 " pdb=" CA ASN I1080 " ideal model delta sigma weight residual 120.94 131.51 -10.57 1.90e+00 2.77e-01 3.09e+01 angle pdb=" O4' DT P 35 " pdb=" C4' DT P 35 " pdb=" C3' DT P 35 " ideal model delta sigma weight residual 106.00 102.67 3.33 6.00e-01 2.78e+00 3.09e+01 angle pdb=" N THR J 212 " pdb=" CA THR J 212 " pdb=" C THR J 212 " ideal model delta sigma weight residual 114.56 107.57 6.99 1.27e+00 6.20e-01 3.03e+01 ... (remaining 50300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.60: 20284 23.60 - 47.19: 1579 47.19 - 70.79: 343 70.79 - 94.39: 49 94.39 - 117.98: 2 Dihedral angle restraints: 22257 sinusoidal: 9828 harmonic: 12429 Sorted by residual: dihedral pdb=" O5' A R 14 " pdb=" C5' A R 14 " pdb=" C4' A R 14 " pdb=" C3' A R 14 " ideal model delta sinusoidal sigma weight residual 60.00 119.16 -59.16 3 6.40e+00 2.44e-02 5.21e+01 dihedral pdb=" C5' ADP A2000 " pdb=" O5' ADP A2000 " pdb=" PA ADP A2000 " pdb=" O2A ADP A2000 " ideal model delta sinusoidal sigma weight residual -60.00 54.94 -114.94 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" CA ASN I 519 " pdb=" C ASN I 519 " pdb=" N PRO I 520 " pdb=" CA PRO I 520 " ideal model delta harmonic sigma weight residual 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 22254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 5314 0.118 - 0.235: 402 0.235 - 0.353: 23 0.353 - 0.471: 1 0.471 - 0.589: 1 Chirality restraints: 5741 Sorted by residual: chirality pdb=" CG LEU J 527 " pdb=" CB LEU J 527 " pdb=" CD1 LEU J 527 " pdb=" CD2 LEU J 527 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.66e+00 chirality pdb=" CB ILE I 11 " pdb=" CA ILE I 11 " pdb=" CG1 ILE I 11 " pdb=" CG2 ILE I 11 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CB ILE J1248 " pdb=" CA ILE J1248 " pdb=" CG1 ILE J1248 " pdb=" CG2 ILE J1248 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 5738 not shown) Planarity restraints: 6190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I1229 " -0.032 2.00e-02 2.50e+03 2.63e-02 1.39e+01 pdb=" CG TYR I1229 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR I1229 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR I1229 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR I1229 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR I1229 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR I1229 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR I1229 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 759 " -0.058 5.00e-02 4.00e+02 8.72e-02 1.22e+01 pdb=" N PRO A 760 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 876 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ASP A 876 " 0.056 2.00e-02 2.50e+03 pdb=" O ASP A 876 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE A 877 " -0.019 2.00e-02 2.50e+03 ... (remaining 6187 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 199 2.45 - 3.06: 22687 3.06 - 3.68: 58364 3.68 - 4.29: 80744 4.29 - 4.90: 130546 Nonbonded interactions: 292540 Sorted by model distance: nonbonded pdb=" O ARG J 709 " pdb=" OD1 ASP J 710 " model vdw 1.840 3.040 nonbonded pdb=" O ASN J 206 " pdb=" OE1 GLU J 207 " model vdw 1.967 3.040 nonbonded pdb=" O3' A R 20 " pdb="MG MG J1501 " model vdw 2.033 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.035 2.170 nonbonded pdb=" OD2 ASP J 460 " pdb="MG MG J1501 " model vdw 2.138 2.170 ... (remaining 292535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 5 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 135 or (resid 136 and (name N or na \ me CA or name C or name O or name CB )) or resid 137 through 158 or resid 170 th \ rough 232)) selection = (chain 'H' and (resid 5 through 187 or (resid 188 through 191 and (name N or nam \ e CA or name C or name O or name CB )) or resid 192 through 193 or (resid 194 an \ d (name N or name CA or name C or name O or name CB )) or resid 195 through 232) \ ) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 46.000 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.107 36844 Z= 0.469 Angle : 1.213 13.967 50311 Z= 0.703 Chirality : 0.066 0.589 5741 Planarity : 0.007 0.087 6190 Dihedral : 17.154 117.983 14245 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.03 % Favored : 91.71 % Rotamer: Outliers : 0.19 % Allowed : 0.94 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.11), residues: 4294 helix: -1.66 (0.11), residues: 1456 sheet: -1.44 (0.20), residues: 605 loop : -1.97 (0.12), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG I 371 TYR 0.062 0.003 TYR I1229 PHE 0.043 0.003 PHE I 80 TRP 0.036 0.004 TRP I 997 HIS 0.012 0.002 HIS A 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00905 / 0.47 (36837) covalent geometry : angle 1.21228 / 0.70 (50305) hydrogen bonds : bond 0.15492 / 10.55 ( 1520) hydrogen bonds : angle 6.84200 / 4.74 ( 4160) metal coordination : bond 0.02112 / 0.95 ( 7) metal coordination : angle 3.85745 / 2.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 417 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 922 MET cc_start: 0.7667 (ptp) cc_final: 0.7143 (ptp) REVERT: G 8 PHE cc_start: 0.8172 (m-80) cc_final: 0.7947 (m-80) REVERT: I 85 CYS cc_start: 0.8767 (m) cc_final: 0.8517 (m) REVERT: I 642 SER cc_start: 0.8149 (t) cc_final: 0.7899 (p) REVERT: I 704 MET cc_start: 0.8403 (mmm) cc_final: 0.8075 (tpp) REVERT: I 1230 MET cc_start: 0.8259 (ttt) cc_final: 0.8006 (ttt) REVERT: J 118 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8399 (mtmt) REVERT: J 320 ASN cc_start: 0.5678 (t0) cc_final: 0.5419 (t0) REVERT: J 644 MET cc_start: 0.6526 (mpp) cc_final: 0.6310 (mtm) REVERT: J 822 MET cc_start: 0.7794 (mmt) cc_final: 0.7575 (mmp) REVERT: J 868 TRP cc_start: 0.7931 (m100) cc_final: 0.7725 (m100) REVERT: J 1371 ARG cc_start: 0.7857 (ppt170) cc_final: 0.7095 (tpm170) REVERT: K 26 ARG cc_start: 0.8421 (tmt-80) cc_final: 0.8163 (tpm170) REVERT: K 30 MET cc_start: 0.7896 (mmm) cc_final: 0.7575 (mmt) REVERT: K 31 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7773 (tm-30) outliers start: 7 outliers final: 2 residues processed: 423 average time/residue: 0.2327 time to fit residues: 163.3801 Evaluate side-chains 317 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 315 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain J residue 850 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 432 optimal weight: 40.0000 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 0.0270 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN ** I 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 573 ASN ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 861 ASN J1049 GLN ** J1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1326 GLN K 15 ASN K 72 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.106199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.082482 restraints weight = 120410.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.083451 restraints weight = 66435.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.083891 restraints weight = 43449.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.084113 restraints weight = 40774.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.084152 restraints weight = 37456.361| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 36844 Z= 0.166 Angle : 0.748 12.095 50311 Z= 0.387 Chirality : 0.047 0.216 5741 Planarity : 0.005 0.067 6190 Dihedral : 16.145 115.340 5945 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.50 % Favored : 93.41 % Rotamer: Outliers : 0.77 % Allowed : 9.21 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.12), residues: 4294 helix: -0.77 (0.12), residues: 1497 sheet: -1.32 (0.21), residues: 614 loop : -1.75 (0.13), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J1330 TYR 0.026 0.002 TYR G 185 PHE 0.016 0.001 PHE I1270 TRP 0.015 0.001 TRP A 73 HIS 0.009 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (36837) covalent geometry : angle 0.74627 / 0.39 (50305) hydrogen bonds : bond 0.04936 / 3.33 ( 1520) hydrogen bonds : angle 5.47386 / 3.83 ( 4160) metal coordination : bond 0.01370 / 0.67 ( 7) metal coordination : angle 4.87526 / 2.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 367 time to evaluate : 1.634 Fit side-chains revert: symmetry clash REVERT: A 426 MET cc_start: 0.7751 (tpp) cc_final: 0.7298 (tpp) REVERT: A 443 LEU cc_start: 0.9049 (tp) cc_final: 0.8756 (tt) REVERT: G 7 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6674 (mm-30) REVERT: H 117 HIS cc_start: 0.8202 (t-90) cc_final: 0.7919 (t-90) REVERT: H 125 LYS cc_start: 0.7510 (tptt) cc_final: 0.7296 (tttp) REVERT: I 85 CYS cc_start: 0.8955 (m) cc_final: 0.8609 (m) REVERT: I 315 MET cc_start: 0.8190 (mmm) cc_final: 0.7808 (tpt) REVERT: I 488 MET cc_start: 0.8205 (mmt) cc_final: 0.7538 (mmt) REVERT: I 642 SER cc_start: 0.8343 (t) cc_final: 0.8119 (p) REVERT: I 685 MET cc_start: 0.7687 (mtm) cc_final: 0.7463 (mtm) REVERT: I 741 MET cc_start: 0.8011 (tpp) cc_final: 0.7762 (mmm) REVERT: I 1066 MET cc_start: 0.8292 (ptp) cc_final: 0.8088 (ptm) REVERT: I 1229 TYR cc_start: 0.8434 (m-10) cc_final: 0.8228 (m-10) REVERT: J 29 MET cc_start: 0.8992 (mtt) cc_final: 0.8733 (ptp) REVERT: J 118 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8366 (mtmt) REVERT: J 180 MET cc_start: 0.7676 (tpp) cc_final: 0.7348 (tpp) REVERT: J 320 ASN cc_start: 0.5548 (t0) cc_final: 0.5243 (t0) REVERT: J 644 MET cc_start: 0.6601 (mpp) cc_final: 0.6359 (mtm) REVERT: J 868 TRP cc_start: 0.7834 (m100) cc_final: 0.7562 (m100) REVERT: J 1124 ILE cc_start: 0.8307 (mt) cc_final: 0.7983 (mm) REVERT: J 1371 ARG cc_start: 0.7962 (ppt170) cc_final: 0.7082 (tpm170) REVERT: K 30 MET cc_start: 0.7531 (mmm) cc_final: 0.7278 (mmt) REVERT: K 31 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7174 (tm-30) outliers start: 28 outliers final: 16 residues processed: 386 average time/residue: 0.2157 time to fit residues: 141.6491 Evaluate side-chains 332 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 315 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1287 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 302 optimal weight: 20.0000 chunk 366 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 41 optimal weight: 30.0000 chunk 169 optimal weight: 4.9990 chunk 392 optimal weight: 20.0000 chunk 128 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 199 optimal weight: 0.6980 chunk 417 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1299 ASN ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.104942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.080745 restraints weight = 122514.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.081897 restraints weight = 70034.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.081884 restraints weight = 46715.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.082163 restraints weight = 46985.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.082237 restraints weight = 41397.100| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 36844 Z= 0.216 Angle : 0.723 11.104 50311 Z= 0.373 Chirality : 0.046 0.269 5741 Planarity : 0.005 0.073 6190 Dihedral : 15.911 116.527 5941 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.17 % Favored : 92.73 % Rotamer: Outliers : 1.69 % Allowed : 12.76 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.12), residues: 4294 helix: -0.38 (0.13), residues: 1500 sheet: -1.37 (0.20), residues: 648 loop : -1.70 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 312 TYR 0.024 0.002 TYR G 185 PHE 0.016 0.002 PHE J1319 TRP 0.012 0.001 TRP A 260 HIS 0.006 0.001 HIS A 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.22 (36837) covalent geometry : angle 0.72178 / 0.37 (50305) hydrogen bonds : bond 0.04693 / 3.16 ( 1520) hydrogen bonds : angle 5.24401 / 3.68 ( 4160) metal coordination : bond 0.01428 / 0.67 ( 7) metal coordination : angle 4.49236 / 2.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 334 time to evaluate : 1.416 Fit side-chains REVERT: A 130 MET cc_start: 0.7704 (ppp) cc_final: 0.7470 (ppp) REVERT: A 426 MET cc_start: 0.7749 (tpp) cc_final: 0.7279 (tpp) REVERT: A 443 LEU cc_start: 0.9108 (tp) cc_final: 0.8810 (tt) REVERT: A 918 HIS cc_start: 0.8639 (t70) cc_final: 0.8301 (t70) REVERT: A 967 MET cc_start: 0.7564 (tpp) cc_final: 0.7336 (tpp) REVERT: H 117 HIS cc_start: 0.8305 (t-90) cc_final: 0.7891 (t-90) REVERT: H 205 MET cc_start: 0.8889 (tpp) cc_final: 0.8102 (ttt) REVERT: I 85 CYS cc_start: 0.8965 (m) cc_final: 0.8602 (m) REVERT: I 224 PHE cc_start: 0.8342 (m-10) cc_final: 0.8071 (m-80) REVERT: I 492 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7748 (mmm) REVERT: I 644 LEU cc_start: 0.8638 (tp) cc_final: 0.8232 (tp) REVERT: I 741 MET cc_start: 0.8023 (tpp) cc_final: 0.7720 (mmm) REVERT: I 839 VAL cc_start: 0.8760 (m) cc_final: 0.8454 (p) REVERT: J 118 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8379 (mtmt) REVERT: J 180 MET cc_start: 0.7723 (tpp) cc_final: 0.7441 (tpp) REVERT: J 320 ASN cc_start: 0.5721 (t0) cc_final: 0.5369 (t0) REVERT: J 868 TRP cc_start: 0.7831 (m100) cc_final: 0.7476 (m100) REVERT: J 1040 MET cc_start: 0.5867 (ttt) cc_final: 0.5268 (ttp) REVERT: J 1189 MET cc_start: 0.7391 (tpp) cc_final: 0.7133 (tpp) REVERT: J 1371 ARG cc_start: 0.8080 (ppt170) cc_final: 0.7271 (tpm170) REVERT: K 30 MET cc_start: 0.7575 (mmm) cc_final: 0.7330 (mmt) REVERT: K 31 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7118 (tm-30) outliers start: 61 outliers final: 33 residues processed: 377 average time/residue: 0.2211 time to fit residues: 141.3310 Evaluate side-chains 353 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 319 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1347 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 391 optimal weight: 5.9990 chunk 320 optimal weight: 9.9990 chunk 359 optimal weight: 7.9990 chunk 370 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 312 optimal weight: 4.9990 chunk 347 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 375 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1209 GLN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 495 ASN J 680 ASN ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.103523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.077695 restraints weight = 120975.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.079678 restraints weight = 59459.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.080939 restraints weight = 38362.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.081702 restraints weight = 29606.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.082145 restraints weight = 25580.190| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 36844 Z= 0.338 Angle : 0.809 13.026 50311 Z= 0.416 Chirality : 0.048 0.261 5741 Planarity : 0.006 0.077 6190 Dihedral : 15.905 116.779 5941 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.96 % Favored : 91.97 % Rotamer: Outliers : 2.55 % Allowed : 15.63 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.12), residues: 4294 helix: -0.40 (0.13), residues: 1486 sheet: -1.44 (0.20), residues: 644 loop : -1.69 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1076 TYR 0.035 0.002 TYR I1229 PHE 0.021 0.002 PHE I 828 TRP 0.021 0.002 TRP I1276 HIS 0.014 0.002 HIS I1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00729 / 0.34 (36837) covalent geometry : angle 0.80705 / 0.42 (50305) hydrogen bonds : bond 0.05084 / 3.40 ( 1520) hydrogen bonds : angle 5.34288 / 3.74 ( 4160) metal coordination : bond 0.01844 / 0.84 ( 7) metal coordination : angle 4.93548 / 2.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 319 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.8567 (mmm) cc_final: 0.8322 (mmm) REVERT: A 426 MET cc_start: 0.7890 (tpp) cc_final: 0.7359 (tpp) REVERT: A 443 LEU cc_start: 0.9303 (tp) cc_final: 0.9032 (tt) REVERT: A 636 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: H 117 HIS cc_start: 0.8177 (t-90) cc_final: 0.7739 (t-90) REVERT: H 205 MET cc_start: 0.8949 (tpp) cc_final: 0.8352 (ttt) REVERT: I 85 CYS cc_start: 0.9008 (m) cc_final: 0.8580 (m) REVERT: I 221 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9159 (mm) REVERT: I 1274 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: J 29 MET cc_start: 0.8922 (mtt) cc_final: 0.8696 (ptp) REVERT: J 118 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8302 (mtmt) REVERT: J 192 MET cc_start: 0.7727 (tpt) cc_final: 0.7471 (tpt) REVERT: J 320 ASN cc_start: 0.5886 (t0) cc_final: 0.5481 (t0) REVERT: J 740 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8960 (tp) REVERT: J 746 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8490 (mt) REVERT: J 868 TRP cc_start: 0.7583 (m100) cc_final: 0.7318 (m100) REVERT: J 1040 MET cc_start: 0.6277 (ttt) cc_final: 0.6024 (ttp) REVERT: J 1146 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7606 (tm-30) REVERT: J 1203 ARG cc_start: 0.8215 (ppt170) cc_final: 0.7981 (tmm-80) REVERT: J 1327 GLU cc_start: 0.8366 (tt0) cc_final: 0.7630 (tt0) REVERT: J 1330 ARG cc_start: 0.8789 (ptt180) cc_final: 0.8393 (ptt180) REVERT: J 1371 ARG cc_start: 0.8176 (ppt170) cc_final: 0.7385 (tpm170) REVERT: K 26 ARG cc_start: 0.8519 (tmt-80) cc_final: 0.8151 (tmt-80) REVERT: K 31 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7161 (tm-30) outliers start: 92 outliers final: 55 residues processed: 384 average time/residue: 0.2118 time to fit residues: 138.0848 Evaluate side-chains 365 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 305 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 921 GLN Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1347 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 22 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 351 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 360 optimal weight: 0.9980 chunk 408 optimal weight: 0.1980 chunk 63 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 372 optimal weight: 9.9990 chunk 378 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1019 ASN J1238 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.105938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.080410 restraints weight = 119063.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.082514 restraints weight = 56844.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.083835 restraints weight = 36020.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.084634 restraints weight = 27566.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.085022 restraints weight = 23669.586| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 36844 Z= 0.154 Angle : 0.678 12.909 50311 Z= 0.347 Chirality : 0.045 0.207 5741 Planarity : 0.005 0.082 6190 Dihedral : 15.760 120.820 5941 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.29 % Favored : 93.67 % Rotamer: Outliers : 2.16 % Allowed : 17.46 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.12), residues: 4294 helix: -0.13 (0.13), residues: 1513 sheet: -1.29 (0.20), residues: 636 loop : -1.58 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 478 TYR 0.028 0.002 TYR I1229 PHE 0.015 0.001 PHE I 224 TRP 0.013 0.001 TRP A 334 HIS 0.005 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (36837) covalent geometry : angle 0.67681 / 0.35 (50305) hydrogen bonds : bond 0.04129 / 2.78 ( 1520) hydrogen bonds : angle 5.00194 / 3.51 ( 4160) metal coordination : bond 0.00989 / 0.48 ( 7) metal coordination : angle 3.75404 / 2.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 353 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.7851 (tpp) cc_final: 0.7324 (tpp) REVERT: A 443 LEU cc_start: 0.9262 (tp) cc_final: 0.8976 (tt) REVERT: A 622 MET cc_start: 0.7623 (mtp) cc_final: 0.7089 (mmm) REVERT: A 636 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: A 918 HIS cc_start: 0.8781 (t70) cc_final: 0.8296 (t70) REVERT: G 51 MET cc_start: 0.8815 (mmm) cc_final: 0.8454 (mpp) REVERT: G 97 GLU cc_start: 0.8397 (tt0) cc_final: 0.8163 (tt0) REVERT: G 152 TYR cc_start: 0.9216 (t80) cc_final: 0.8996 (t80) REVERT: H 48 LEU cc_start: 0.9374 (mm) cc_final: 0.9095 (mm) REVERT: H 117 HIS cc_start: 0.8181 (t-90) cc_final: 0.7685 (t-90) REVERT: H 205 MET cc_start: 0.8906 (tpp) cc_final: 0.8254 (ttt) REVERT: I 85 CYS cc_start: 0.8933 (m) cc_final: 0.8541 (m) REVERT: I 210 LEU cc_start: 0.9490 (mm) cc_final: 0.9273 (mm) REVERT: I 488 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7038 (mmm) REVERT: I 542 ARG cc_start: 0.7181 (tpp-160) cc_final: 0.6940 (tpp-160) REVERT: I 700 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8945 (m) REVERT: I 741 MET cc_start: 0.8107 (tpp) cc_final: 0.7785 (mmm) REVERT: I 768 MET cc_start: 0.8321 (mtp) cc_final: 0.7866 (mtp) REVERT: I 1070 HIS cc_start: 0.9385 (OUTLIER) cc_final: 0.9083 (p-80) REVERT: I 1274 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: J 29 MET cc_start: 0.8891 (mtt) cc_final: 0.8227 (ptp) REVERT: J 118 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8378 (mtmt) REVERT: J 164 GLN cc_start: 0.9335 (tm-30) cc_final: 0.9069 (tm-30) REVERT: J 180 MET cc_start: 0.8176 (tpp) cc_final: 0.7432 (tpp) REVERT: J 192 MET cc_start: 0.7498 (tpt) cc_final: 0.7271 (tpt) REVERT: J 320 ASN cc_start: 0.5593 (t0) cc_final: 0.5308 (t0) REVERT: J 740 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8925 (tp) REVERT: J 868 TRP cc_start: 0.7693 (m100) cc_final: 0.7229 (m100) REVERT: J 1146 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7440 (tm-30) REVERT: J 1203 ARG cc_start: 0.8195 (ppt170) cc_final: 0.7634 (ptp-110) REVERT: J 1327 GLU cc_start: 0.8260 (tt0) cc_final: 0.7417 (tm-30) REVERT: J 1330 ARG cc_start: 0.8736 (ptt180) cc_final: 0.7915 (ptt180) REVERT: J 1371 ARG cc_start: 0.8136 (ppt170) cc_final: 0.7339 (tpm170) REVERT: K 26 ARG cc_start: 0.8459 (tmt-80) cc_final: 0.7396 (tmt-80) REVERT: K 30 MET cc_start: 0.7529 (mmm) cc_final: 0.7139 (mmm) REVERT: K 31 GLN cc_start: 0.7837 (tm-30) cc_final: 0.7112 (tm-30) outliers start: 78 outliers final: 41 residues processed: 413 average time/residue: 0.2077 time to fit residues: 144.7106 Evaluate side-chains 375 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 328 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 224 PHE Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 1070 HIS Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1347 LEU Chi-restraints excluded: chain J residue 1351 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 184 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 431 optimal weight: 20.0000 chunk 93 optimal weight: 0.0980 chunk 350 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 420 optimal weight: 7.9990 chunk 229 optimal weight: 8.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 477 GLN ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1238 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.104630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.078965 restraints weight = 119305.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.080968 restraints weight = 58274.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.082249 restraints weight = 37561.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.083008 restraints weight = 28889.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083461 restraints weight = 24972.879| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 36844 Z= 0.277 Angle : 0.748 12.842 50311 Z= 0.382 Chirality : 0.046 0.228 5741 Planarity : 0.005 0.075 6190 Dihedral : 15.754 123.155 5941 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.85 % Favored : 92.08 % Rotamer: Outliers : 3.27 % Allowed : 17.79 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.12), residues: 4294 helix: -0.15 (0.13), residues: 1519 sheet: -1.37 (0.21), residues: 630 loop : -1.64 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 202 TYR 0.026 0.002 TYR I1229 PHE 0.017 0.002 PHE I 828 TRP 0.020 0.002 TRP I1276 HIS 0.010 0.001 HIS I1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.28 (36837) covalent geometry : angle 0.74652 / 0.38 (50305) hydrogen bonds : bond 0.04544 / 3.04 ( 1520) hydrogen bonds : angle 5.10111 / 3.58 ( 4160) metal coordination : bond 0.01516 / 0.70 ( 7) metal coordination : angle 4.11668 / 2.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 322 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.7810 (ppp) cc_final: 0.7573 (ppp) REVERT: A 443 LEU cc_start: 0.9239 (tp) cc_final: 0.8955 (tt) REVERT: A 527 HIS cc_start: 0.9090 (OUTLIER) cc_final: 0.8536 (p90) REVERT: A 622 MET cc_start: 0.7254 (mtp) cc_final: 0.6728 (mmt) REVERT: A 636 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: H 117 HIS cc_start: 0.8269 (t-90) cc_final: 0.7798 (t-90) REVERT: H 205 MET cc_start: 0.8970 (tpp) cc_final: 0.8374 (ttt) REVERT: I 85 CYS cc_start: 0.8969 (m) cc_final: 0.8559 (m) REVERT: I 221 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9159 (mm) REVERT: I 488 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7270 (mmm) REVERT: I 542 ARG cc_start: 0.7344 (tpp-160) cc_final: 0.6654 (tpp-160) REVERT: I 606 LEU cc_start: 0.9255 (tp) cc_final: 0.9015 (tp) REVERT: I 700 VAL cc_start: 0.9334 (OUTLIER) cc_final: 0.9130 (m) REVERT: I 741 MET cc_start: 0.8076 (tpp) cc_final: 0.7852 (mmm) REVERT: I 978 VAL cc_start: 0.5681 (OUTLIER) cc_final: 0.5464 (t) REVERT: I 1070 HIS cc_start: 0.9399 (OUTLIER) cc_final: 0.9092 (p-80) REVERT: I 1274 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: J 118 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8372 (mtmt) REVERT: J 164 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8977 (tm-30) REVERT: J 180 MET cc_start: 0.8110 (tpp) cc_final: 0.7815 (tpp) REVERT: J 192 MET cc_start: 0.7547 (tpt) cc_final: 0.7324 (tpt) REVERT: J 320 ASN cc_start: 0.5625 (t0) cc_final: 0.5367 (t0) REVERT: J 740 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8961 (tp) REVERT: J 746 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8465 (mt) REVERT: J 868 TRP cc_start: 0.7606 (m100) cc_final: 0.7292 (m100) REVERT: J 1146 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7468 (tm-30) REVERT: J 1203 ARG cc_start: 0.8252 (ppt170) cc_final: 0.7731 (ptp-110) REVERT: J 1327 GLU cc_start: 0.8289 (tt0) cc_final: 0.6976 (tt0) REVERT: J 1330 ARG cc_start: 0.8787 (ptt180) cc_final: 0.8111 (ptt180) REVERT: J 1371 ARG cc_start: 0.8147 (ppt170) cc_final: 0.7337 (tpm170) REVERT: K 26 ARG cc_start: 0.8521 (tmt-80) cc_final: 0.7544 (tpm170) REVERT: K 31 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7123 (tm-30) outliers start: 118 outliers final: 76 residues processed: 412 average time/residue: 0.2119 time to fit residues: 148.4901 Evaluate side-chains 394 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 308 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 224 PHE Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1070 HIS Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain I residue 1325 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1347 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 22 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 149 optimal weight: 20.0000 chunk 342 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 295 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 181 optimal weight: 20.0000 chunk 241 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 962 ASN J1238 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.105984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.080551 restraints weight = 118736.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.082596 restraints weight = 57546.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.083890 restraints weight = 36849.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.084705 restraints weight = 28292.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.085086 restraints weight = 24300.887| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 36844 Z= 0.174 Angle : 0.689 16.830 50311 Z= 0.350 Chirality : 0.045 0.258 5741 Planarity : 0.004 0.075 6190 Dihedral : 15.689 126.811 5941 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.66 % Favored : 93.27 % Rotamer: Outliers : 2.68 % Allowed : 18.90 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.12), residues: 4294 helix: 0.00 (0.13), residues: 1517 sheet: -1.34 (0.20), residues: 633 loop : -1.59 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 624 TYR 0.026 0.002 TYR I1229 PHE 0.019 0.001 PHE I 828 TRP 0.018 0.001 TRP I1276 HIS 0.005 0.001 HIS I1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (36837) covalent geometry : angle 0.68808 / 0.35 (50305) hydrogen bonds : bond 0.04066 / 2.74 ( 1520) hydrogen bonds : angle 4.93841 / 3.48 ( 4160) metal coordination : bond 0.01061 / 0.50 ( 7) metal coordination : angle 3.45257 / 2.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 349 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.8019 (ppp) cc_final: 0.7770 (ppp) REVERT: A 426 MET cc_start: 0.8175 (tpp) cc_final: 0.7756 (tpp) REVERT: A 443 LEU cc_start: 0.9213 (tp) cc_final: 0.8934 (tt) REVERT: A 527 HIS cc_start: 0.9062 (OUTLIER) cc_final: 0.8452 (p90) REVERT: A 622 MET cc_start: 0.7293 (mtp) cc_final: 0.6939 (mmt) REVERT: A 636 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: A 639 MET cc_start: 0.8166 (mmp) cc_final: 0.7883 (mmp) REVERT: H 117 HIS cc_start: 0.8380 (t-90) cc_final: 0.8020 (t-90) REVERT: H 205 MET cc_start: 0.8930 (tpp) cc_final: 0.8272 (ttt) REVERT: I 85 CYS cc_start: 0.8917 (m) cc_final: 0.8517 (m) REVERT: I 488 MET cc_start: 0.7985 (mmp) cc_final: 0.7272 (mmm) REVERT: I 492 MET cc_start: 0.8383 (mmm) cc_final: 0.7950 (mmm) REVERT: I 542 ARG cc_start: 0.7288 (tpp-160) cc_final: 0.6988 (tpp-160) REVERT: I 606 LEU cc_start: 0.9240 (tp) cc_final: 0.8984 (tp) REVERT: I 685 MET cc_start: 0.8152 (mtp) cc_final: 0.7525 (mtm) REVERT: I 700 VAL cc_start: 0.9195 (OUTLIER) cc_final: 0.8988 (m) REVERT: I 927 THR cc_start: 0.9145 (m) cc_final: 0.8797 (p) REVERT: I 1070 HIS cc_start: 0.9355 (OUTLIER) cc_final: 0.9051 (p-80) REVERT: I 1274 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7939 (mt-10) REVERT: I 1279 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8352 (mt-10) REVERT: J 29 MET cc_start: 0.8867 (mtt) cc_final: 0.8651 (ptp) REVERT: J 118 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8408 (mtmt) REVERT: J 164 GLN cc_start: 0.9221 (tm-30) cc_final: 0.8926 (tm-30) REVERT: J 180 MET cc_start: 0.8117 (tpp) cc_final: 0.7785 (tpp) REVERT: J 320 ASN cc_start: 0.5614 (t0) cc_final: 0.5354 (t0) REVERT: J 330 MET cc_start: 0.8815 (ptp) cc_final: 0.8526 (ptp) REVERT: J 349 TYR cc_start: 0.8854 (m-10) cc_final: 0.8590 (m-10) REVERT: J 740 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8859 (tp) REVERT: J 868 TRP cc_start: 0.7594 (m100) cc_final: 0.7258 (m100) REVERT: J 1146 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7419 (tm-30) REVERT: J 1203 ARG cc_start: 0.8240 (ppt170) cc_final: 0.7728 (ptp-110) REVERT: J 1371 ARG cc_start: 0.8094 (ppt170) cc_final: 0.7247 (tpm170) REVERT: K 26 ARG cc_start: 0.8529 (tmt-80) cc_final: 0.7512 (tpm170) REVERT: K 31 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7019 (tm-30) outliers start: 97 outliers final: 70 residues processed: 426 average time/residue: 0.2132 time to fit residues: 154.2617 Evaluate side-chains 405 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 329 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1070 HIS Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 560 ASN Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 1068 THR Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1347 LEU Chi-restraints excluded: chain J residue 1351 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 189 optimal weight: 20.0000 chunk 313 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 305 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 238 optimal weight: 0.0670 chunk 171 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 573 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 477 GLN J 777 HIS J1238 GLN K 29 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.107675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.082212 restraints weight = 118114.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.084318 restraints weight = 56801.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.085666 restraints weight = 36252.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.086466 restraints weight = 27751.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.086945 restraints weight = 23875.545| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36844 Z= 0.126 Angle : 0.683 16.162 50311 Z= 0.341 Chirality : 0.044 0.270 5741 Planarity : 0.004 0.070 6190 Dihedral : 15.571 131.018 5941 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.31 % Favored : 93.64 % Rotamer: Outliers : 2.46 % Allowed : 19.26 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.13), residues: 4294 helix: 0.13 (0.13), residues: 1530 sheet: -1.22 (0.21), residues: 621 loop : -1.51 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 200 TYR 0.024 0.001 TYR I1229 PHE 0.019 0.001 PHE I 224 TRP 0.017 0.001 TRP I1276 HIS 0.004 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (36837) covalent geometry : angle 0.68255 / 0.34 (50305) hydrogen bonds : bond 0.03751 / 2.53 ( 1520) hydrogen bonds : angle 4.78685 / 3.37 ( 4160) metal coordination : bond 0.00627 / 0.31 ( 7) metal coordination : angle 2.52330 / 1.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 379 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 LEU cc_start: 0.8379 (tp) cc_final: 0.8081 (tt) REVERT: A 426 MET cc_start: 0.8154 (tpp) cc_final: 0.7682 (tpp) REVERT: A 443 LEU cc_start: 0.9314 (tp) cc_final: 0.9005 (tt) REVERT: A 527 HIS cc_start: 0.9056 (OUTLIER) cc_final: 0.8415 (p90) REVERT: A 636 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: A 639 MET cc_start: 0.8159 (mmp) cc_final: 0.7772 (mmp) REVERT: A 759 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9050 (mm) REVERT: A 918 HIS cc_start: 0.8782 (t70) cc_final: 0.8349 (t70) REVERT: A 959 LEU cc_start: 0.8988 (tp) cc_final: 0.8739 (tp) REVERT: A 997 LEU cc_start: 0.8766 (pp) cc_final: 0.8460 (pp) REVERT: G 8 PHE cc_start: 0.8083 (m-80) cc_final: 0.7500 (m-80) REVERT: H 117 HIS cc_start: 0.8411 (t-90) cc_final: 0.8091 (t-90) REVERT: H 205 MET cc_start: 0.8901 (tpp) cc_final: 0.8245 (ttt) REVERT: I 85 CYS cc_start: 0.8975 (m) cc_final: 0.8619 (m) REVERT: I 315 MET cc_start: 0.8179 (mmm) cc_final: 0.7902 (tpt) REVERT: I 396 ASP cc_start: 0.8494 (t0) cc_final: 0.8247 (t0) REVERT: I 492 MET cc_start: 0.8343 (mmm) cc_final: 0.7962 (mmm) REVERT: I 542 ARG cc_start: 0.7165 (tpp-160) cc_final: 0.6884 (tpp-160) REVERT: I 581 THR cc_start: 0.8835 (m) cc_final: 0.8609 (t) REVERT: I 685 MET cc_start: 0.8127 (mtp) cc_final: 0.7410 (mtm) REVERT: I 700 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8928 (m) REVERT: I 755 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8278 (tppt) REVERT: I 768 MET cc_start: 0.8137 (mtm) cc_final: 0.7910 (mtp) REVERT: I 918 LEU cc_start: 0.6400 (OUTLIER) cc_final: 0.6147 (pt) REVERT: I 927 THR cc_start: 0.9045 (m) cc_final: 0.8786 (p) REVERT: I 978 VAL cc_start: 0.5575 (OUTLIER) cc_final: 0.5352 (t) REVERT: I 1070 HIS cc_start: 0.9261 (OUTLIER) cc_final: 0.9006 (p-80) REVERT: I 1229 TYR cc_start: 0.8449 (m-10) cc_final: 0.7961 (m-10) REVERT: I 1236 ASN cc_start: 0.9151 (t0) cc_final: 0.8794 (t0) REVERT: I 1274 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: I 1279 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8307 (mt-10) REVERT: J 29 MET cc_start: 0.8925 (mtt) cc_final: 0.8649 (ptp) REVERT: J 77 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7179 (mmm160) REVERT: J 118 LYS cc_start: 0.8622 (mtmt) cc_final: 0.8370 (mtmt) REVERT: J 164 GLN cc_start: 0.9204 (tm-30) cc_final: 0.8896 (tm-30) REVERT: J 180 MET cc_start: 0.8136 (tpp) cc_final: 0.7756 (tpp) REVERT: J 320 ASN cc_start: 0.5584 (t0) cc_final: 0.5317 (t0) REVERT: J 349 TYR cc_start: 0.8679 (m-10) cc_final: 0.8397 (m-10) REVERT: J 491 LEU cc_start: 0.8925 (mp) cc_final: 0.8551 (mt) REVERT: J 868 TRP cc_start: 0.7567 (m100) cc_final: 0.7208 (m100) REVERT: J 1040 MET cc_start: 0.5500 (ttt) cc_final: 0.4883 (ttp) REVERT: J 1146 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7456 (tm-30) REVERT: J 1203 ARG cc_start: 0.8264 (ppt170) cc_final: 0.7709 (ptp-110) REVERT: J 1371 ARG cc_start: 0.8131 (ppt170) cc_final: 0.7290 (tpm170) REVERT: K 26 ARG cc_start: 0.8524 (tmt-80) cc_final: 0.7587 (tpm170) REVERT: K 30 MET cc_start: 0.7683 (mmm) cc_final: 0.7240 (mmt) REVERT: K 31 GLN cc_start: 0.7686 (tm-30) cc_final: 0.6940 (tm-30) outliers start: 89 outliers final: 57 residues processed: 443 average time/residue: 0.2226 time to fit residues: 166.3297 Evaluate side-chains 407 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 341 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1070 HIS Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1068 THR Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1347 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 39 optimal weight: 3.9990 chunk 317 optimal weight: 0.0570 chunk 305 optimal weight: 0.0470 chunk 335 optimal weight: 0.0870 chunk 20 optimal weight: 20.0000 chunk 307 optimal weight: 0.8980 chunk 249 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 408 optimal weight: 0.6980 chunk 435 optimal weight: 20.0000 chunk 358 optimal weight: 2.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 573 ASN I 799 ASN ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS J 861 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.107859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.082285 restraints weight = 119289.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.084436 restraints weight = 57038.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.085806 restraints weight = 36128.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.086640 restraints weight = 27543.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.087097 restraints weight = 23624.099| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36844 Z= 0.120 Angle : 0.688 15.926 50311 Z= 0.341 Chirality : 0.044 0.201 5741 Planarity : 0.004 0.069 6190 Dihedral : 15.483 133.495 5941 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.78 % Favored : 94.18 % Rotamer: Outliers : 2.13 % Allowed : 20.06 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.13), residues: 4294 helix: 0.25 (0.13), residues: 1523 sheet: -1.08 (0.21), residues: 614 loop : -1.46 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I1106 TYR 0.022 0.001 TYR I1229 PHE 0.021 0.001 PHE I 224 TRP 0.021 0.001 TRP I1276 HIS 0.008 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (36837) covalent geometry : angle 0.68738 / 0.34 (50305) hydrogen bonds : bond 0.03605 / 2.44 ( 1520) hydrogen bonds : angle 4.69784 / 3.30 ( 4160) metal coordination : bond 0.00461 / 0.23 ( 7) metal coordination : angle 2.05207 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 378 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7952 (ppp) cc_final: 0.7501 (ppp) REVERT: A 426 MET cc_start: 0.8178 (tpp) cc_final: 0.7698 (tpp) REVERT: A 443 LEU cc_start: 0.9349 (tp) cc_final: 0.9039 (tt) REVERT: A 527 HIS cc_start: 0.9137 (OUTLIER) cc_final: 0.8519 (p90) REVERT: A 636 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: A 639 MET cc_start: 0.8233 (mmp) cc_final: 0.7837 (mmp) REVERT: A 759 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9115 (mm) REVERT: A 867 CYS cc_start: 0.8695 (p) cc_final: 0.8479 (p) REVERT: A 945 LEU cc_start: 0.9459 (tp) cc_final: 0.9100 (tp) REVERT: G 8 PHE cc_start: 0.8126 (m-80) cc_final: 0.7397 (m-80) REVERT: H 117 HIS cc_start: 0.8434 (t-90) cc_final: 0.8106 (t-90) REVERT: H 205 MET cc_start: 0.8884 (tpp) cc_final: 0.8404 (ttt) REVERT: I 85 CYS cc_start: 0.8958 (m) cc_final: 0.8590 (m) REVERT: I 396 ASP cc_start: 0.8505 (t0) cc_final: 0.8258 (t0) REVERT: I 488 MET cc_start: 0.7934 (mmp) cc_final: 0.6945 (mmm) REVERT: I 492 MET cc_start: 0.8535 (mmm) cc_final: 0.8177 (mmm) REVERT: I 542 ARG cc_start: 0.7107 (tpp-160) cc_final: 0.6858 (tpp-160) REVERT: I 581 THR cc_start: 0.8759 (m) cc_final: 0.8463 (t) REVERT: I 685 MET cc_start: 0.8071 (mtp) cc_final: 0.7780 (mtm) REVERT: I 768 MET cc_start: 0.8218 (mtm) cc_final: 0.7866 (mtp) REVERT: I 978 VAL cc_start: 0.5582 (OUTLIER) cc_final: 0.5360 (t) REVERT: I 1070 HIS cc_start: 0.9253 (OUTLIER) cc_final: 0.8939 (p-80) REVERT: I 1229 TYR cc_start: 0.8409 (m-10) cc_final: 0.8174 (m-10) REVERT: I 1236 ASN cc_start: 0.9136 (t0) cc_final: 0.8761 (t0) REVERT: I 1274 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: I 1279 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8314 (mt-10) REVERT: J 29 MET cc_start: 0.8901 (mtt) cc_final: 0.8608 (ptp) REVERT: J 77 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7252 (mmm160) REVERT: J 118 LYS cc_start: 0.8634 (mtmt) cc_final: 0.8321 (mtmt) REVERT: J 164 GLN cc_start: 0.9223 (tm-30) cc_final: 0.8898 (tm-30) REVERT: J 180 MET cc_start: 0.8155 (tpp) cc_final: 0.7717 (tpp) REVERT: J 320 ASN cc_start: 0.5710 (t0) cc_final: 0.5416 (t0) REVERT: J 491 LEU cc_start: 0.8849 (mp) cc_final: 0.8459 (mt) REVERT: J 582 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8849 (tt) REVERT: J 868 TRP cc_start: 0.7517 (m100) cc_final: 0.7194 (m100) REVERT: J 1040 MET cc_start: 0.5407 (ttt) cc_final: 0.4986 (ttt) REVERT: J 1146 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7448 (tm-30) REVERT: J 1203 ARG cc_start: 0.8222 (ppt170) cc_final: 0.7659 (ttm-80) REVERT: J 1327 GLU cc_start: 0.8322 (tt0) cc_final: 0.7920 (tt0) REVERT: J 1371 ARG cc_start: 0.8140 (ppt170) cc_final: 0.7287 (tpm170) REVERT: K 26 ARG cc_start: 0.8504 (tmt-80) cc_final: 0.7565 (tpm170) REVERT: K 30 MET cc_start: 0.7589 (mmm) cc_final: 0.7146 (mmt) REVERT: K 31 GLN cc_start: 0.7721 (tm-30) cc_final: 0.6907 (tm-30) outliers start: 77 outliers final: 58 residues processed: 434 average time/residue: 0.2230 time to fit residues: 163.5454 Evaluate side-chains 406 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 340 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1070 HIS Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1068 THR Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain K residue 4 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 60 optimal weight: 0.6980 chunk 279 optimal weight: 0.0870 chunk 188 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 205 optimal weight: 0.0770 chunk 423 optimal weight: 8.9990 chunk 287 optimal weight: 0.8980 chunk 392 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 519 ASN I 573 ASN I 799 ASN ** I1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.108059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.082695 restraints weight = 119466.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.084856 restraints weight = 56930.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.086213 restraints weight = 35991.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.087061 restraints weight = 27414.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.087450 restraints weight = 23452.330| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 36844 Z= 0.124 Angle : 0.704 15.690 50311 Z= 0.346 Chirality : 0.045 0.364 5741 Planarity : 0.004 0.079 6190 Dihedral : 15.415 134.798 5941 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.25 % Rotamer: Outliers : 2.02 % Allowed : 20.56 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 4294 helix: 0.30 (0.13), residues: 1520 sheet: -1.09 (0.21), residues: 623 loop : -1.43 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 929 TYR 0.021 0.001 TYR I1229 PHE 0.021 0.001 PHE I 224 TRP 0.016 0.001 TRP J 580 HIS 0.005 0.001 HIS I 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (36837) covalent geometry : angle 0.70349 / 0.35 (50305) hydrogen bonds : bond 0.03551 / 2.40 ( 1520) hydrogen bonds : angle 4.65738 / 3.27 ( 4160) metal coordination : bond 0.00439 / 0.22 ( 7) metal coordination : angle 1.91269 / 1.08 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 352 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7862 (ppp) cc_final: 0.7400 (ppp) REVERT: A 174 MET cc_start: 0.8232 (mmm) cc_final: 0.7715 (mmm) REVERT: A 443 LEU cc_start: 0.9342 (tp) cc_final: 0.9029 (tt) REVERT: A 527 HIS cc_start: 0.9121 (OUTLIER) cc_final: 0.8521 (p90) REVERT: A 636 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7121 (tm-30) REVERT: A 639 MET cc_start: 0.8245 (mmp) cc_final: 0.7839 (mmp) REVERT: A 759 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9120 (mm) REVERT: A 765 MET cc_start: 0.9213 (ttm) cc_final: 0.8781 (tmm) REVERT: A 773 LEU cc_start: 0.8983 (tp) cc_final: 0.8765 (tp) REVERT: A 867 CYS cc_start: 0.8628 (p) cc_final: 0.8422 (p) REVERT: A 945 LEU cc_start: 0.9458 (tp) cc_final: 0.9092 (tp) REVERT: A 959 LEU cc_start: 0.8806 (tp) cc_final: 0.8379 (tp) REVERT: G 8 PHE cc_start: 0.8122 (m-80) cc_final: 0.7291 (m-80) REVERT: G 71 LYS cc_start: 0.8811 (tppt) cc_final: 0.8531 (tppt) REVERT: H 117 HIS cc_start: 0.8471 (t-90) cc_final: 0.8225 (t-90) REVERT: H 205 MET cc_start: 0.8932 (tpp) cc_final: 0.8272 (ttt) REVERT: I 36 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8536 (mm110) REVERT: I 85 CYS cc_start: 0.8950 (m) cc_final: 0.8586 (m) REVERT: I 396 ASP cc_start: 0.8483 (t0) cc_final: 0.8249 (t0) REVERT: I 488 MET cc_start: 0.7972 (mmp) cc_final: 0.7010 (mmm) REVERT: I 492 MET cc_start: 0.8532 (mmm) cc_final: 0.8171 (mmm) REVERT: I 542 ARG cc_start: 0.7086 (tpp-160) cc_final: 0.6852 (tpp-160) REVERT: I 685 MET cc_start: 0.8010 (mtp) cc_final: 0.7704 (mtm) REVERT: I 800 MET cc_start: 0.8119 (mtp) cc_final: 0.7918 (mtp) REVERT: I 978 VAL cc_start: 0.5587 (OUTLIER) cc_final: 0.5363 (t) REVERT: I 1070 HIS cc_start: 0.9271 (OUTLIER) cc_final: 0.9008 (p-80) REVERT: I 1229 TYR cc_start: 0.8316 (m-10) cc_final: 0.7891 (m-10) REVERT: I 1236 ASN cc_start: 0.9110 (t0) cc_final: 0.8714 (t0) REVERT: I 1274 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7713 (mt-10) REVERT: I 1279 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8357 (mt-10) REVERT: J 29 MET cc_start: 0.8885 (mtt) cc_final: 0.8578 (ptp) REVERT: J 118 LYS cc_start: 0.8659 (mtmt) cc_final: 0.8341 (mtmt) REVERT: J 164 GLN cc_start: 0.9213 (tm-30) cc_final: 0.8887 (tm-30) REVERT: J 180 MET cc_start: 0.8172 (tpp) cc_final: 0.7705 (tpp) REVERT: J 320 ASN cc_start: 0.5715 (t0) cc_final: 0.5408 (t0) REVERT: J 491 LEU cc_start: 0.8843 (mp) cc_final: 0.8459 (mt) REVERT: J 582 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8859 (tt) REVERT: J 868 TRP cc_start: 0.7476 (m100) cc_final: 0.7138 (m100) REVERT: J 1040 MET cc_start: 0.5213 (ttt) cc_final: 0.4925 (ttt) REVERT: J 1146 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7429 (tm-30) REVERT: J 1174 ARG cc_start: 0.6787 (ptp90) cc_final: 0.6168 (ptp-110) REVERT: J 1327 GLU cc_start: 0.8281 (tt0) cc_final: 0.7904 (tt0) REVERT: J 1371 ARG cc_start: 0.8258 (ppt170) cc_final: 0.7299 (tpm170) REVERT: K 26 ARG cc_start: 0.8498 (tmt-80) cc_final: 0.7567 (tpm170) REVERT: K 30 MET cc_start: 0.7526 (mmm) cc_final: 0.7083 (mmt) REVERT: K 31 GLN cc_start: 0.7713 (tm-30) cc_final: 0.6940 (tm-30) outliers start: 73 outliers final: 57 residues processed: 408 average time/residue: 0.2136 time to fit residues: 147.2469 Evaluate side-chains 399 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 335 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1070 HIS Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1068 THR Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain K residue 4 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 213 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 435 optimal weight: 20.0000 chunk 405 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 222 optimal weight: 0.6980 chunk 206 optimal weight: 0.0270 chunk 137 optimal weight: 20.0000 overall best weight: 2.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.107808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.082397 restraints weight = 119108.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.084522 restraints weight = 57100.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.085873 restraints weight = 36337.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.086696 restraints weight = 27750.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.087072 restraints weight = 23825.272| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.307 36844 Z= 0.177 Angle : 0.786 59.199 50311 Z= 0.409 Chirality : 0.046 0.614 5741 Planarity : 0.004 0.083 6190 Dihedral : 15.418 134.770 5941 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.68 % Favored : 94.27 % Rotamer: Outliers : 1.99 % Allowed : 20.84 % Favored : 77.17 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.13), residues: 4294 helix: 0.29 (0.13), residues: 1520 sheet: -1.10 (0.21), residues: 623 loop : -1.44 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 77 TYR 0.022 0.001 TYR I1229 PHE 0.021 0.001 PHE I 224 TRP 0.016 0.001 TRP I1276 HIS 0.018 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (36837) covalent geometry : angle 0.78624 / 0.41 (50305) hydrogen bonds : bond 0.03558 / 2.40 ( 1520) hydrogen bonds : angle 4.65255 / 3.27 ( 4160) metal coordination : bond 0.00589 / 0.27 ( 7) metal coordination : angle 1.90422 / 1.07 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6824.18 seconds wall clock time: 118 minutes 34.85 seconds (7114.85 seconds total)