Starting phenix.real_space_refine on Fri Mar 6 15:34:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mkj_23897/03_2026/7mkj_23897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mkj_23897/03_2026/7mkj_23897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mkj_23897/03_2026/7mkj_23897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mkj_23897/03_2026/7mkj_23897.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mkj_23897/03_2026/7mkj_23897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mkj_23897/03_2026/7mkj_23897.map" } resolution = 2.9 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= 0.003 sd= 0.127 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 118 5.49 5 Mg 1 5.21 5 S 130 5.16 5 C 19726 2.51 5 N 5655 2.21 5 O 6375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 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: 32007 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1808 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1710 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Chain: "J" Number of atoms: 10386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10386 Classifications: {'peptide': 1336} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 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: "L" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3835 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 455} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1278 Classifications: {'DNA': 62} Link IDs: {'rna3p': 61} Chain: "Q" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1140 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain breaks: 1 Chain: "R" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14534 SG CYS J 70 49.377 125.817 73.852 1.00 66.30 S ATOM 14548 SG CYS J 72 52.392 127.808 72.074 1.00 69.18 S ATOM 14656 SG CYS J 85 48.312 126.204 73.071 1.00 77.60 S ATOM 20368 SG CYS J 814 21.527 74.188 106.018 1.00 55.32 S ATOM 20933 SG CYS J 888 25.051 74.948 105.131 1.00 49.66 S ATOM 21005 SG CYS J 898 24.199 73.207 108.089 1.00 41.44 S Time building chain proxies: 6.76, per 1000 atoms: 0.21 Number of scatterers: 32007 At special positions: 0 Unit cell: (151.58, 193.98, 192.92, 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 130 16.00 P 118 15.00 Mg 1 11.99 O 6375 8.00 N 5655 7.00 C 19726 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: 2.53 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 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6970 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 49 sheets defined 41.7% alpha, 13.9% beta 48 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.788A 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 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.718A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.543A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.997A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE I 35 " --> pdb=" O GLN I 31 " (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 213 removed outlier: 3.893A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 293 removed outlier: 3.876A pdb=" N ILE I 292 " --> pdb=" O VAL I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.611A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 removed outlier: 3.727A pdb=" N GLU I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.100A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE I 390 " --> pdb=" O GLU I 386 " (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 480 removed outlier: 3.852A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 removed outlier: 3.535A pdb=" N GLU I 523 " --> pdb=" O ASN I 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.756A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 614 removed outlier: 4.137A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 609 through 614' Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.632A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 860 through 864 removed outlier: 3.593A pdb=" N SER I 863 " --> pdb=" O ALA I 860 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS I 864 " --> pdb=" O ALA I 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 860 through 864' Processing helix chain 'I' and resid 896 through 907 Processing helix chain 'I' and resid 942 through 981 removed outlier: 4.088A pdb=" N ILE I 966 " --> pdb=" O GLU I 962 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 999 removed outlier: 3.923A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU I 999 " --> pdb=" O ARG I 996 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 4.249A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1099 through 1103 removed outlier: 3.676A 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: 3.746A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.589A pdb=" N PHE I1164 " --> pdb=" O LEU I1161 " (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 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.845A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.716A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.754A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.728A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 removed outlier: 3.641A pdb=" N ARG J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) 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 208 removed outlier: 3.809A pdb=" N ASN J 206 " --> pdb=" O ARG J 202 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR J 208 " --> pdb=" O GLU J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 removed outlier: 3.994A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.509A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.757A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 386 removed outlier: 3.524A pdb=" N LYS J 384 " --> pdb=" O PHE J 380 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU J 386 " --> pdb=" O TYR J 382 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 401 removed outlier: 3.600A pdb=" N VAL J 401 " --> pdb=" O ALA J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 416 removed outlier: 3.729A pdb=" N GLU J 414 " --> pdb=" O ASP J 410 " (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 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 475 through 483 removed outlier: 3.596A pdb=" N ARG J 481 " --> pdb=" O GLN J 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 506 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.823A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 598 through 610 removed outlier: 3.683A pdb=" N CYS J 608 " --> pdb=" O MET J 604 " (cutoff:3.500A) Processing helix chain 'J' and resid 613 through 634 removed outlier: 3.773A pdb=" N THR J 617 " --> pdb=" O GLY J 613 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP J 622 " --> pdb=" O VAL J 618 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET J 625 " --> pdb=" O ALA J 621 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 658 Processing helix chain 'J' and resid 663 through 670 Processing helix chain 'J' and resid 674 through 702 removed outlier: 4.074A pdb=" N ASN J 680 " --> pdb=" O GLY J 676 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP J 684 " --> pdb=" O ASN J 680 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE J 685 " --> pdb=" O LYS J 681 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA J 688 " --> pdb=" O ASP J 684 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP J 691 " --> pdb=" O ALA J 687 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG J 692 " --> pdb=" O ALA J 688 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS J 695 " --> pdb=" O ASP J 691 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET J 698 " --> pdb=" O SER J 694 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 removed outlier: 3.696A pdb=" N MET J 725 " --> pdb=" O SER J 721 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 775 removed outlier: 3.636A pdb=" N ILE J 774 " --> pdb=" O LEU J 770 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER J 775 " --> pdb=" O GLN J 771 " (cutoff:3.500A) Processing helix chain 'J' and resid 776 through 786 removed outlier: 3.636A pdb=" N GLY J 782 " --> pdb=" O GLY J 778 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR J 786 " --> pdb=" O GLY J 782 " (cutoff:3.500A) Processing helix chain 'J' and resid 788 through 805 removed outlier: 3.609A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG J 798 " --> pdb=" O GLY J 794 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA J 804 " --> pdb=" O LEU J 800 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.607A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 867 through 875 removed outlier: 3.705A pdb=" N LEU J 871 " --> pdb=" O GLN J 867 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU J 872 " --> pdb=" O TRP J 868 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU J 873 " --> pdb=" O CYS J 869 " (cutoff:3.500A) Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.795A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA J 920 " --> pdb=" O GLY J 916 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE J 923 " --> pdb=" O ALA J 919 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1068 through 1073 removed outlier: 4.098A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1146 removed outlier: 3.656A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1225 removed outlier: 3.694A pdb=" N ILE J1220 " --> pdb=" O ALA J1216 " (cutoff:3.500A) Processing helix chain 'J' and resid 1225 through 1237 removed outlier: 3.748A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) Processing helix chain 'J' and resid 1237 through 1243 removed outlier: 3.644A pdb=" N TYR J1241 " --> pdb=" O VAL J1237 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1259 removed outlier: 3.856A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.861A pdb=" N ASN J1289 " --> pdb=" O VAL J1285 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG J1290 " --> pdb=" O LYS J1286 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU J1291 " --> pdb=" O ILE J1287 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU J1292 " --> pdb=" O ALA J1288 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU J1293 " --> pdb=" O ASN J1289 " (cutoff:3.500A) Processing helix chain 'J' and resid 1319 through 1324 Processing helix chain 'J' and resid 1327 through 1338 removed outlier: 3.571A pdb=" N GLU J1334 " --> pdb=" O ARG J1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 4.140A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1362 through 1373 Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.539A 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 78 Processing helix chain 'L' and resid 96 through 106 Processing helix chain 'L' and resid 112 through 135 removed outlier: 3.954A pdb=" N ILE L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 153 removed outlier: 3.696A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 235 Processing helix chain 'L' and resid 243 through 257 removed outlier: 4.185A pdb=" N GLU L 247 " --> pdb=" O ALA L 243 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU L 250 " --> pdb=" O GLN L 246 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU L 254 " --> pdb=" O LEU L 250 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL L 255 " --> pdb=" O LYS L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 292 removed outlier: 3.647A pdb=" N ASP L 267 " --> pdb=" O PRO L 263 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR L 268 " --> pdb=" O LYS L 264 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET L 276 " --> pdb=" O SER L 272 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU L 286 " --> pdb=" O THR L 282 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET L 288 " --> pdb=" O GLU L 284 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 305 Processing helix chain 'L' and resid 329 through 348 removed outlier: 4.394A pdb=" N VAL L 333 " --> pdb=" O LYS L 329 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU L 335 " --> pdb=" O HIS L 331 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLU L 336 " --> pdb=" O ASP L 332 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG L 339 " --> pdb=" O GLU L 335 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU L 348 " --> pdb=" O LEU L 344 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 383 removed outlier: 4.230A pdb=" N ARG L 364 " --> pdb=" O ASP L 360 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA L 370 " --> pdb=" O SER L 366 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 392 removed outlier: 3.831A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE L 388 " --> pdb=" O LEU L 384 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 419 removed outlier: 3.533A pdb=" N GLU L 407 " --> pdb=" O ASP L 403 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN L 409 " --> pdb=" O ILE L 405 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE L 410 " --> pdb=" O GLN L 406 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP L 417 " --> pdb=" O MET L 413 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS L 418 " --> pdb=" O LYS L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 424 removed outlier: 3.621A pdb=" N ARG L 423 " --> pdb=" O GLU L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 447 removed outlier: 3.768A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP L 445 " --> pdb=" O ARG L 441 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 470 removed outlier: 3.673A pdb=" N THR L 459 " --> pdb=" O HIS L 455 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS L 462 " --> pdb=" O GLU L 458 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG L 468 " --> pdb=" O ASN L 464 " (cutoff:3.500A) Processing helix chain 'L' and resid 470 through 475 Processing helix chain 'L' and resid 479 through 488 removed outlier: 3.597A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 490 through 499 Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.908A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 550 removed outlier: 3.593A pdb=" N GLU L 538 " --> pdb=" O SER L 534 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA L 542 " --> pdb=" O GLU L 538 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS L 545 " --> pdb=" O ARG L 541 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU L 548 " --> pdb=" O THR L 544 " (cutoff:3.500A) Processing helix chain 'L' and resid 554 through 563 removed outlier: 3.888A pdb=" N ARG L 560 " --> pdb=" O ALA L 556 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 581 removed outlier: 3.613A pdb=" N LYS L 578 " --> pdb=" O GLU L 574 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN L 579 " --> pdb=" O GLU L 575 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 600 removed outlier: 3.967A pdb=" N HIS L 600 " --> pdb=" O ARG L 596 " (cutoff:3.500A) Processing helix chain 'L' and resid 606 through 611 removed outlier: 3.551A pdb=" N LEU L 611 " --> pdb=" O ARG L 608 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 261 removed outlier: 3.638A pdb=" N LEU R 260 " --> pdb=" O VAL R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 273 Processing helix chain 'R' and resid 277 through 284 Processing helix chain 'R' and resid 285 through 292 removed outlier: 3.701A pdb=" N THR R 292 " --> pdb=" O GLU R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 310 Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 20 removed outlier: 3.936A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU G 31 " --> pdb=" O ASP G 199 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 111 removed outlier: 5.076A pdb=" N ALA G 138 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N GLY G 108 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N GLU G 136 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 11.804A pdb=" N VAL G 110 " --> pdb=" O THR G 134 " (cutoff:3.500A) removed outlier: 10.929A pdb=" N THR G 134 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY G 53 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AA4, first strand: chain 'H' and resid 15 through 16 removed outlier: 6.299A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 15 through 16 removed outlier: 6.299A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 99 through 101 removed outlier: 6.845A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AA9, first strand: chain 'H' and resid 109 through 111 removed outlier: 7.072A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.339A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.950A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'I' and resid 184 through 188 Processing sheet with id=AB8, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB9, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AC1, first strand: chain 'I' and resid 250 through 251 removed outlier: 3.799A pdb=" N ALA I 251 " --> pdb=" O ARG I 267 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG I 267 " --> pdb=" O ALA I 251 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'I' and resid 255 through 257 removed outlier: 3.803A pdb=" N VAL I 263 " --> pdb=" O ILE I 255 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.507A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC6, first strand: chain 'I' and resid 616 through 617 Processing sheet with id=AC7, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.328A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.616A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AD1, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AD2, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.425A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 846 through 847 removed outlier: 6.433A pdb=" N ASP I 842 " --> pdb=" O VAL I1046 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL I1046 " --> pdb=" O ASP I 842 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 882 through 884 Processing sheet with id=AD5, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD6, first strand: chain 'I' and resid 1268 through 1270 Processing sheet with id=AD7, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AD8, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.589A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.369A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AE1, first strand: chain 'J' and resid 261 through 262 Processing sheet with id=AE2, first strand: chain 'J' and resid 350 through 356 Processing sheet with id=AE3, first strand: chain 'J' and resid 547 through 556 Processing sheet with id=AE4, first strand: chain 'J' and resid 706 through 709 Processing sheet with id=AE5, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE6, first strand: chain 'J' and resid 825 through 826 removed outlier: 3.608A pdb=" N GLU J 833 " --> pdb=" O VAL J 825 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.994A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 949 through 950 removed outlier: 4.473A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL J 966 " --> pdb=" O VAL J 974 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 991 through 997 removed outlier: 3.916A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER J 961 " --> pdb=" O GLU J 981 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1049 through 1050 Processing sheet with id=AF2, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AF3, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.391A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP J1305 " --> pdb=" O LYS J1263 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 162 through 165 removed outlier: 5.813A pdb=" N ARG L 260 " --> pdb=" O THR L 163 " (cutoff:3.500A) 1179 hydrogen bonds defined for protein. 3285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 116 hydrogen bonds 232 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 8.35 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9968 1.34 - 1.46: 6351 1.46 - 1.58: 15936 1.58 - 1.70: 244 1.70 - 1.83: 235 Bond restraints: 32734 Sorted by residual: bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.827 -0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" C19 1N7 G 401 " pdb=" C3 1N7 G 401 " ideal model delta sigma weight residual 1.532 1.821 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.819 -0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" C3 1N7 J1504 " pdb=" C4 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.740 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C3 1N7 G 401 " pdb=" C4 1N7 G 401 " ideal model delta sigma weight residual 1.532 1.727 -0.195 2.00e-02 2.50e+03 9.54e+01 ... (remaining 32729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 43825 2.01 - 4.03: 784 4.03 - 6.04: 90 6.04 - 8.05: 19 8.05 - 10.07: 4 Bond angle restraints: 44722 Sorted by residual: angle pdb=" N GLY I1261 " pdb=" CA GLY I1261 " pdb=" C GLY I1261 " ideal model delta sigma weight residual 111.03 120.21 -9.18 1.40e+00 5.10e-01 4.30e+01 angle pdb=" C LEU J 903 " pdb=" N ALA J 904 " pdb=" CA ALA J 904 " ideal model delta sigma weight residual 121.54 131.11 -9.57 1.91e+00 2.74e-01 2.51e+01 angle pdb=" N ILE L 367 " pdb=" CA ILE L 367 " pdb=" C ILE L 367 " ideal model delta sigma weight residual 111.81 107.72 4.09 8.60e-01 1.35e+00 2.27e+01 angle pdb=" C LEU I 484 " pdb=" N ASP I 485 " pdb=" CA ASP I 485 " ideal model delta sigma weight residual 121.70 129.63 -7.93 1.80e+00 3.09e-01 1.94e+01 angle pdb=" C ASP I 696 " pdb=" N LYS I 697 " pdb=" CA LYS I 697 " ideal model delta sigma weight residual 121.80 131.87 -10.07 2.44e+00 1.68e-01 1.70e+01 ... (remaining 44717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 19233 35.74 - 71.47: 783 71.47 - 107.21: 27 107.21 - 142.94: 2 142.94 - 178.68: 3 Dihedral angle restraints: 20048 sinusoidal: 9239 harmonic: 10809 Sorted by residual: dihedral pdb=" CA ALA J 904 " pdb=" C ALA J 904 " pdb=" N ARG J 905 " pdb=" CA ARG J 905 " ideal model delta harmonic sigma weight residual 180.00 147.49 32.51 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA SER I 398 " pdb=" C SER I 398 " pdb=" N ALA I 399 " pdb=" CA ALA I 399 " ideal model delta harmonic sigma weight residual 180.00 151.47 28.53 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA VAL K 32 " pdb=" C VAL K 32 " pdb=" N GLY K 33 " pdb=" CA GLY K 33 " ideal model delta harmonic sigma weight residual -180.00 -151.50 -28.50 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 20045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4773 0.086 - 0.172: 336 0.172 - 0.257: 5 0.257 - 0.343: 5 0.343 - 0.429: 3 Chirality restraints: 5122 Sorted by residual: chirality pdb=" C19 1N7 J1504 " pdb=" C18 1N7 J1504 " pdb=" C2 1N7 J1504 " pdb=" C3 1N7 J1504 " both_signs ideal model delta sigma weight residual False -2.53 -2.96 0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" C19 1N7 G 401 " pdb=" C18 1N7 G 401 " pdb=" C2 1N7 G 401 " pdb=" C3 1N7 G 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.95 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.92 0.39 2.00e-01 2.50e+01 3.74e+00 ... (remaining 5119 not shown) Planarity restraints: 5408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS I 551 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO I 552 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO I 552 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 552 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE I 514 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C PHE I 514 " -0.036 2.00e-02 2.50e+03 pdb=" O PHE I 514 " 0.013 2.00e-02 2.50e+03 pdb=" N MET I 515 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS I 496 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO I 497 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO I 497 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO I 497 " -0.028 5.00e-02 4.00e+02 ... (remaining 5405 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 2307 2.74 - 3.28: 29773 3.28 - 3.82: 50795 3.82 - 4.36: 63736 4.36 - 4.90: 109295 Nonbonded interactions: 255906 Sorted by model distance: nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.195 2.170 nonbonded pdb=" OG1 THR I 843 " pdb=" O GLY I 846 " model vdw 2.248 3.040 nonbonded pdb=" O ILE I 11 " pdb=" OH TYR I1149 " model vdw 2.250 3.040 nonbonded pdb=" NH1 ARG I1246 " pdb=" OD1 ASP J 348 " model vdw 2.252 3.120 nonbonded pdb=" OG SER J 353 " pdb=" O LYS J 445 " model vdw 2.253 3.040 ... (remaining 255901 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 158 or resid 167 through 233)) selection = (chain 'H' and resid 5 through 233) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 37.040 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 : 0.007 0.295 32740 Z= 0.312 Angle : 0.672 10.068 44722 Z= 0.395 Chirality : 0.046 0.429 5122 Planarity : 0.004 0.052 5408 Dihedral : 16.515 178.678 13078 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.61 % Rotamer: Outliers : 3.83 % Allowed : 8.24 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.98 (0.13), residues: 3730 helix: -1.10 (0.13), residues: 1444 sheet: -1.02 (0.25), residues: 417 loop : -1.48 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 610 TYR 0.013 0.002 TYR I1281 PHE 0.013 0.002 PHE K 17 TRP 0.005 0.001 TRP J1193 HIS 0.006 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00659 (32734) covalent geometry : angle 0.67238 (44722) hydrogen bonds : bond 0.23257 ( 1287) hydrogen bonds : angle 8.02137 ( 3517) metal coordination : bond 0.00345 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 347 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 38 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7477 (t) REVERT: H 114 ASP cc_start: 0.7972 (m-30) cc_final: 0.7599 (m-30) REVERT: H 183 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8558 (tp) REVERT: I 119 GLU cc_start: 0.8598 (tt0) cc_final: 0.8324 (tt0) REVERT: I 189 ASP cc_start: 0.7057 (p0) cc_final: 0.6796 (p0) REVERT: I 200 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7904 (mmm-85) REVERT: I 342 ASP cc_start: 0.8287 (t0) cc_final: 0.8054 (t70) REVERT: I 365 GLU cc_start: 0.6905 (tp30) cc_final: 0.6631 (tp30) REVERT: I 538 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8102 (pp) REVERT: I 859 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7574 (tp30) REVERT: I 895 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7280 (pp) REVERT: J 151 MET cc_start: 0.6302 (OUTLIER) cc_final: 0.5483 (ppp) REVERT: J 320 ASN cc_start: 0.7467 (m-40) cc_final: 0.7257 (m-40) REVERT: J 992 LYS cc_start: 0.7378 (tppp) cc_final: 0.6565 (tppp) REVERT: J 1189 MET cc_start: 0.7388 (mmp) cc_final: 0.7182 (mmp) REVERT: K 56 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: L 104 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7455 (mm-30) REVERT: L 137 TYR cc_start: 0.6521 (OUTLIER) cc_final: 0.5552 (m-80) REVERT: L 149 ASP cc_start: 0.3748 (OUTLIER) cc_final: 0.3540 (m-30) REVERT: L 261 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6846 (tt) REVERT: L 468 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7777 (ptt-90) REVERT: L 489 MET cc_start: 0.8480 (ptp) cc_final: 0.8081 (ptp) outliers start: 123 outliers final: 55 residues processed: 443 average time/residue: 0.6435 time to fit residues: 339.3282 Evaluate side-chains 342 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 275 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 859 GLU Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 261 LEU Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 103 ASN H 132 HIS H 186 ASN I 83 GLN I 193 ASN I 649 GLN I 799 ASN J 792 ASN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.197363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.128388 restraints weight = 34495.909| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.26 r_work: 0.3229 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 32740 Z= 0.242 Angle : 0.643 9.364 44722 Z= 0.339 Chirality : 0.045 0.202 5122 Planarity : 0.005 0.043 5408 Dihedral : 17.540 178.992 5753 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 4.32 % Allowed : 11.01 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.54 (0.13), residues: 3730 helix: -0.47 (0.13), residues: 1473 sheet: -0.92 (0.25), residues: 414 loop : -1.46 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I1223 TYR 0.012 0.002 TYR I1231 PHE 0.017 0.002 PHE J 620 TRP 0.005 0.001 TRP J 868 HIS 0.008 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00592 (32734) covalent geometry : angle 0.64272 (44722) hydrogen bonds : bond 0.05167 ( 1287) hydrogen bonds : angle 4.96829 ( 3517) metal coordination : bond 0.00533 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 291 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 13 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6598 (pp) REVERT: H 38 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7880 (t) REVERT: H 183 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8565 (tp) REVERT: I 200 ARG cc_start: 0.8685 (mtp85) cc_final: 0.8469 (mmm-85) REVERT: I 342 ASP cc_start: 0.8340 (t0) cc_final: 0.8053 (t70) REVERT: I 412 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6881 (pm20) REVERT: I 538 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8200 (pp) REVERT: I 845 LEU cc_start: 0.7738 (mp) cc_final: 0.7525 (mp) REVERT: I 859 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7646 (tp30) REVERT: I 895 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7454 (pp) REVERT: I 1107 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8612 (mtp) REVERT: I 1154 ASP cc_start: 0.8270 (t0) cc_final: 0.7805 (t0) REVERT: J 151 MET cc_start: 0.6482 (OUTLIER) cc_final: 0.5453 (ppp) REVERT: J 163 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: J 314 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7272 (ptt180) REVERT: J 714 GLU cc_start: 0.8276 (tt0) cc_final: 0.8043 (tt0) REVERT: J 992 LYS cc_start: 0.7376 (tppp) cc_final: 0.6514 (tppp) REVERT: K 68 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6601 (tt0) REVERT: L 104 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7520 (mm-30) REVERT: L 137 TYR cc_start: 0.6485 (OUTLIER) cc_final: 0.5219 (m-80) REVERT: L 261 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6961 (tt) REVERT: L 274 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7458 (mmm160) REVERT: L 489 MET cc_start: 0.8419 (ptp) cc_final: 0.7948 (ptp) REVERT: L 505 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8495 (mp) outliers start: 139 outliers final: 73 residues processed: 394 average time/residue: 0.6355 time to fit residues: 298.6453 Evaluate side-chains 365 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 277 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 685 ILE Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 261 LEU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 305 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 230 optimal weight: 0.8980 chunk 370 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 319 optimal weight: 5.9990 chunk 58 optimal weight: 0.2980 chunk 267 optimal weight: 0.3980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN G 147 GLN H 103 ASN H 132 HIS I 193 ASN I 649 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1259 GLN L 131 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.200425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.131436 restraints weight = 34548.961| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.32 r_work: 0.3270 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32740 Z= 0.138 Angle : 0.546 8.272 44722 Z= 0.290 Chirality : 0.041 0.211 5122 Planarity : 0.004 0.043 5408 Dihedral : 17.090 179.993 5730 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.79 % Allowed : 12.75 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % 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: -1.14 (0.13), residues: 3730 helix: 0.06 (0.14), residues: 1477 sheet: -0.93 (0.24), residues: 431 loop : -1.36 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J1173 TYR 0.012 0.001 TYR H 152 PHE 0.014 0.001 PHE I 405 TRP 0.004 0.001 TRP I1276 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00323 (32734) covalent geometry : angle 0.54640 (44722) hydrogen bonds : bond 0.04033 ( 1287) hydrogen bonds : angle 4.46343 ( 3517) metal coordination : bond 0.00263 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 294 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.8727 (mmt180) cc_final: 0.8360 (ttp-110) REVERT: G 62 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7736 (t0) REVERT: H 13 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6546 (pp) REVERT: H 38 THR cc_start: 0.7954 (OUTLIER) cc_final: 0.7503 (t) REVERT: H 183 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8455 (tp) REVERT: I 118 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6946 (mtpp) REVERT: I 200 ARG cc_start: 0.8531 (mtp85) cc_final: 0.8291 (mmm-85) REVERT: I 222 ASP cc_start: 0.7439 (t0) cc_final: 0.7211 (t0) REVERT: I 342 ASP cc_start: 0.8292 (t0) cc_final: 0.7991 (t70) REVERT: I 412 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6730 (pm20) REVERT: I 492 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8282 (ptp) REVERT: I 538 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8286 (pp) REVERT: I 681 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7994 (mtt) REVERT: I 895 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7354 (pp) REVERT: I 1107 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8470 (mtp) REVERT: I 1143 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7544 (tp30) REVERT: I 1154 ASP cc_start: 0.8157 (t0) cc_final: 0.7697 (t0) REVERT: J 151 MET cc_start: 0.6345 (OUTLIER) cc_final: 0.5376 (ppp) REVERT: J 163 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: J 225 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7555 (mm-30) REVERT: J 603 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7723 (pttp) REVERT: J 697 MET cc_start: 0.8436 (ttp) cc_final: 0.8115 (ttp) REVERT: J 714 GLU cc_start: 0.8026 (tt0) cc_final: 0.7737 (tt0) REVERT: J 992 LYS cc_start: 0.7257 (tppp) cc_final: 0.6302 (tppp) REVERT: J 1231 ARG cc_start: 0.7321 (mtp85) cc_final: 0.6426 (mtt180) REVERT: K 35 LYS cc_start: 0.7618 (mptp) cc_final: 0.7301 (mmtt) REVERT: L 104 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7361 (mm-30) REVERT: L 261 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7190 (tt) REVERT: L 274 ARG cc_start: 0.7978 (mtt-85) cc_final: 0.7366 (mmm160) REVERT: L 489 MET cc_start: 0.8293 (ptp) cc_final: 0.7850 (ptp) REVERT: R 260 LEU cc_start: 0.5624 (pt) cc_final: 0.4673 (mt) outliers start: 122 outliers final: 65 residues processed: 379 average time/residue: 0.7114 time to fit residues: 317.5308 Evaluate side-chains 359 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 277 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 603 LYS Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 261 LEU Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 146 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 71 optimal weight: 0.1980 chunk 235 optimal weight: 0.7980 chunk 187 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 chunk 322 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 234 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 103 ASN H 132 HIS I 193 ASN I 649 GLN I1116 HIS ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 362 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.202064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133404 restraints weight = 34340.568| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.30 r_work: 0.3301 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32740 Z= 0.114 Angle : 0.516 8.137 44722 Z= 0.275 Chirality : 0.040 0.214 5122 Planarity : 0.004 0.041 5408 Dihedral : 16.858 179.641 5719 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.04 % Allowed : 13.34 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % 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: -0.82 (0.14), residues: 3730 helix: 0.44 (0.14), residues: 1479 sheet: -0.77 (0.25), residues: 428 loop : -1.30 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 596 TYR 0.013 0.001 TYR H 152 PHE 0.017 0.001 PHE I 645 TRP 0.004 0.001 TRP J 33 HIS 0.004 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00259 (32734) covalent geometry : angle 0.51559 (44722) hydrogen bonds : bond 0.03526 ( 1287) hydrogen bonds : angle 4.19091 ( 3517) metal coordination : bond 0.00198 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 307 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.8834 (mmt180) cc_final: 0.8306 (ttp-110) REVERT: G 62 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8064 (t0) REVERT: H 13 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6444 (pp) REVERT: H 38 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7635 (t) REVERT: H 180 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8537 (t) REVERT: I 60 GLN cc_start: 0.7497 (mt0) cc_final: 0.7072 (mm-40) REVERT: I 200 ARG cc_start: 0.8625 (mtp85) cc_final: 0.8395 (mmm-85) REVERT: I 222 ASP cc_start: 0.7576 (t0) cc_final: 0.7336 (t0) REVERT: I 342 ASP cc_start: 0.8316 (t0) cc_final: 0.7995 (t70) REVERT: I 473 ARG cc_start: 0.7118 (mtp180) cc_final: 0.6836 (mtm180) REVERT: I 514 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7876 (m-80) REVERT: I 538 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8519 (pp) REVERT: I 681 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8126 (mtt) REVERT: I 895 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7396 (pp) REVERT: I 1107 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8460 (mtp) REVERT: I 1143 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7771 (tp30) REVERT: I 1154 ASP cc_start: 0.8309 (t0) cc_final: 0.7830 (t0) REVERT: J 151 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.5350 (ppp) REVERT: J 225 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7599 (mm-30) REVERT: J 314 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7368 (ptt180) REVERT: J 388 ARG cc_start: 0.8193 (mmt90) cc_final: 0.7820 (mmt90) REVERT: J 422 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8807 (mp) REVERT: J 697 MET cc_start: 0.8514 (ttp) cc_final: 0.8300 (ttp) REVERT: J 714 GLU cc_start: 0.8141 (tt0) cc_final: 0.7870 (tt0) REVERT: J 802 ASP cc_start: 0.8139 (m-30) cc_final: 0.7880 (m-30) REVERT: J 992 LYS cc_start: 0.7305 (tppp) cc_final: 0.6329 (tppp) REVERT: K 35 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7330 (mmtt) REVERT: K 68 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6535 (tt0) REVERT: L 274 ARG cc_start: 0.7999 (mtt-85) cc_final: 0.7385 (mmm160) REVERT: L 456 MET cc_start: 0.8363 (tpp) cc_final: 0.8108 (tpt) REVERT: L 489 MET cc_start: 0.8180 (ptp) cc_final: 0.7797 (ptp) REVERT: L 568 ASN cc_start: 0.7469 (m110) cc_final: 0.7093 (t0) REVERT: R 260 LEU cc_start: 0.5674 (OUTLIER) cc_final: 0.4847 (mt) outliers start: 130 outliers final: 63 residues processed: 392 average time/residue: 0.6765 time to fit residues: 312.6434 Evaluate side-chains 363 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 284 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1212 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 362 ASN Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 71 optimal weight: 20.0000 chunk 190 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 336 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 229 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 274 optimal weight: 0.0030 chunk 202 optimal weight: 0.1980 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 103 ASN H 132 HIS I 193 ASN I 649 GLN I1038 GLN J 335 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1235 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.201660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.133879 restraints weight = 34421.451| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.17 r_work: 0.3316 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32740 Z= 0.128 Angle : 0.522 8.337 44722 Z= 0.277 Chirality : 0.041 0.210 5122 Planarity : 0.004 0.040 5408 Dihedral : 16.735 179.258 5697 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.32 % Allowed : 13.62 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % 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: -0.66 (0.14), residues: 3730 helix: 0.61 (0.14), residues: 1480 sheet: -0.73 (0.25), residues: 434 loop : -1.22 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J1231 TYR 0.014 0.001 TYR H 152 PHE 0.013 0.001 PHE I 645 TRP 0.004 0.001 TRP J 409 HIS 0.004 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00301 (32734) covalent geometry : angle 0.52227 (44722) hydrogen bonds : bond 0.03529 ( 1287) hydrogen bonds : angle 4.08736 ( 3517) metal coordination : bond 0.00242 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 291 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 13 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7779 (tt) REVERT: G 33 ARG cc_start: 0.8819 (mmt180) cc_final: 0.8325 (ttp-110) REVERT: G 62 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.8003 (t0) REVERT: G 101 THR cc_start: 0.8780 (m) cc_final: 0.8383 (p) REVERT: H 13 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6475 (pp) REVERT: H 38 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7544 (t) REVERT: H 168 ILE cc_start: 0.6776 (OUTLIER) cc_final: 0.6533 (tt) REVERT: H 183 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8398 (tp) REVERT: I 60 GLN cc_start: 0.7511 (mt0) cc_final: 0.7073 (mm-40) REVERT: I 200 ARG cc_start: 0.8619 (mtp85) cc_final: 0.8386 (mmm-85) REVERT: I 222 ASP cc_start: 0.7585 (t0) cc_final: 0.7323 (t0) REVERT: I 342 ASP cc_start: 0.8313 (t0) cc_final: 0.7995 (t70) REVERT: I 473 ARG cc_start: 0.7106 (mtp180) cc_final: 0.6819 (mtm180) REVERT: I 514 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: I 538 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8512 (pp) REVERT: I 681 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8139 (mtt) REVERT: I 799 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8616 (p0) REVERT: I 895 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7389 (pp) REVERT: I 1107 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8466 (mtp) REVERT: I 1143 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7728 (tp30) REVERT: I 1154 ASP cc_start: 0.8317 (t0) cc_final: 0.7853 (t0) REVERT: I 1264 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8228 (pm20) REVERT: J 151 MET cc_start: 0.6267 (OUTLIER) cc_final: 0.5330 (ppp) REVERT: J 213 LYS cc_start: 0.7758 (mmtm) cc_final: 0.7550 (mmtp) REVERT: J 225 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7656 (mm-30) REVERT: J 314 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7352 (ptt180) REVERT: J 388 ARG cc_start: 0.8196 (mmt90) cc_final: 0.7918 (mmt90) REVERT: J 390 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8493 (mt) REVERT: J 422 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8814 (mp) REVERT: J 697 MET cc_start: 0.8496 (ttp) cc_final: 0.8273 (ttp) REVERT: J 714 GLU cc_start: 0.8101 (tt0) cc_final: 0.7823 (tt0) REVERT: J 802 ASP cc_start: 0.8189 (m-30) cc_final: 0.7971 (m-30) REVERT: J 992 LYS cc_start: 0.7289 (tppp) cc_final: 0.6408 (tppp) REVERT: J 1152 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7504 (tm-30) REVERT: J 1231 ARG cc_start: 0.7389 (mtp85) cc_final: 0.6419 (mtt180) REVERT: K 35 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7280 (mmtt) REVERT: K 56 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: K 68 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6540 (tt0) REVERT: L 274 ARG cc_start: 0.8021 (mtt-85) cc_final: 0.7357 (mmm160) REVERT: L 456 MET cc_start: 0.8351 (tpp) cc_final: 0.8092 (tpt) REVERT: L 489 MET cc_start: 0.8224 (ptp) cc_final: 0.7802 (ptp) REVERT: R 260 LEU cc_start: 0.5682 (OUTLIER) cc_final: 0.4940 (mt) outliers start: 139 outliers final: 68 residues processed: 389 average time/residue: 0.6944 time to fit residues: 319.2013 Evaluate side-chains 373 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 283 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 168 ILE Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1264 GLN Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1361 THR Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 26 optimal weight: 3.9990 chunk 346 optimal weight: 4.9990 chunk 354 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 0.1980 chunk 210 optimal weight: 0.0470 chunk 173 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 296 optimal weight: 8.9990 chunk 170 optimal weight: 0.8980 chunk 315 optimal weight: 4.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 103 ASN I 649 GLN J 335 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 362 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.203636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135006 restraints weight = 34339.479| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.28 r_work: 0.3331 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32740 Z= 0.103 Angle : 0.500 8.568 44722 Z= 0.266 Chirality : 0.040 0.203 5122 Planarity : 0.003 0.041 5408 Dihedral : 16.597 178.715 5694 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.83 % Allowed : 14.68 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % 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: -0.40 (0.14), residues: 3730 helix: 0.92 (0.14), residues: 1468 sheet: -0.65 (0.25), residues: 434 loop : -1.14 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 596 TYR 0.012 0.001 TYR I1231 PHE 0.014 0.001 PHE I 645 TRP 0.004 0.001 TRP J 33 HIS 0.004 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00230 (32734) covalent geometry : angle 0.49992 (44722) hydrogen bonds : bond 0.03167 ( 1287) hydrogen bonds : angle 3.92436 ( 3517) metal coordination : bond 0.00165 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 302 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 13 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7925 (tt) REVERT: G 33 ARG cc_start: 0.8821 (mmt180) cc_final: 0.8232 (ttp-110) REVERT: G 62 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.8020 (t0) REVERT: G 101 THR cc_start: 0.8684 (m) cc_final: 0.8311 (p) REVERT: H 13 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6400 (pp) REVERT: H 38 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7535 (t) REVERT: H 183 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8324 (tp) REVERT: I 60 GLN cc_start: 0.7516 (mt0) cc_final: 0.7119 (mm-40) REVERT: I 200 ARG cc_start: 0.8603 (mtp85) cc_final: 0.8374 (mmm-85) REVERT: I 222 ASP cc_start: 0.7580 (t0) cc_final: 0.7340 (t0) REVERT: I 412 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6892 (pm20) REVERT: I 429 MET cc_start: 0.8100 (mtp) cc_final: 0.7877 (mtm) REVERT: I 473 ARG cc_start: 0.7057 (mtp180) cc_final: 0.6830 (mtm180) REVERT: I 514 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7840 (m-80) REVERT: I 538 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8541 (pp) REVERT: I 681 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8101 (mtt) REVERT: I 895 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7399 (pp) REVERT: I 1143 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: I 1154 ASP cc_start: 0.8293 (t0) cc_final: 0.7858 (t0) REVERT: J 60 ARG cc_start: 0.8775 (ptm-80) cc_final: 0.8564 (ttt-90) REVERT: J 81 ARG cc_start: 0.8034 (ttp-110) cc_final: 0.7351 (ttp80) REVERT: J 151 MET cc_start: 0.6104 (OUTLIER) cc_final: 0.5236 (ppp) REVERT: J 213 LYS cc_start: 0.7707 (mmtm) cc_final: 0.7462 (mmtp) REVERT: J 225 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7624 (mm-30) REVERT: J 314 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7370 (ptt180) REVERT: J 388 ARG cc_start: 0.8216 (mmt90) cc_final: 0.7804 (mmt90) REVERT: J 390 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8477 (mt) REVERT: J 677 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6143 (mt-10) REVERT: J 684 ASP cc_start: 0.8061 (m-30) cc_final: 0.7667 (m-30) REVERT: J 697 MET cc_start: 0.8434 (ttp) cc_final: 0.8220 (ttp) REVERT: J 714 GLU cc_start: 0.8125 (tt0) cc_final: 0.7864 (tt0) REVERT: J 788 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6436 (pp) REVERT: J 802 ASP cc_start: 0.8168 (m-30) cc_final: 0.7964 (m-30) REVERT: J 992 LYS cc_start: 0.7235 (tppp) cc_final: 0.6332 (tppp) REVERT: J 1152 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7545 (tm-30) REVERT: J 1231 ARG cc_start: 0.7395 (mtp85) cc_final: 0.7080 (ttm110) REVERT: K 35 LYS cc_start: 0.7614 (mptp) cc_final: 0.7245 (mmtt) REVERT: L 273 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.6535 (tmt) REVERT: L 274 ARG cc_start: 0.8104 (mtt-85) cc_final: 0.7422 (mmm160) REVERT: L 364 ARG cc_start: 0.7996 (mtm110) cc_final: 0.7469 (ptp-170) REVERT: L 456 MET cc_start: 0.8383 (tpp) cc_final: 0.8110 (tpt) REVERT: L 489 MET cc_start: 0.8137 (ptp) cc_final: 0.7850 (ptp) REVERT: R 260 LEU cc_start: 0.5516 (OUTLIER) cc_final: 0.4943 (mt) outliers start: 123 outliers final: 55 residues processed: 389 average time/residue: 0.6579 time to fit residues: 302.9285 Evaluate side-chains 351 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 278 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 677 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1361 THR Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 273 MET Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 225 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 347 optimal weight: 0.7980 chunk 284 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 321 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 103 ASN I 649 GLN I 799 ASN J 335 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.190268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.130087 restraints weight = 34068.354| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.08 r_work: 0.3273 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32740 Z= 0.151 Angle : 0.540 10.826 44722 Z= 0.283 Chirality : 0.041 0.208 5122 Planarity : 0.004 0.052 5408 Dihedral : 16.631 178.429 5687 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.61 % Allowed : 15.27 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % 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: -0.43 (0.14), residues: 3730 helix: 0.87 (0.14), residues: 1474 sheet: -0.63 (0.25), residues: 419 loop : -1.16 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 596 TYR 0.013 0.001 TYR H 152 PHE 0.014 0.001 PHE I 645 TRP 0.003 0.001 TRP J 409 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00363 (32734) covalent geometry : angle 0.54011 (44722) hydrogen bonds : bond 0.03558 ( 1287) hydrogen bonds : angle 3.95588 ( 3517) metal coordination : bond 0.00283 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 280 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 13 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7932 (tt) REVERT: G 33 ARG cc_start: 0.8749 (mmt180) cc_final: 0.8357 (ttp-110) REVERT: G 62 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7871 (t0) REVERT: G 101 THR cc_start: 0.8716 (m) cc_final: 0.8384 (p) REVERT: H 13 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6612 (pp) REVERT: H 38 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7602 (t) REVERT: H 183 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8441 (tp) REVERT: H 232 VAL cc_start: 0.8800 (m) cc_final: 0.8598 (t) REVERT: I 60 GLN cc_start: 0.7590 (mt0) cc_final: 0.7261 (mm-40) REVERT: I 119 GLU cc_start: 0.8412 (tt0) cc_final: 0.8178 (tt0) REVERT: I 200 ARG cc_start: 0.8650 (mtp85) cc_final: 0.8430 (mmm-85) REVERT: I 222 ASP cc_start: 0.7693 (t0) cc_final: 0.7461 (t0) REVERT: I 342 ASP cc_start: 0.8408 (t0) cc_final: 0.8162 (t70) REVERT: I 412 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6971 (pm20) REVERT: I 473 ARG cc_start: 0.7147 (mtp180) cc_final: 0.6847 (mtm180) REVERT: I 514 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: I 525 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8772 (p) REVERT: I 538 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8603 (pp) REVERT: I 895 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7622 (pp) REVERT: I 1143 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7730 (tp30) REVERT: I 1154 ASP cc_start: 0.8196 (t0) cc_final: 0.7804 (t0) REVERT: J 77 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6677 (mtm180) REVERT: J 81 ARG cc_start: 0.7961 (ttp-110) cc_final: 0.7402 (ttp80) REVERT: J 151 MET cc_start: 0.6149 (OUTLIER) cc_final: 0.5298 (ppp) REVERT: J 225 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7732 (mm-30) REVERT: J 314 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7370 (ptt180) REVERT: J 388 ARG cc_start: 0.8316 (mmt90) cc_final: 0.8035 (mmt90) REVERT: J 390 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8425 (mt) REVERT: J 677 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6402 (mt-10) REVERT: J 680 ASN cc_start: 0.8281 (m-40) cc_final: 0.7564 (m110) REVERT: J 684 ASP cc_start: 0.8007 (m-30) cc_final: 0.7546 (m-30) REVERT: J 697 MET cc_start: 0.8421 (ttp) cc_final: 0.8197 (ttp) REVERT: J 802 ASP cc_start: 0.8199 (m-30) cc_final: 0.7987 (m-30) REVERT: J 992 LYS cc_start: 0.7309 (tppp) cc_final: 0.6401 (tppp) REVERT: J 1152 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7617 (tm-30) REVERT: J 1231 ARG cc_start: 0.7554 (mtp85) cc_final: 0.6606 (mtt180) REVERT: J 1334 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: K 35 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7250 (mmtt) REVERT: K 68 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6660 (tt0) REVERT: L 137 TYR cc_start: 0.6407 (OUTLIER) cc_final: 0.5615 (m-80) REVERT: L 149 ASP cc_start: 0.5261 (OUTLIER) cc_final: 0.4599 (t0) REVERT: L 274 ARG cc_start: 0.7881 (mtt-85) cc_final: 0.7241 (mmm160) REVERT: L 364 ARG cc_start: 0.8007 (mtm110) cc_final: 0.7463 (ptp-170) REVERT: L 456 MET cc_start: 0.8516 (tpp) cc_final: 0.8258 (tpt) REVERT: L 468 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7861 (ptt-90) REVERT: L 489 MET cc_start: 0.8289 (ptp) cc_final: 0.7964 (ptp) REVERT: R 260 LEU cc_start: 0.5442 (OUTLIER) cc_final: 0.4888 (mt) outliers start: 116 outliers final: 64 residues processed: 365 average time/residue: 0.6792 time to fit residues: 293.2442 Evaluate side-chains 364 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 277 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 677 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1361 THR Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 468 ARG Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 335 optimal weight: 30.0000 chunk 171 optimal weight: 2.9990 chunk 326 optimal weight: 7.9990 chunk 131 optimal weight: 0.1980 chunk 146 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 301 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 103 ASN I 649 GLN I 725 GLN J 335 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.192686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.131834 restraints weight = 33776.235| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.01 r_work: 0.3273 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 32740 Z= 0.157 Angle : 0.549 11.504 44722 Z= 0.287 Chirality : 0.042 0.208 5122 Planarity : 0.004 0.045 5408 Dihedral : 16.648 178.085 5687 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.64 % Allowed : 15.43 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.43 (0.14), residues: 3730 helix: 0.87 (0.14), residues: 1474 sheet: -0.62 (0.25), residues: 419 loop : -1.16 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 596 TYR 0.012 0.001 TYR I1231 PHE 0.013 0.001 PHE I 645 TRP 0.004 0.001 TRP J 868 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00382 (32734) covalent geometry : angle 0.54866 (44722) hydrogen bonds : bond 0.03635 ( 1287) hydrogen bonds : angle 3.96072 ( 3517) metal coordination : bond 0.00300 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 285 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 12 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7964 (ptp90) REVERT: G 13 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7878 (tt) REVERT: G 33 ARG cc_start: 0.8827 (mmt180) cc_final: 0.8413 (ttp-110) REVERT: G 62 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7838 (t0) REVERT: G 101 THR cc_start: 0.8786 (m) cc_final: 0.8430 (p) REVERT: H 13 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6662 (pp) REVERT: H 38 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7656 (t) REVERT: H 183 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8469 (tp) REVERT: I 60 GLN cc_start: 0.7583 (mt0) cc_final: 0.7237 (mm-40) REVERT: I 119 GLU cc_start: 0.8443 (tt0) cc_final: 0.8200 (tt0) REVERT: I 200 ARG cc_start: 0.8643 (mtp85) cc_final: 0.8422 (mmm-85) REVERT: I 222 ASP cc_start: 0.7700 (t0) cc_final: 0.7470 (t0) REVERT: I 342 ASP cc_start: 0.8414 (t0) cc_final: 0.8169 (t70) REVERT: I 412 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6976 (pm20) REVERT: I 473 ARG cc_start: 0.7063 (mtp180) cc_final: 0.6781 (mtm180) REVERT: I 514 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.7856 (m-80) REVERT: I 525 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8763 (p) REVERT: I 538 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8578 (pp) REVERT: I 895 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7592 (pp) REVERT: I 1154 ASP cc_start: 0.8165 (t0) cc_final: 0.7784 (t0) REVERT: J 77 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6676 (mtm180) REVERT: J 151 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.5250 (ppp) REVERT: J 225 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7755 (mm-30) REVERT: J 314 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7389 (ptt180) REVERT: J 388 ARG cc_start: 0.8366 (mmt90) cc_final: 0.8106 (mmt90) REVERT: J 390 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8394 (mt) REVERT: J 677 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6419 (mt-10) REVERT: J 680 ASN cc_start: 0.8337 (m-40) cc_final: 0.7609 (m110) REVERT: J 684 ASP cc_start: 0.8019 (m-30) cc_final: 0.7538 (m-30) REVERT: J 697 MET cc_start: 0.8490 (ttp) cc_final: 0.8280 (ttp) REVERT: J 992 LYS cc_start: 0.7303 (tppp) cc_final: 0.6393 (tppp) REVERT: J 1152 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7615 (tm-30) REVERT: J 1334 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7960 (mm-30) REVERT: K 35 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7401 (mmtt) REVERT: K 68 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6672 (tt0) REVERT: L 149 ASP cc_start: 0.5195 (OUTLIER) cc_final: 0.4545 (t0) REVERT: L 274 ARG cc_start: 0.7906 (mtt-85) cc_final: 0.7229 (mmm160) REVERT: L 364 ARG cc_start: 0.8015 (mtm110) cc_final: 0.7443 (ptp-170) REVERT: L 456 MET cc_start: 0.8494 (tpp) cc_final: 0.8211 (tpt) REVERT: L 489 MET cc_start: 0.8348 (ptp) cc_final: 0.7993 (ptp) REVERT: R 260 LEU cc_start: 0.5419 (OUTLIER) cc_final: 0.4905 (mt) outliers start: 117 outliers final: 70 residues processed: 366 average time/residue: 0.6812 time to fit residues: 295.5285 Evaluate side-chains 366 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 275 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 677 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain J residue 1361 THR Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 112 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 371 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 368 optimal weight: 10.0000 chunk 277 optimal weight: 6.9990 chunk 79 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 103 ASN I 649 GLN I1038 GLN J 335 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.194073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.133185 restraints weight = 33489.773| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.08 r_work: 0.3285 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32740 Z= 0.127 Angle : 0.529 10.643 44722 Z= 0.277 Chirality : 0.041 0.203 5122 Planarity : 0.004 0.040 5408 Dihedral : 16.570 177.583 5687 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.33 % Allowed : 15.99 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.30 (0.14), residues: 3730 helix: 1.01 (0.14), residues: 1473 sheet: -0.55 (0.25), residues: 428 loop : -1.12 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J1231 TYR 0.012 0.001 TYR I1231 PHE 0.016 0.001 PHE I 645 TRP 0.004 0.001 TRP J 409 HIS 0.004 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00299 (32734) covalent geometry : angle 0.52916 (44722) hydrogen bonds : bond 0.03365 ( 1287) hydrogen bonds : angle 3.88490 ( 3517) metal coordination : bond 0.00231 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 286 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 13 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7919 (tt) REVERT: G 33 ARG cc_start: 0.8854 (mmt180) cc_final: 0.8387 (ttp-110) REVERT: G 62 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7833 (t0) REVERT: G 101 THR cc_start: 0.8671 (m) cc_final: 0.8356 (p) REVERT: H 13 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6627 (pp) REVERT: H 38 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7580 (t) REVERT: H 183 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8418 (tp) REVERT: I 60 GLN cc_start: 0.7589 (mt0) cc_final: 0.7281 (mm-40) REVERT: I 119 GLU cc_start: 0.8438 (tt0) cc_final: 0.8123 (tt0) REVERT: I 200 ARG cc_start: 0.8628 (mtp85) cc_final: 0.8410 (mmm-85) REVERT: I 222 ASP cc_start: 0.7701 (t0) cc_final: 0.7482 (t0) REVERT: I 342 ASP cc_start: 0.8407 (t0) cc_final: 0.8160 (t70) REVERT: I 412 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.7006 (pm20) REVERT: I 473 ARG cc_start: 0.7154 (mtp180) cc_final: 0.6936 (mtm180) REVERT: I 514 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7827 (m-80) REVERT: I 538 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8611 (pp) REVERT: I 849 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7904 (tt0) REVERT: I 895 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7585 (pp) REVERT: I 1143 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7742 (tp30) REVERT: I 1154 ASP cc_start: 0.8199 (t0) cc_final: 0.7829 (t0) REVERT: J 81 ARG cc_start: 0.7968 (ttp-110) cc_final: 0.7444 (ttp80) REVERT: J 151 MET cc_start: 0.6038 (OUTLIER) cc_final: 0.5267 (ppp) REVERT: J 225 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7753 (mm-30) REVERT: J 314 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7397 (ptt180) REVERT: J 388 ARG cc_start: 0.8327 (mmt90) cc_final: 0.8056 (mmt90) REVERT: J 390 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8384 (mt) REVERT: J 677 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6310 (mt-10) REVERT: J 680 ASN cc_start: 0.8161 (m-40) cc_final: 0.7404 (m110) REVERT: J 684 ASP cc_start: 0.8014 (m-30) cc_final: 0.7528 (m-30) REVERT: J 697 MET cc_start: 0.8438 (ttp) cc_final: 0.8223 (ttp) REVERT: J 992 LYS cc_start: 0.7325 (tppp) cc_final: 0.6431 (tppp) REVERT: J 1152 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7617 (tm-30) REVERT: J 1231 ARG cc_start: 0.7632 (mtp85) cc_final: 0.6705 (mtt180) REVERT: K 35 LYS cc_start: 0.7674 (mptp) cc_final: 0.7410 (mmtt) REVERT: L 149 ASP cc_start: 0.5183 (OUTLIER) cc_final: 0.4542 (t0) REVERT: L 364 ARG cc_start: 0.8076 (mtm110) cc_final: 0.7621 (ptp-170) REVERT: L 456 MET cc_start: 0.8542 (tpp) cc_final: 0.8173 (tpt) REVERT: R 260 LEU cc_start: 0.5390 (OUTLIER) cc_final: 0.4899 (mt) outliers start: 107 outliers final: 68 residues processed: 360 average time/residue: 0.6728 time to fit residues: 286.1718 Evaluate side-chains 359 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 275 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 677 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1361 THR Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 134 optimal weight: 5.9990 chunk 229 optimal weight: 4.9990 chunk 311 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 351 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 152 optimal weight: 0.0870 chunk 215 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN I 649 GLN J 335 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.192824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.132012 restraints weight = 33596.842| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.99 r_work: 0.3271 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32740 Z= 0.160 Angle : 0.558 10.461 44722 Z= 0.291 Chirality : 0.042 0.206 5122 Planarity : 0.004 0.050 5408 Dihedral : 16.603 177.573 5687 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.99 % Allowed : 16.24 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % 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: -0.33 (0.14), residues: 3730 helix: 0.99 (0.14), residues: 1468 sheet: -0.56 (0.25), residues: 425 loop : -1.14 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J1372 TYR 0.015 0.001 TYR I1231 PHE 0.013 0.001 PHE I 645 TRP 0.004 0.001 TRP J 868 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00388 (32734) covalent geometry : angle 0.55850 (44722) hydrogen bonds : bond 0.03626 ( 1287) hydrogen bonds : angle 3.93132 ( 3517) metal coordination : bond 0.00308 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7460 Ramachandran restraints generated. 3730 Oldfield, 0 Emsley, 3730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 279 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7884 (tt) REVERT: G 33 ARG cc_start: 0.8851 (mmt180) cc_final: 0.8372 (ttp-110) REVERT: G 62 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7842 (t0) REVERT: G 101 THR cc_start: 0.8792 (m) cc_final: 0.8428 (p) REVERT: H 13 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6631 (pp) REVERT: H 38 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7638 (t) REVERT: H 143 ARG cc_start: 0.8422 (mtp-110) cc_final: 0.8030 (mtm-85) REVERT: H 183 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8451 (tp) REVERT: I 60 GLN cc_start: 0.7568 (mt0) cc_final: 0.7227 (mm-40) REVERT: I 119 GLU cc_start: 0.8451 (tt0) cc_final: 0.8153 (tt0) REVERT: I 200 ARG cc_start: 0.8630 (mtp85) cc_final: 0.8417 (mmm-85) REVERT: I 222 ASP cc_start: 0.7685 (t0) cc_final: 0.7462 (t0) REVERT: I 342 ASP cc_start: 0.8415 (t0) cc_final: 0.8163 (t70) REVERT: I 412 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: I 473 ARG cc_start: 0.7056 (mtp180) cc_final: 0.6844 (mtm180) REVERT: I 514 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: I 525 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8777 (p) REVERT: I 538 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8563 (pp) REVERT: I 895 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7559 (pp) REVERT: I 1143 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7754 (tp30) REVERT: I 1154 ASP cc_start: 0.8184 (t0) cc_final: 0.7820 (t0) REVERT: J 77 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6665 (mtm180) REVERT: J 151 MET cc_start: 0.6029 (OUTLIER) cc_final: 0.5271 (ppp) REVERT: J 225 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7750 (mm-30) REVERT: J 314 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7430 (ptt180) REVERT: J 388 ARG cc_start: 0.8358 (mmt90) cc_final: 0.8111 (mmt90) REVERT: J 390 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8412 (mt) REVERT: J 677 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6383 (mt-10) REVERT: J 680 ASN cc_start: 0.8296 (m-40) cc_final: 0.7491 (m110) REVERT: J 684 ASP cc_start: 0.7978 (m-30) cc_final: 0.7491 (m-30) REVERT: J 697 MET cc_start: 0.8463 (ttp) cc_final: 0.8248 (ttp) REVERT: J 992 LYS cc_start: 0.7359 (tppp) cc_final: 0.6440 (tppp) REVERT: J 1152 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7634 (tm-30) REVERT: J 1231 ARG cc_start: 0.7614 (mtp85) cc_final: 0.6663 (mtt180) REVERT: K 35 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7425 (mmtt) REVERT: L 149 ASP cc_start: 0.5120 (OUTLIER) cc_final: 0.4526 (t0) REVERT: L 364 ARG cc_start: 0.8078 (mtm110) cc_final: 0.7620 (ptp-170) REVERT: L 456 MET cc_start: 0.8512 (tpp) cc_final: 0.8218 (tpt) REVERT: R 260 LEU cc_start: 0.5201 (OUTLIER) cc_final: 0.4686 (mt) outliers start: 96 outliers final: 72 residues processed: 350 average time/residue: 0.6893 time to fit residues: 284.9713 Evaluate side-chains 369 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 278 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 895 LEU Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 677 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1284 ARG Chi-restraints excluded: chain J residue 1361 THR Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 70 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 272 optimal weight: 10.0000 chunk 262 optimal weight: 0.0670 chunk 294 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN I 649 GLN I1038 GLN J 335 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.192860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131437 restraints weight = 33600.657| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.02 r_work: 0.3273 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32740 Z= 0.153 Angle : 0.554 10.247 44722 Z= 0.289 Chirality : 0.041 0.205 5122 Planarity : 0.004 0.064 5408 Dihedral : 16.604 177.627 5687 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.30 % Allowed : 15.93 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.11 % 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: -0.32 (0.14), residues: 3730 helix: 1.00 (0.14), residues: 1475 sheet: -0.55 (0.25), residues: 425 loop : -1.13 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J1372 TYR 0.012 0.001 TYR H 152 PHE 0.015 0.001 PHE I 645 TRP 0.004 0.001 TRP R 321 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00369 (32734) covalent geometry : angle 0.55377 (44722) hydrogen bonds : bond 0.03559 ( 1287) hydrogen bonds : angle 3.91407 ( 3517) metal coordination : bond 0.00311 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13131.49 seconds wall clock time: 223 minutes 8.43 seconds (13388.43 seconds total)