Starting phenix.real_space_refine on Sat Mar 7 01:44:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x4w_22043/03_2026/6x4w_22043.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x4w_22043/03_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_22043/03_2026/6x4w_22043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x4w_22043/03_2026/6x4w_22043.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x4w_22043/03_2026/6x4w_22043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x4w_22043/03_2026/6x4w_22043.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: {'RNA': 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: 7.12, per 1000 atoms: 0.20 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: 2.97 Conformation dependent library (CDL) restraints added in 1.4 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: 4.89 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: 9.34 Time building geometry restraints manager: 3.92 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=" 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=" O3' DT P 24 " pdb=" P DA P 25 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.50e-02 4.44e+03 1.62e+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=" CA GLU I 672 " pdb=" C GLU I 672 " ideal model delta sigma weight residual 1.522 1.467 0.055 1.38e-02 5.25e+03 1.57e+01 bond pdb=" CA THR A 762 " pdb=" C THR A 762 " ideal model delta sigma weight residual 1.522 1.468 0.054 1.39e-02 5.18e+03 1.53e+01 ... (remaining 36832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 48463 2.79 - 5.59: 1582 5.59 - 8.38: 206 8.38 - 11.17: 44 11.17 - 13.97: 10 Bond angle restraints: 50305 Sorted by residual: 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=" 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 angle pdb=" C GLY I 112 " pdb=" N THR I 113 " pdb=" CA THR I 113 " ideal model delta sigma weight residual 121.80 131.04 -9.24 1.71e+00 3.42e-01 2.92e+01 angle pdb=" N VAL A 156 " pdb=" CA VAL A 156 " pdb=" C VAL A 156 " ideal model delta sigma weight residual 109.30 116.35 -7.05 1.31e+00 5.83e-01 2.90e+01 ... (remaining 50300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.60: 20306 23.60 - 47.19: 1579 47.19 - 70.79: 354 70.79 - 94.39: 50 94.39 - 117.98: 2 Dihedral angle restraints: 22291 sinusoidal: 9862 harmonic: 12429 Sorted by residual: 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 dihedral pdb=" CA VAL G 14 " pdb=" C VAL G 14 " pdb=" N ASP G 15 " pdb=" CA ASP G 15 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 22288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 5345 0.118 - 0.235: 375 0.235 - 0.353: 19 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.590 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 41.040 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.080 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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= 0.410 Angle : 1.199 13.967 50311 Z= 0.660 Chirality : 0.064 0.589 5741 Planarity : 0.007 0.087 6190 Dihedral : 17.227 117.983 14279 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 covalent geometry : bond 0.00893 (36837) covalent geometry : angle 1.19799 (50305) hydrogen bonds : bond 0.15492 ( 1520) hydrogen bonds : angle 6.84200 ( 4160) metal coordination : bond 0.02112 ( 7) metal coordination : angle 3.85745 ( 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 : 0.978 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: 0.2077 time to fit residues: 145.3587 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 : 1.209 ------------------------------------------------------------------------------- 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: ** 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 I 573 ASN ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS J 861 ASN J1049 GLN J1126 GLN J1238 GLN J1326 GLN K 72 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.106433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.082806 restraints weight = 121167.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083778 restraints weight = 66355.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.084159 restraints weight = 43540.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.084406 restraints weight = 41250.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.084443 restraints weight = 37641.386| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1302 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= 0.157 Angle : 0.696 11.992 50311 Z= 0.360 Chirality : 0.044 0.179 5741 Planarity : 0.005 0.069 6190 Dihedral : 16.180 123.046 5979 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.96 % Favored : 93.97 % Rotamer: Outliers : 0.91 % Allowed : 9.02 % Favored : 90.07 % 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: -1.94 (0.12), residues: 4294 helix: -0.65 (0.12), residues: 1506 sheet: -1.33 (0.20), residues: 630 loop : -1.71 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J1330 TYR 0.024 0.002 TYR G 185 PHE 0.016 0.001 PHE I1270 TRP 0.014 0.001 TRP A 73 HIS 0.007 0.001 HIS G 117 Details of bonding type rmsd covalent geometry : bond 0.00344 (36837) covalent geometry : angle 0.69466 (50305) hydrogen bonds : bond 0.04442 ( 1520) hydrogen bonds : angle 5.23241 ( 4160) metal coordination : bond 0.01185 ( 7) metal coordination : angle 4.35761 ( 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 412 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 379 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 MET cc_start: 0.8683 (tpp) cc_final: 0.8459 (tpp) REVERT: A 426 MET cc_start: 0.7883 (tpp) cc_final: 0.7461 (tpp) REVERT: A 443 LEU cc_start: 0.9034 (tp) cc_final: 0.8743 (tt) REVERT: H 117 HIS cc_start: 0.8253 (t-90) cc_final: 0.7944 (t-90) REVERT: H 125 LYS cc_start: 0.7602 (tptt) cc_final: 0.7196 (tptt) REVERT: H 205 MET cc_start: 0.8845 (tpp) cc_final: 0.8034 (ttt) REVERT: I 85 CYS cc_start: 0.8928 (m) cc_final: 0.8598 (m) REVERT: I 315 MET cc_start: 0.8310 (mmm) cc_final: 0.7938 (tpt) REVERT: I 642 SER cc_start: 0.8351 (t) cc_final: 0.8103 (p) REVERT: I 704 MET cc_start: 0.8522 (mmm) cc_final: 0.8309 (tpp) REVERT: I 1229 TYR cc_start: 0.8408 (m-10) cc_final: 0.8118 (m-10) REVERT: I 1236 ASN cc_start: 0.9099 (t0) cc_final: 0.8595 (t0) REVERT: J 29 MET cc_start: 0.9033 (mtt) cc_final: 0.8799 (ptp) REVERT: J 118 LYS cc_start: 0.8661 (mtmt) cc_final: 0.8373 (mtmt) REVERT: J 180 MET cc_start: 0.7911 (tpp) cc_final: 0.7673 (tpp) REVERT: J 320 ASN cc_start: 0.5626 (t0) cc_final: 0.5308 (t0) REVERT: J 644 MET cc_start: 0.6728 (mpp) cc_final: 0.6436 (mtm) REVERT: J 801 VAL cc_start: 0.9317 (p) cc_final: 0.9093 (p) REVERT: J 868 TRP cc_start: 0.7832 (m100) cc_final: 0.7522 (m100) REVERT: J 1124 ILE cc_start: 0.8286 (mt) cc_final: 0.7962 (mm) REVERT: J 1371 ARG cc_start: 0.8039 (ppt170) cc_final: 0.7113 (tpm170) REVERT: K 30 MET cc_start: 0.7474 (mmm) cc_final: 0.7198 (mmt) REVERT: K 31 GLN cc_start: 0.7846 (tm-30) cc_final: 0.7246 (tm-30) outliers start: 33 outliers final: 18 residues processed: 397 average time/residue: 0.1929 time to fit residues: 129.1577 Evaluate side-chains 336 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 318 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 790 VAL 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 21 SER Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 550 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 661 VAL 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 1238 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 302 optimal weight: 8.9990 chunk 366 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 392 optimal weight: 30.0000 chunk 128 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 417 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 HIS ** 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 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1299 ASN J 777 HIS J1019 ASN ** J1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.106257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.081962 restraints weight = 122101.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083778 restraints weight = 66241.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.084057 restraints weight = 40257.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.084256 restraints weight = 38176.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.084547 restraints weight = 36030.179| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36844 Z= 0.160 Angle : 0.661 11.652 50311 Z= 0.339 Chirality : 0.043 0.236 5741 Planarity : 0.005 0.087 6190 Dihedral : 15.958 126.945 5975 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.43 % Favored : 93.50 % Rotamer: Outliers : 1.44 % Allowed : 12.84 % Favored : 85.72 % 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: -1.59 (0.12), residues: 4294 helix: -0.20 (0.13), residues: 1509 sheet: -1.31 (0.20), residues: 634 loop : -1.57 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 182 TYR 0.024 0.001 TYR G 185 PHE 0.014 0.001 PHE I 80 TRP 0.014 0.001 TRP I1276 HIS 0.016 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00354 (36837) covalent geometry : angle 0.65973 (50305) hydrogen bonds : bond 0.04125 ( 1520) hydrogen bonds : angle 4.97192 ( 4160) metal coordination : bond 0.01073 ( 7) metal coordination : angle 3.49372 ( 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 418 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 366 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 MET cc_start: 0.8675 (tpp) cc_final: 0.8290 (tpp) REVERT: A 426 MET cc_start: 0.7914 (tpp) cc_final: 0.7366 (tpp) REVERT: A 443 LEU cc_start: 0.9078 (tp) cc_final: 0.8789 (tt) REVERT: A 918 HIS cc_start: 0.8645 (t70) cc_final: 0.8426 (t70) REVERT: G 152 TYR cc_start: 0.9251 (t80) cc_final: 0.8950 (t80) REVERT: H 8 PHE cc_start: 0.8392 (m-80) cc_final: 0.8183 (m-80) REVERT: H 117 HIS cc_start: 0.8279 (t-90) cc_final: 0.7865 (t-90) REVERT: H 125 LYS cc_start: 0.7775 (tptt) cc_final: 0.7288 (tmtt) REVERT: H 205 MET cc_start: 0.8838 (tpp) cc_final: 0.8070 (ttt) REVERT: I 85 CYS cc_start: 0.8918 (m) cc_final: 0.8577 (m) REVERT: I 644 LEU cc_start: 0.8606 (tp) cc_final: 0.8153 (tp) REVERT: I 685 MET cc_start: 0.7917 (mtm) cc_final: 0.7641 (mtm) REVERT: I 1236 ASN cc_start: 0.9080 (t0) cc_final: 0.8637 (t0) REVERT: J 29 MET cc_start: 0.9052 (mtt) cc_final: 0.8850 (mtt) REVERT: J 118 LYS cc_start: 0.8648 (mtmt) cc_final: 0.8335 (mtmt) REVERT: J 180 MET cc_start: 0.7863 (tpp) cc_final: 0.7492 (tpp) REVERT: J 192 MET cc_start: 0.7414 (tpt) cc_final: 0.7168 (tpt) REVERT: J 320 ASN cc_start: 0.5655 (t0) cc_final: 0.5303 (t0) REVERT: J 698 MET cc_start: 0.9008 (mmm) cc_final: 0.8808 (tpp) REVERT: J 868 TRP cc_start: 0.7778 (m100) cc_final: 0.7415 (m100) REVERT: J 1040 MET cc_start: 0.5901 (ttt) cc_final: 0.5379 (ttp) REVERT: J 1146 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7419 (tm-30) REVERT: J 1327 GLU cc_start: 0.8102 (tt0) cc_final: 0.7897 (tm-30) REVERT: J 1371 ARG cc_start: 0.8018 (ppt170) cc_final: 0.7228 (tpm170) REVERT: K 31 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7241 (tm-30) outliers start: 52 outliers final: 29 residues processed: 401 average time/residue: 0.1917 time to fit residues: 129.2262 Evaluate side-chains 360 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 331 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 225 GLU 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 49 SER 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 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 661 VAL Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 903 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 1347 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 391 optimal weight: 2.9990 chunk 320 optimal weight: 9.9990 chunk 359 optimal weight: 9.9990 chunk 370 optimal weight: 6.9990 chunk 31 optimal weight: 0.1980 chunk 312 optimal weight: 0.5980 chunk 347 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 149 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 375 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 318 GLN ** 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 494 ASN ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1209 GLN J 777 HIS ** J1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.106406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.080612 restraints weight = 119940.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.082711 restraints weight = 57791.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084043 restraints weight = 36902.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.084842 restraints weight = 28276.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.085310 restraints weight = 24339.201| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 36844 Z= 0.184 Angle : 0.659 13.508 50311 Z= 0.336 Chirality : 0.043 0.195 5741 Planarity : 0.004 0.081 6190 Dihedral : 15.862 130.942 5975 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.50 % Favored : 93.46 % Rotamer: Outliers : 1.96 % Allowed : 15.05 % Favored : 82.98 % 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: -1.42 (0.13), residues: 4294 helix: -0.04 (0.13), residues: 1526 sheet: -1.18 (0.21), residues: 613 loop : -1.51 (0.13), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 542 TYR 0.026 0.002 TYR I1229 PHE 0.013 0.001 PHE I 80 TRP 0.010 0.001 TRP J 115 HIS 0.009 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00410 (36837) covalent geometry : angle 0.65787 (50305) hydrogen bonds : bond 0.03970 ( 1520) hydrogen bonds : angle 4.83357 ( 4160) metal coordination : bond 0.01104 ( 7) metal coordination : angle 3.13011 ( 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 415 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 344 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.7853 (ppp) cc_final: 0.7364 (ppp) REVERT: A 413 MET cc_start: 0.8903 (tpp) cc_final: 0.8665 (tpp) REVERT: A 443 LEU cc_start: 0.9251 (tp) cc_final: 0.8960 (tt) REVERT: A 636 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7086 (tm-30) REVERT: A 845 MET cc_start: 0.8470 (ppp) cc_final: 0.7768 (ppp) REVERT: A 918 HIS cc_start: 0.8815 (t70) cc_final: 0.8525 (t70) REVERT: A 967 MET cc_start: 0.8327 (mmm) cc_final: 0.8122 (mmm) REVERT: H 8 PHE cc_start: 0.8672 (m-80) cc_final: 0.8455 (m-80) REVERT: H 48 LEU cc_start: 0.9351 (mm) cc_final: 0.9149 (mm) REVERT: H 117 HIS cc_start: 0.8341 (t-90) cc_final: 0.7910 (t-90) REVERT: H 205 MET cc_start: 0.8909 (tpp) cc_final: 0.8350 (ttt) REVERT: I 85 CYS cc_start: 0.8954 (m) cc_final: 0.8551 (m) REVERT: I 542 ARG cc_start: 0.7585 (tpp-160) cc_final: 0.7177 (tpp-160) REVERT: I 644 LEU cc_start: 0.8725 (tp) cc_final: 0.8301 (tp) REVERT: I 704 MET cc_start: 0.8416 (tpp) cc_final: 0.8175 (tpp) REVERT: I 927 THR cc_start: 0.9104 (m) cc_final: 0.8737 (p) REVERT: I 1229 TYR cc_start: 0.8557 (m-10) cc_final: 0.8287 (m-10) REVERT: I 1236 ASN cc_start: 0.9319 (t0) cc_final: 0.8890 (t0) REVERT: I 1274 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: J 29 MET cc_start: 0.9048 (mtt) cc_final: 0.8825 (mtt) REVERT: J 118 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8332 (mtmt) REVERT: J 180 MET cc_start: 0.7911 (tpp) cc_final: 0.7465 (tpp) REVERT: J 192 MET cc_start: 0.7530 (tpt) cc_final: 0.7319 (tpt) REVERT: J 282 LEU cc_start: 0.9579 (tp) cc_final: 0.9266 (tt) REVERT: J 320 ASN cc_start: 0.5878 (t0) cc_final: 0.5460 (t0) REVERT: J 349 TYR cc_start: 0.8833 (m-10) cc_final: 0.8514 (m-10) REVERT: J 491 LEU cc_start: 0.9209 (mt) cc_final: 0.8929 (mt) REVERT: J 536 LEU cc_start: 0.9109 (tp) cc_final: 0.8903 (tp) REVERT: J 644 MET cc_start: 0.6665 (mtm) cc_final: 0.6406 (mtm) REVERT: J 868 TRP cc_start: 0.7640 (m100) cc_final: 0.7388 (m100) REVERT: J 1146 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7430 (tm-30) REVERT: J 1306 LEU cc_start: 0.9292 (tp) cc_final: 0.8911 (tt) REVERT: J 1327 GLU cc_start: 0.8167 (tt0) cc_final: 0.7502 (tm-30) REVERT: J 1371 ARG cc_start: 0.8045 (ppt170) cc_final: 0.7246 (tpm170) REVERT: K 26 ARG cc_start: 0.8507 (tmt-80) cc_final: 0.7663 (tpm170) REVERT: K 31 GLN cc_start: 0.7735 (tm-30) cc_final: 0.7032 (tm-30) outliers start: 71 outliers final: 43 residues processed: 392 average time/residue: 0.1915 time to fit residues: 126.7339 Evaluate side-chains 370 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 325 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 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 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 I residue 79 VAL Chi-restraints excluded: chain I residue 155 VAL 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 484 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1151 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 392 THR Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 903 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 1347 LEU Chi-restraints excluded: chain J residue 1351 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 351 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 360 optimal weight: 5.9990 chunk 408 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 372 optimal weight: 10.0000 chunk 378 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS J1238 GLN K 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.106374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.080755 restraints weight = 119639.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.082858 restraints weight = 57453.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.084192 restraints weight = 36581.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.084997 restraints weight = 27933.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.085438 restraints weight = 23982.350| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 36844 Z= 0.173 Angle : 0.646 12.667 50311 Z= 0.329 Chirality : 0.043 0.184 5741 Planarity : 0.004 0.079 6190 Dihedral : 15.791 133.945 5975 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.17 % Favored : 93.76 % Rotamer: Outliers : 2.19 % Allowed : 16.41 % Favored : 81.41 % 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: -1.32 (0.13), residues: 4294 helix: 0.08 (0.13), residues: 1524 sheet: -1.12 (0.21), residues: 612 loop : -1.49 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 52 TYR 0.022 0.001 TYR G 152 PHE 0.014 0.001 PHE I 80 TRP 0.010 0.001 TRP A 334 HIS 0.008 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00386 (36837) covalent geometry : angle 0.64512 (50305) hydrogen bonds : bond 0.03842 ( 1520) hydrogen bonds : angle 4.74453 ( 4160) metal coordination : bond 0.00991 ( 7) metal coordination : angle 2.82998 ( 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 433 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 354 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.7928 (ppp) cc_final: 0.7446 (ppp) REVERT: A 413 MET cc_start: 0.8983 (tpp) cc_final: 0.8533 (tpp) REVERT: A 426 MET cc_start: 0.8106 (tpp) cc_final: 0.7633 (tpp) REVERT: A 443 LEU cc_start: 0.9247 (tp) cc_final: 0.8955 (tt) REVERT: A 622 MET cc_start: 0.7219 (mtp) cc_final: 0.6723 (mmm) REVERT: A 636 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7197 (tm-30) REVERT: A 895 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8864 (pp30) REVERT: A 918 HIS cc_start: 0.8851 (t70) cc_final: 0.8504 (t70) REVERT: A 945 LEU cc_start: 0.9501 (tp) cc_final: 0.9144 (tp) REVERT: A 967 MET cc_start: 0.8281 (mmm) cc_final: 0.8076 (mmm) REVERT: G 77 ASP cc_start: 0.8514 (m-30) cc_final: 0.8292 (m-30) REVERT: H 8 PHE cc_start: 0.8688 (m-80) cc_final: 0.8466 (m-80) REVERT: H 48 LEU cc_start: 0.9337 (mm) cc_final: 0.9073 (mm) REVERT: H 117 HIS cc_start: 0.8351 (t-90) cc_final: 0.7884 (t-90) REVERT: H 205 MET cc_start: 0.8913 (tpp) cc_final: 0.8350 (ttt) REVERT: I 85 CYS cc_start: 0.8942 (m) cc_final: 0.8583 (m) REVERT: I 488 MET cc_start: 0.8087 (mmp) cc_final: 0.7320 (mmm) REVERT: I 542 ARG cc_start: 0.7506 (tpp-160) cc_final: 0.7037 (tpp-160) REVERT: I 581 THR cc_start: 0.8901 (m) cc_final: 0.8689 (t) REVERT: I 606 LEU cc_start: 0.9230 (tp) cc_final: 0.8992 (tp) REVERT: I 685 MET cc_start: 0.8134 (mtp) cc_final: 0.7527 (mtm) REVERT: I 704 MET cc_start: 0.8427 (tpp) cc_final: 0.8204 (tpp) REVERT: I 768 MET cc_start: 0.8510 (mtp) cc_final: 0.8115 (mtm) REVERT: I 927 THR cc_start: 0.9081 (m) cc_final: 0.8753 (p) REVERT: I 1229 TYR cc_start: 0.8576 (m-10) cc_final: 0.8358 (m-10) REVERT: I 1236 ASN cc_start: 0.9309 (t0) cc_final: 0.8953 (t0) REVERT: I 1274 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7992 (mt-10) REVERT: J 29 MET cc_start: 0.8982 (mtt) cc_final: 0.8743 (mtt) REVERT: J 118 LYS cc_start: 0.8669 (mtmt) cc_final: 0.8356 (mtmt) REVERT: J 164 GLN cc_start: 0.9270 (tm-30) cc_final: 0.8986 (tm-30) REVERT: J 180 MET cc_start: 0.7917 (tpp) cc_final: 0.7436 (tpp) REVERT: J 282 LEU cc_start: 0.9577 (tp) cc_final: 0.9301 (tt) REVERT: J 320 ASN cc_start: 0.5632 (t0) cc_final: 0.5370 (t0) REVERT: J 644 MET cc_start: 0.6768 (mtm) cc_final: 0.6042 (mtm) REVERT: J 707 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7850 (tp) REVERT: J 740 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8924 (tp) REVERT: J 868 TRP cc_start: 0.7657 (m100) cc_final: 0.7376 (m100) REVERT: J 1146 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7414 (tm-30) REVERT: J 1203 ARG cc_start: 0.8233 (ppt170) cc_final: 0.7962 (tmm-80) REVERT: J 1327 GLU cc_start: 0.8170 (tt0) cc_final: 0.7187 (tm-30) REVERT: J 1330 ARG cc_start: 0.8880 (ptt180) cc_final: 0.7955 (ptt180) REVERT: J 1371 ARG cc_start: 0.8013 (ppt170) cc_final: 0.7251 (tpm170) REVERT: K 26 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7627 (tpm170) REVERT: K 31 GLN cc_start: 0.7698 (tm-30) cc_final: 0.7159 (tm-30) outliers start: 79 outliers final: 54 residues processed: 412 average time/residue: 0.1915 time to fit residues: 133.1015 Evaluate side-chains 385 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 325 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 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 895 GLN Chi-restraints excluded: chain A residue 1052 LEU 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 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 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 484 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 814 ASP 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 1066 MET Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1227 VAL 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 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 661 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 707 ILE 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 903 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 1347 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 26 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 184 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 431 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 350 optimal weight: 0.0070 chunk 87 optimal weight: 7.9990 chunk 420 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 overall best weight: 4.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 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 477 GLN J 680 ASN J1238 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.104407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.078877 restraints weight = 119849.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.080894 restraints weight = 58164.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.082177 restraints weight = 37319.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.082920 restraints weight = 28657.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.083380 restraints weight = 24764.044| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 36844 Z= 0.268 Angle : 0.718 12.701 50311 Z= 0.366 Chirality : 0.045 0.203 5741 Planarity : 0.005 0.076 6190 Dihedral : 15.842 136.203 5975 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.24 % Favored : 92.69 % Rotamer: Outliers : 2.85 % Allowed : 17.46 % Favored : 79.69 % 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: -1.38 (0.13), residues: 4294 helix: 0.05 (0.13), residues: 1507 sheet: -1.25 (0.20), residues: 637 loop : -1.49 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 542 TYR 0.021 0.002 TYR I1229 PHE 0.016 0.002 PHE I 156 TRP 0.020 0.002 TRP I1276 HIS 0.028 0.002 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00590 (36837) covalent geometry : angle 0.71709 (50305) hydrogen bonds : bond 0.04301 ( 1520) hydrogen bonds : angle 4.89252 ( 4160) metal coordination : bond 0.01485 ( 7) metal coordination : angle 3.51663 ( 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 434 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 331 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8706 (mmm) cc_final: 0.8216 (mmt) REVERT: A 130 MET cc_start: 0.8020 (ppp) cc_final: 0.7516 (ppp) REVERT: A 413 MET cc_start: 0.9002 (tpp) cc_final: 0.8600 (tpp) REVERT: A 426 MET cc_start: 0.7880 (tpp) cc_final: 0.7576 (tpp) REVERT: A 443 LEU cc_start: 0.9284 (tp) cc_final: 0.9011 (tt) REVERT: A 527 HIS cc_start: 0.9053 (OUTLIER) cc_final: 0.8640 (p90) REVERT: A 622 MET cc_start: 0.7715 (mtp) cc_final: 0.7249 (mmt) REVERT: A 636 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: A 967 MET cc_start: 0.8301 (mmm) cc_final: 0.8101 (mmm) REVERT: G 8 PHE cc_start: 0.8825 (m-80) cc_final: 0.8424 (m-80) REVERT: H 8 PHE cc_start: 0.8766 (m-80) cc_final: 0.8556 (m-80) REVERT: H 48 LEU cc_start: 0.9301 (mm) cc_final: 0.9074 (mm) REVERT: H 117 HIS cc_start: 0.8394 (t-90) cc_final: 0.8114 (t-90) REVERT: H 205 MET cc_start: 0.8944 (tpp) cc_final: 0.8479 (ttt) REVERT: I 85 CYS cc_start: 0.9034 (m) cc_final: 0.8564 (m) REVERT: I 488 MET cc_start: 0.8098 (mmp) cc_final: 0.7222 (mmm) REVERT: I 492 MET cc_start: 0.8335 (mmm) cc_final: 0.8042 (mmm) REVERT: I 542 ARG cc_start: 0.7472 (tpp-160) cc_final: 0.7012 (tpp-160) REVERT: I 606 LEU cc_start: 0.9232 (tp) cc_final: 0.8960 (tp) REVERT: I 685 MET cc_start: 0.8191 (mtp) cc_final: 0.7639 (mtm) REVERT: I 704 MET cc_start: 0.8560 (tpp) cc_final: 0.8160 (tpp) REVERT: I 768 MET cc_start: 0.8476 (mtp) cc_final: 0.8018 (mtm) REVERT: I 1070 HIS cc_start: 0.9339 (OUTLIER) cc_final: 0.9050 (p-80) REVERT: I 1229 TYR cc_start: 0.8690 (m-10) cc_final: 0.8438 (m-10) REVERT: I 1274 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: J 29 MET cc_start: 0.8952 (mtt) cc_final: 0.8700 (mtt) REVERT: J 118 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8396 (mtmt) REVERT: J 164 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8955 (tm-30) REVERT: J 282 LEU cc_start: 0.9613 (tp) cc_final: 0.9344 (tt) REVERT: J 320 ASN cc_start: 0.5631 (t0) cc_final: 0.5358 (t0) REVERT: J 349 TYR cc_start: 0.8887 (m-10) cc_final: 0.8586 (m-10) REVERT: J 644 MET cc_start: 0.6909 (mtm) cc_final: 0.6006 (mtm) REVERT: J 740 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8934 (tp) REVERT: J 746 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8465 (mt) REVERT: J 868 TRP cc_start: 0.7462 (m100) cc_final: 0.7102 (m100) REVERT: J 1040 MET cc_start: 0.5696 (ttt) cc_final: 0.5410 (ttp) REVERT: J 1146 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7487 (tm-30) REVERT: J 1203 ARG cc_start: 0.8217 (ppt170) cc_final: 0.7700 (ptp-110) REVERT: J 1327 GLU cc_start: 0.8309 (tt0) cc_final: 0.7541 (tt0) REVERT: J 1330 ARG cc_start: 0.8913 (ptt180) cc_final: 0.8369 (ptt180) REVERT: J 1371 ARG cc_start: 0.8009 (ppt170) cc_final: 0.7232 (tpm170) REVERT: K 31 GLN cc_start: 0.7833 (tm-30) cc_final: 0.7270 (tm-30) REVERT: K 73 GLN cc_start: 0.7191 (tt0) cc_final: 0.6683 (pt0) outliers start: 103 outliers final: 72 residues processed: 407 average time/residue: 0.1895 time to fit residues: 131.4728 Evaluate side-chains 393 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 315 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 346 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 515 ASN 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 773 LEU 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 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 27 THR 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 91 THR Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 224 PHE 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 429 MET Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 814 ASP 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 1060 ILE Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1070 HIS Chi-restraints excluded: chain I residue 1151 LEU 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 253 VAL Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 307 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 701 LEU 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 825 VAL Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 903 LEU 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 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 Chi-restraints excluded: chain K residue 26 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 149 optimal weight: 2.9990 chunk 342 optimal weight: 0.0020 chunk 113 optimal weight: 0.9980 chunk 118 optimal weight: 0.0000 chunk 295 optimal weight: 0.9990 chunk 296 optimal weight: 20.0000 chunk 197 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 329 optimal weight: 0.8980 chunk 181 optimal weight: 20.0000 chunk 241 optimal weight: 7.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 519 ASN ** I1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 477 GLN J 777 HIS J 962 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.107922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.082519 restraints weight = 119042.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.084692 restraints weight = 56533.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.086057 restraints weight = 35650.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.086856 restraints weight = 27118.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.087374 restraints weight = 23275.132| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36844 Z= 0.117 Angle : 0.631 14.560 50311 Z= 0.317 Chirality : 0.042 0.175 5741 Planarity : 0.004 0.072 6190 Dihedral : 15.633 139.537 5975 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.43 % Rotamer: Outliers : 1.99 % Allowed : 18.68 % Favored : 79.33 % 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: -1.08 (0.13), residues: 4294 helix: 0.34 (0.13), residues: 1530 sheet: -0.96 (0.21), residues: 614 loop : -1.41 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 52 TYR 0.016 0.001 TYR G 152 PHE 0.014 0.001 PHE I 80 TRP 0.018 0.001 TRP I1276 HIS 0.006 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00260 (36837) covalent geometry : angle 0.63063 (50305) hydrogen bonds : bond 0.03511 ( 1520) hydrogen bonds : angle 4.60142 ( 4160) metal coordination : bond 0.00439 ( 7) metal coordination : angle 1.86427 ( 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 465 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 393 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8730 (mmm) cc_final: 0.8207 (mmt) REVERT: A 174 MET cc_start: 0.8471 (mmm) cc_final: 0.8063 (mmm) REVERT: A 413 MET cc_start: 0.9060 (tpp) cc_final: 0.8845 (tpp) REVERT: A 443 LEU cc_start: 0.9229 (tp) cc_final: 0.8950 (tt) REVERT: A 729 ASP cc_start: 0.8950 (t70) cc_final: 0.8645 (t70) REVERT: A 945 LEU cc_start: 0.9446 (tp) cc_final: 0.9087 (tp) REVERT: G 8 PHE cc_start: 0.8588 (m-80) cc_final: 0.7759 (m-80) REVERT: G 71 LYS cc_start: 0.8801 (tppt) cc_final: 0.8501 (tppt) REVERT: G 185 TYR cc_start: 0.8969 (p90) cc_final: 0.8611 (p90) REVERT: H 48 LEU cc_start: 0.9244 (mm) cc_final: 0.8960 (mm) REVERT: H 117 HIS cc_start: 0.8425 (t-90) cc_final: 0.8179 (t-90) REVERT: H 205 MET cc_start: 0.8876 (tpp) cc_final: 0.8292 (ttt) REVERT: I 36 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8334 (mm110) REVERT: I 85 CYS cc_start: 0.8964 (m) cc_final: 0.8571 (m) REVERT: I 315 MET cc_start: 0.8220 (tpt) cc_final: 0.7893 (mmm) REVERT: I 349 GLU cc_start: 0.8707 (mp0) cc_final: 0.8457 (mp0) REVERT: I 488 MET cc_start: 0.7964 (mmp) cc_final: 0.7145 (mmm) REVERT: I 492 MET cc_start: 0.8334 (mmm) cc_final: 0.8028 (mmm) REVERT: I 542 ARG cc_start: 0.7428 (tpp-160) cc_final: 0.6978 (tpp-160) REVERT: I 581 THR cc_start: 0.8825 (m) cc_final: 0.8554 (t) REVERT: I 685 MET cc_start: 0.8060 (mtp) cc_final: 0.7538 (mtm) REVERT: I 704 MET cc_start: 0.8417 (tpp) cc_final: 0.8191 (tpp) REVERT: I 800 MET cc_start: 0.8292 (mtp) cc_final: 0.8069 (mtp) REVERT: I 1064 ASP cc_start: 0.8295 (m-30) cc_final: 0.8069 (m-30) REVERT: I 1236 ASN cc_start: 0.9199 (t0) cc_final: 0.8776 (t0) REVERT: I 1274 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: I 1279 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8384 (mt-10) REVERT: J 29 MET cc_start: 0.8968 (mtt) cc_final: 0.8763 (mtt) REVERT: J 118 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8373 (mtmt) REVERT: J 164 GLN cc_start: 0.9216 (tm-30) cc_final: 0.8880 (tm-30) REVERT: J 180 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7664 (tpp) REVERT: J 320 ASN cc_start: 0.5661 (t0) cc_final: 0.5385 (t0) REVERT: J 644 MET cc_start: 0.6866 (mtm) cc_final: 0.6073 (mtm) REVERT: J 740 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8890 (tp) REVERT: J 868 TRP cc_start: 0.7497 (m100) cc_final: 0.7119 (m100) REVERT: J 1040 MET cc_start: 0.5374 (ttt) cc_final: 0.4703 (ttp) REVERT: J 1146 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7444 (tm-30) REVERT: J 1203 ARG cc_start: 0.8190 (ppt170) cc_final: 0.7564 (ttm-80) REVERT: J 1371 ARG cc_start: 0.8002 (ppt170) cc_final: 0.7205 (tpm170) REVERT: K 26 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7767 (tpm170) REVERT: K 30 MET cc_start: 0.7658 (mmt) cc_final: 0.7128 (mmt) REVERT: K 31 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7209 (tm-30) REVERT: K 73 GLN cc_start: 0.7187 (tt0) cc_final: 0.6711 (pt0) outliers start: 72 outliers final: 50 residues processed: 440 average time/residue: 0.1935 time to fit residues: 143.9409 Evaluate side-chains 393 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 339 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 626 VAL Chi-restraints excluded: chain A residue 773 LEU 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 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain H residue 21 SER 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 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 472 GLU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1066 MET 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 180 MET Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 453 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 825 VAL Chi-restraints excluded: chain J residue 1068 THR Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1347 LEU Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 49 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 189 optimal weight: 5.9990 chunk 313 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 243 optimal weight: 0.0670 chunk 161 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 305 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 238 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN ** 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 = 0.3833 r_free = 0.3833 target = 0.107626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.082157 restraints weight = 118812.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.084283 restraints weight = 57046.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.085584 restraints weight = 36233.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.086439 restraints weight = 27763.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.086879 restraints weight = 23783.051| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2543 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= 0.128 Angle : 0.644 17.223 50311 Z= 0.322 Chirality : 0.042 0.175 5741 Planarity : 0.004 0.070 6190 Dihedral : 15.556 139.882 5975 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.01 % Favored : 93.95 % Rotamer: Outliers : 2.02 % Allowed : 19.48 % Favored : 78.50 % 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: -1.02 (0.13), residues: 4294 helix: 0.46 (0.13), residues: 1524 sheet: -1.04 (0.21), residues: 613 loop : -1.38 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 52 TYR 0.016 0.001 TYR I1229 PHE 0.015 0.001 PHE I 80 TRP 0.037 0.001 TRP I1276 HIS 0.003 0.001 HIS J 865 Details of bonding type rmsd covalent geometry : bond 0.00290 (36837) covalent geometry : angle 0.64325 (50305) hydrogen bonds : bond 0.03459 ( 1520) hydrogen bonds : angle 4.54952 ( 4160) metal coordination : bond 0.00548 ( 7) metal coordination : angle 1.79906 ( 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 420 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 347 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8718 (mmm) cc_final: 0.8201 (mmt) REVERT: A 174 MET cc_start: 0.8487 (mmm) cc_final: 0.8157 (mmm) REVERT: A 413 MET cc_start: 0.9094 (tpp) cc_final: 0.8863 (tpp) REVERT: A 443 LEU cc_start: 0.9353 (tp) cc_final: 0.9039 (tt) REVERT: A 759 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9069 (mm) REVERT: A 773 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8839 (mm) REVERT: A 945 LEU cc_start: 0.9464 (tp) cc_final: 0.9096 (tp) REVERT: A 967 MET cc_start: 0.8295 (mmm) cc_final: 0.7758 (tmm) REVERT: G 51 MET cc_start: 0.8786 (mmm) cc_final: 0.8415 (mpp) REVERT: G 71 LYS cc_start: 0.8816 (tppt) cc_final: 0.8508 (tppt) REVERT: H 29 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7780 (tm-30) REVERT: H 48 LEU cc_start: 0.9260 (mm) cc_final: 0.8945 (mm) REVERT: H 117 HIS cc_start: 0.8409 (t-90) cc_final: 0.8158 (t-90) REVERT: H 205 MET cc_start: 0.8799 (tpp) cc_final: 0.8185 (ttt) REVERT: I 36 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8368 (mm110) REVERT: I 85 CYS cc_start: 0.9000 (m) cc_final: 0.8592 (m) REVERT: I 349 GLU cc_start: 0.8719 (mp0) cc_final: 0.8493 (mp0) REVERT: I 488 MET cc_start: 0.8020 (mmp) cc_final: 0.7238 (mmm) REVERT: I 492 MET cc_start: 0.8415 (mmm) cc_final: 0.8106 (mmm) REVERT: I 542 ARG cc_start: 0.7474 (tpp-160) cc_final: 0.6971 (tpp-160) REVERT: I 685 MET cc_start: 0.8031 (mtp) cc_final: 0.7552 (mtm) REVERT: I 704 MET cc_start: 0.8418 (tpp) cc_final: 0.8209 (tpp) REVERT: I 768 MET cc_start: 0.8163 (mtm) cc_final: 0.7766 (mtp) REVERT: I 1064 ASP cc_start: 0.8218 (m-30) cc_final: 0.7987 (m-30) REVERT: I 1236 ASN cc_start: 0.9184 (t0) cc_final: 0.8729 (t0) REVERT: I 1274 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7807 (mt-10) REVERT: I 1279 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8475 (mt-10) REVERT: J 29 MET cc_start: 0.8932 (mtt) cc_final: 0.8666 (mtt) REVERT: J 102 MET cc_start: 0.6368 (mmp) cc_final: 0.6094 (mmp) REVERT: J 118 LYS cc_start: 0.8662 (mtmt) cc_final: 0.8389 (mtmt) REVERT: J 164 GLN cc_start: 0.9182 (tm-30) cc_final: 0.8833 (tm-30) REVERT: J 180 MET cc_start: 0.8267 (tpp) cc_final: 0.7720 (tpp) REVERT: J 320 ASN cc_start: 0.5665 (t0) cc_final: 0.5370 (t0) REVERT: J 330 MET cc_start: 0.8607 (ptp) cc_final: 0.8291 (pmm) REVERT: J 644 MET cc_start: 0.6847 (mtm) cc_final: 0.6069 (mtm) REVERT: J 740 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8929 (tp) REVERT: J 868 TRP cc_start: 0.7528 (m100) cc_final: 0.7144 (m100) REVERT: J 1040 MET cc_start: 0.5298 (ttt) cc_final: 0.4843 (ttp) REVERT: J 1146 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7411 (tm-30) REVERT: J 1151 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8441 (pttt) REVERT: J 1203 ARG cc_start: 0.8034 (ppt170) cc_final: 0.7532 (ttm-80) REVERT: J 1371 ARG cc_start: 0.8010 (ppt170) cc_final: 0.7204 (tpm170) REVERT: K 26 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7779 (tpm170) REVERT: K 30 MET cc_start: 0.7447 (mmt) cc_final: 0.6901 (mmt) REVERT: K 31 GLN cc_start: 0.7729 (tm-30) cc_final: 0.7201 (tm-30) REVERT: K 73 GLN cc_start: 0.7220 (tt0) cc_final: 0.6724 (pt0) outliers start: 73 outliers final: 54 residues processed: 397 average time/residue: 0.1921 time to fit residues: 128.9678 Evaluate side-chains 394 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 335 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 759 ILE Chi-restraints excluded: chain A residue 773 LEU 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 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 59 VAL 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 394 ARG Chi-restraints excluded: chain I residue 400 VAL 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 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 828 PHE Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1096 ILE 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 253 VAL Chi-restraints excluded: chain J residue 265 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 661 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 740 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 1248 ILE Chi-restraints excluded: chain J residue 1347 LEU Chi-restraints excluded: chain K residue 26 ARG 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: 7.9990 chunk 305 optimal weight: 7.9990 chunk 335 optimal weight: 0.0370 chunk 20 optimal weight: 0.1980 chunk 307 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 408 optimal weight: 0.6980 chunk 435 optimal weight: 7.9990 chunk 358 optimal weight: 1.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 41 ASN H 186 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.107637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.082183 restraints weight = 119472.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.084301 restraints weight = 57416.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.085641 restraints weight = 36453.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.086440 restraints weight = 27824.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.086934 restraints weight = 23916.326| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36844 Z= 0.133 Angle : 0.657 16.998 50311 Z= 0.324 Chirality : 0.043 0.191 5741 Planarity : 0.004 0.069 6190 Dihedral : 15.488 140.042 5975 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.88 % Rotamer: Outliers : 2.08 % Allowed : 19.59 % Favored : 78.33 % 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: -0.99 (0.13), residues: 4294 helix: 0.46 (0.13), residues: 1532 sheet: -1.06 (0.21), residues: 620 loop : -1.35 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 52 TYR 0.016 0.001 TYR H 185 PHE 0.015 0.001 PHE I 80 TRP 0.039 0.001 TRP I1276 HIS 0.004 0.001 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00302 (36837) covalent geometry : angle 0.65694 (50305) hydrogen bonds : bond 0.03417 ( 1520) hydrogen bonds : angle 4.54377 ( 4160) metal coordination : bond 0.00574 ( 7) metal coordination : angle 1.74736 ( 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 421 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 346 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8712 (mmm) cc_final: 0.8233 (mmt) REVERT: A 174 MET cc_start: 0.8563 (mmm) cc_final: 0.8272 (mmm) REVERT: A 759 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.9089 (mm) REVERT: A 773 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8890 (mm) REVERT: A 967 MET cc_start: 0.8252 (mmm) cc_final: 0.8021 (tmm) REVERT: G 8 PHE cc_start: 0.8583 (m-80) cc_final: 0.7723 (m-80) REVERT: G 51 MET cc_start: 0.8808 (mmm) cc_final: 0.8496 (mpp) REVERT: G 71 LYS cc_start: 0.8832 (tppt) cc_final: 0.8553 (tppt) REVERT: H 29 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7822 (tm-30) REVERT: H 48 LEU cc_start: 0.9264 (mm) cc_final: 0.8944 (mm) REVERT: H 205 MET cc_start: 0.8801 (tpp) cc_final: 0.8213 (ttt) REVERT: I 36 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8396 (mm110) REVERT: I 85 CYS cc_start: 0.9008 (m) cc_final: 0.8587 (m) REVERT: I 315 MET cc_start: 0.8052 (mmm) cc_final: 0.7799 (tpt) REVERT: I 349 GLU cc_start: 0.8744 (mp0) cc_final: 0.8517 (mp0) REVERT: I 488 MET cc_start: 0.8032 (mmp) cc_final: 0.7466 (mmm) REVERT: I 492 MET cc_start: 0.8421 (mmm) cc_final: 0.8208 (mmm) REVERT: I 542 ARG cc_start: 0.7475 (tpp-160) cc_final: 0.6970 (tpp-160) REVERT: I 606 LEU cc_start: 0.9214 (tp) cc_final: 0.8914 (tp) REVERT: I 685 MET cc_start: 0.8020 (mtp) cc_final: 0.7552 (mtm) REVERT: I 704 MET cc_start: 0.8404 (tpp) cc_final: 0.8201 (tpp) REVERT: I 978 VAL cc_start: 0.5508 (OUTLIER) cc_final: 0.5279 (t) REVERT: I 1064 ASP cc_start: 0.8263 (m-30) cc_final: 0.8029 (m-30) REVERT: I 1229 TYR cc_start: 0.8268 (m-10) cc_final: 0.7843 (m-10) REVERT: I 1236 ASN cc_start: 0.9209 (t0) cc_final: 0.8766 (t0) REVERT: I 1242 LYS cc_start: 0.8912 (mmtp) cc_final: 0.8500 (mmtm) REVERT: I 1274 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7811 (mt-10) REVERT: I 1279 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8467 (mt-10) REVERT: J 29 MET cc_start: 0.8920 (mtt) cc_final: 0.8654 (mtt) REVERT: J 102 MET cc_start: 0.6635 (OUTLIER) cc_final: 0.6182 (mmp) REVERT: J 118 LYS cc_start: 0.8665 (mtmt) cc_final: 0.8394 (mtmt) REVERT: J 164 GLN cc_start: 0.9220 (tm-30) cc_final: 0.8864 (tm-30) REVERT: J 180 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7601 (tpp) REVERT: J 320 ASN cc_start: 0.5684 (t0) cc_final: 0.5415 (t0) REVERT: J 330 MET cc_start: 0.8622 (ptp) cc_final: 0.8333 (pmm) REVERT: J 644 MET cc_start: 0.6845 (mtm) cc_final: 0.6366 (mtm) REVERT: J 740 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8930 (tp) REVERT: J 746 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8369 (mt) REVERT: J 802 ASP cc_start: 0.8313 (m-30) cc_final: 0.7819 (m-30) REVERT: J 821 MET cc_start: 0.8122 (tpt) cc_final: 0.7817 (tpt) REVERT: J 868 TRP cc_start: 0.7558 (m100) cc_final: 0.7173 (m100) REVERT: J 1040 MET cc_start: 0.5246 (ttt) cc_final: 0.4819 (ttp) REVERT: J 1146 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7380 (tm-30) REVERT: J 1151 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8465 (pttt) REVERT: J 1203 ARG cc_start: 0.8110 (ppt170) cc_final: 0.7635 (ttm-80) REVERT: J 1371 ARG cc_start: 0.8010 (ppt170) cc_final: 0.7266 (tpm170) REVERT: K 26 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7769 (tpm170) REVERT: K 30 MET cc_start: 0.7408 (mmt) cc_final: 0.6821 (mmt) REVERT: K 31 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7187 (tm-30) REVERT: K 73 GLN cc_start: 0.7312 (tt0) cc_final: 0.6860 (pt0) outliers start: 75 outliers final: 62 residues processed: 398 average time/residue: 0.1966 time to fit residues: 131.4912 Evaluate side-chains 403 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 332 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 759 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 1052 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 G residue 202 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 196 THR Chi-restraints excluded: chain H residue 207 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 394 ARG Chi-restraints excluded: chain I residue 400 VAL 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 521 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 624 ASP Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 814 ASP 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 997 TRP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1096 ILE 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 180 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 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 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 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 1347 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 26 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 60 optimal weight: 0.8980 chunk 279 optimal weight: 0.0020 chunk 188 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 423 optimal weight: 7.9990 chunk 287 optimal weight: 2.9990 chunk 392 optimal weight: 20.0000 chunk 191 optimal weight: 3.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A 948 HIS ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.108413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082996 restraints weight = 119283.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.085132 restraints weight = 57180.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.086482 restraints weight = 36219.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.087328 restraints weight = 27583.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.087722 restraints weight = 23602.687| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 36844 Z= 0.121 Angle : 0.659 16.935 50311 Z= 0.324 Chirality : 0.043 0.251 5741 Planarity : 0.004 0.069 6190 Dihedral : 15.410 140.391 5975 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.66 % Favored : 94.29 % Rotamer: Outliers : 1.96 % Allowed : 20.01 % Favored : 78.03 % 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: -0.94 (0.13), residues: 4294 helix: 0.47 (0.13), residues: 1539 sheet: -0.92 (0.21), residues: 606 loop : -1.33 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 52 TYR 0.016 0.001 TYR J 772 PHE 0.015 0.001 PHE I 80 TRP 0.026 0.001 TRP I1276 HIS 0.008 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00273 (36837) covalent geometry : angle 0.65865 (50305) hydrogen bonds : bond 0.03344 ( 1520) hydrogen bonds : angle 4.48867 ( 4160) metal coordination : bond 0.00439 ( 7) metal coordination : angle 1.54542 ( 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 426 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 355 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8679 (mmm) cc_final: 0.8257 (mmt) REVERT: A 130 MET cc_start: 0.7750 (ppp) cc_final: 0.7149 (ppp) REVERT: A 174 MET cc_start: 0.8604 (mmm) cc_final: 0.8317 (mmm) REVERT: A 360 ASP cc_start: 0.7848 (t0) cc_final: 0.7616 (t0) REVERT: A 443 LEU cc_start: 0.9328 (tp) cc_final: 0.9007 (tt) REVERT: A 759 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9086 (mm) REVERT: A 773 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8881 (mm) REVERT: G 8 PHE cc_start: 0.8539 (m-80) cc_final: 0.7626 (m-80) REVERT: G 51 MET cc_start: 0.8790 (mmm) cc_final: 0.8488 (mpp) REVERT: G 71 LYS cc_start: 0.8772 (tppt) cc_final: 0.8456 (tppt) REVERT: H 29 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7806 (tm-30) REVERT: H 48 LEU cc_start: 0.9245 (mm) cc_final: 0.8928 (mm) REVERT: H 205 MET cc_start: 0.8787 (tpp) cc_final: 0.8146 (ttt) REVERT: H 207 THR cc_start: 0.9257 (OUTLIER) cc_final: 0.8908 (t) REVERT: I 36 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8435 (mm110) REVERT: I 85 CYS cc_start: 0.8988 (m) cc_final: 0.8580 (m) REVERT: I 315 MET cc_start: 0.8131 (mmm) cc_final: 0.7877 (tpt) REVERT: I 349 GLU cc_start: 0.8740 (mp0) cc_final: 0.8510 (mp0) REVERT: I 488 MET cc_start: 0.8035 (mmp) cc_final: 0.7265 (mmm) REVERT: I 492 MET cc_start: 0.8317 (mmm) cc_final: 0.7945 (mmm) REVERT: I 503 LYS cc_start: 0.8822 (tttt) cc_final: 0.8442 (tptm) REVERT: I 542 ARG cc_start: 0.7430 (tpp-160) cc_final: 0.6604 (tpp-160) REVERT: I 573 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8704 (m-40) REVERT: I 685 MET cc_start: 0.7961 (mtp) cc_final: 0.7478 (mtm) REVERT: I 704 MET cc_start: 0.8376 (tpp) cc_final: 0.8167 (tpp) REVERT: I 800 MET cc_start: 0.8121 (mtp) cc_final: 0.7861 (mtp) REVERT: I 978 VAL cc_start: 0.5497 (OUTLIER) cc_final: 0.5262 (t) REVERT: I 1064 ASP cc_start: 0.8191 (m-30) cc_final: 0.7959 (m-30) REVERT: I 1229 TYR cc_start: 0.8184 (m-10) cc_final: 0.7771 (m-10) REVERT: I 1236 ASN cc_start: 0.9145 (t0) cc_final: 0.8671 (t0) REVERT: I 1242 LYS cc_start: 0.8810 (mmtp) cc_final: 0.8463 (mmtm) REVERT: I 1274 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: I 1279 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8491 (mt-10) REVERT: J 29 MET cc_start: 0.8972 (mtt) cc_final: 0.8753 (mtt) REVERT: J 102 MET cc_start: 0.6653 (mmp) cc_final: 0.6347 (mmp) REVERT: J 118 LYS cc_start: 0.8659 (mtmt) cc_final: 0.8407 (mtmt) REVERT: J 164 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8844 (tm-30) REVERT: J 180 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7600 (tpp) REVERT: J 238 ILE cc_start: 0.8437 (tp) cc_final: 0.8213 (tp) REVERT: J 320 ASN cc_start: 0.5670 (t0) cc_final: 0.5400 (t0) REVERT: J 330 MET cc_start: 0.8578 (ptp) cc_final: 0.8279 (pmm) REVERT: J 644 MET cc_start: 0.6792 (mtm) cc_final: 0.6317 (mtm) REVERT: J 740 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8958 (tp) REVERT: J 746 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8361 (mt) REVERT: J 802 ASP cc_start: 0.8277 (m-30) cc_final: 0.7941 (m-30) REVERT: J 821 MET cc_start: 0.8198 (tpt) cc_final: 0.7902 (tpt) REVERT: J 868 TRP cc_start: 0.7466 (m100) cc_final: 0.7097 (m100) REVERT: J 1040 MET cc_start: 0.5284 (ttt) cc_final: 0.4895 (ttp) REVERT: J 1146 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7327 (tm-30) REVERT: J 1151 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8433 (pttt) REVERT: J 1203 ARG cc_start: 0.8176 (ppt170) cc_final: 0.7732 (ttm-80) REVERT: J 1371 ARG cc_start: 0.7977 (ppt170) cc_final: 0.7182 (tpm170) REVERT: K 26 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7762 (tpm170) REVERT: K 31 GLN cc_start: 0.7656 (tm-30) cc_final: 0.7136 (tm-30) REVERT: K 71 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7521 (tm-30) outliers start: 71 outliers final: 55 residues processed: 407 average time/residue: 0.1886 time to fit residues: 130.3769 Evaluate side-chains 404 residues out of total 3671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 339 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 626 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 207 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 394 ARG Chi-restraints excluded: chain I residue 400 VAL 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 521 LEU Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 814 ASP 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 997 TRP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1096 ILE 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 180 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 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 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 777 HIS 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 1248 ILE Chi-restraints excluded: chain J residue 1347 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 26 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 213 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 239 optimal weight: 0.9990 chunk 435 optimal weight: 6.9990 chunk 405 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 222 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 799 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.107401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.081762 restraints weight = 119340.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.083853 restraints weight = 57724.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.085171 restraints weight = 36916.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.085999 restraints weight = 28309.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.086449 restraints weight = 24290.962| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36844 Z= 0.155 Angle : 0.672 16.312 50311 Z= 0.332 Chirality : 0.043 0.245 5741 Planarity : 0.004 0.068 6190 Dihedral : 15.386 140.280 5974 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.22 % Favored : 93.74 % Rotamer: Outliers : 1.94 % Allowed : 20.14 % Favored : 77.92 % 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: -0.95 (0.13), residues: 4294 helix: 0.48 (0.13), residues: 1535 sheet: -0.98 (0.21), residues: 611 loop : -1.33 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 52 TYR 0.015 0.001 TYR H 185 PHE 0.014 0.001 PHE I 80 TRP 0.032 0.001 TRP I1276 HIS 0.007 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00349 (36837) covalent geometry : angle 0.67164 (50305) hydrogen bonds : bond 0.03488 ( 1520) hydrogen bonds : angle 4.49672 ( 4160) metal coordination : bond 0.00694 ( 7) metal coordination : angle 1.82963 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6182.87 seconds wall clock time: 107 minutes 23.58 seconds (6443.58 seconds total)