Starting phenix.real_space_refine on Thu May 22 19:59:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hsh_34997/05_2025/8hsh_34997.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hsh_34997/05_2025/8hsh_34997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hsh_34997/05_2025/8hsh_34997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hsh_34997/05_2025/8hsh_34997.map" model { file = "/net/cci-nas-00/data/ceres_data/8hsh_34997/05_2025/8hsh_34997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hsh_34997/05_2025/8hsh_34997.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 62 5.16 5 C 14625 2.51 5 N 4081 2.21 5 O 4301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23072 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1806 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 214} Chain: "H" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1806 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 214} Chain: "I" Number of atoms: 8644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 8644 Classifications: {'peptide': 1096} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1025} Chain breaks: 1 Chain: "J" Number of atoms: 10078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 10078 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 62, 'TRANS': 1215} Chain breaks: 3 Chain: "K" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19413 SG CYS J1112 72.061 87.192 31.746 1.00132.11 S ATOM 20057 SG CYS J1194 71.350 87.254 35.503 1.00128.57 S ATOM 20113 SG CYS J1201 69.505 84.871 33.258 1.00129.94 S ATOM 20137 SG CYS J1204 72.882 84.054 33.956 1.00132.51 S Time building chain proxies: 11.96, per 1000 atoms: 0.52 Number of scatterers: 23072 At special positions: 0 Unit cell: (125.08, 184.44, 139.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 62 16.00 Mg 1 11.99 O 4301 8.00 N 4081 7.00 C 14625 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: 5.31 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1602 " pdb="ZN ZN J1602 " - pdb=" SG CYS J1201 " pdb="ZN ZN J1602 " - pdb=" SG CYS J1204 " pdb="ZN ZN J1602 " - pdb=" SG CYS J1194 " pdb="ZN ZN J1602 " - pdb=" SG CYS J1112 " Number of angles added : 6 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5396 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 40 sheets defined 39.0% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'G' and resid 31 through 47 removed outlier: 3.826A pdb=" N THR G 35 " --> pdb=" O GLY G 31 " (cutoff:3.500A) Proline residue: G 39 - end of helix Processing helix chain 'G' and resid 74 through 84 removed outlier: 3.887A pdb=" N GLU G 84 " --> pdb=" O LEU G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 114 removed outlier: 3.532A pdb=" N ASP G 113 " --> pdb=" O LYS G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 157 removed outlier: 3.935A pdb=" N HIS G 156 " --> pdb=" O PRO G 152 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY G 157 " --> pdb=" O ALA G 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 152 through 157' Processing helix chain 'G' and resid 206 through 223 Processing helix chain 'G' and resid 224 through 227 removed outlier: 3.866A pdb=" N ASN G 227 " --> pdb=" O TYR G 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 224 through 227' Processing helix chain 'H' and resid 31 through 47 removed outlier: 3.627A pdb=" N THR H 35 " --> pdb=" O GLY H 31 " (cutoff:3.500A) Proline residue: H 39 - end of helix Processing helix chain 'H' and resid 74 through 84 removed outlier: 4.110A pdb=" N GLU H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 152 through 157 removed outlier: 4.158A pdb=" N HIS H 156 " --> pdb=" O PRO H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 223 Processing helix chain 'H' and resid 224 through 226 No H-bonds generated for 'chain 'H' and resid 224 through 226' Processing helix chain 'I' and resid 19 through 30 removed outlier: 3.593A pdb=" N VAL I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 79 through 86 Processing helix chain 'I' and resid 193 through 200 Processing helix chain 'I' and resid 203 through 211 Processing helix chain 'I' and resid 215 through 217 No H-bonds generated for 'chain 'I' and resid 215 through 217' Processing helix chain 'I' and resid 218 through 223 Processing helix chain 'I' and resid 232 through 242 removed outlier: 3.576A pdb=" N ILE I 236 " --> pdb=" O GLU I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 279 removed outlier: 3.668A pdb=" N GLU I 279 " --> pdb=" O TYR I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 316 Processing helix chain 'I' and resid 327 through 329 No H-bonds generated for 'chain 'I' and resid 327 through 329' Processing helix chain 'I' and resid 335 through 362 Processing helix chain 'I' and resid 375 through 389 removed outlier: 3.741A pdb=" N SER I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 424 through 429 removed outlier: 4.454A pdb=" N ASP I 429 " --> pdb=" O PHE I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 431 through 435 removed outlier: 3.907A pdb=" N TYR I 435 " --> pdb=" O ARG I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 487 through 492 Processing helix chain 'I' and resid 525 through 529 Processing helix chain 'I' and resid 535 through 540 Processing helix chain 'I' and resid 543 through 547 removed outlier: 3.596A pdb=" N LEU I 546 " --> pdb=" O ASN I 543 " (cutoff:3.500A) Processing helix chain 'I' and resid 554 through 567 removed outlier: 3.501A pdb=" N THR I 566 " --> pdb=" O SER I 562 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN I 567 " --> pdb=" O ASN I 563 " (cutoff:3.500A) Processing helix chain 'I' and resid 583 through 591 Processing helix chain 'I' and resid 692 through 697 Processing helix chain 'I' and resid 732 through 737 removed outlier: 3.593A pdb=" N ARG I 735 " --> pdb=" O ALA I 732 " (cutoff:3.500A) Processing helix chain 'I' and resid 874 through 879 removed outlier: 3.814A pdb=" N SER I 878 " --> pdb=" O LEU I 874 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG I 879 " --> pdb=" O GLY I 875 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 874 through 879' Processing helix chain 'I' and resid 882 through 898 removed outlier: 3.605A pdb=" N PHE I 896 " --> pdb=" O LEU I 892 " (cutoff:3.500A) Processing helix chain 'I' and resid 910 through 932 removed outlier: 3.635A pdb=" N GLU I 932 " --> pdb=" O LYS I 928 " (cutoff:3.500A) Processing helix chain 'I' and resid 937 through 950 Processing helix chain 'I' and resid 958 through 969 Processing helix chain 'I' and resid 1034 through 1043 removed outlier: 3.517A pdb=" N TYR I1043 " --> pdb=" O ALA I1039 " (cutoff:3.500A) Processing helix chain 'I' and resid 1046 through 1054 Processing helix chain 'I' and resid 1059 through 1073 Processing helix chain 'I' and resid 1082 through 1095 removed outlier: 3.506A pdb=" N LEU I1095 " --> pdb=" O GLU I1091 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 22 Processing helix chain 'J' and resid 46 through 51 removed outlier: 3.513A pdb=" N PHE J 50 " --> pdb=" O ASP J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 89 Processing helix chain 'J' and resid 102 through 107 Processing helix chain 'J' and resid 110 through 116 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 155 through 163 removed outlier: 3.757A pdb=" N TYR J 163 " --> pdb=" O ARG J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 423 through 426 Processing helix chain 'J' and resid 456 through 468 removed outlier: 3.891A pdb=" N ALA J 460 " --> pdb=" O MET J 456 " (cutoff:3.500A) Processing helix chain 'J' and resid 469 through 483 Processing helix chain 'J' and resid 485 through 505 removed outlier: 3.576A pdb=" N ARG J 489 " --> pdb=" O SER J 485 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS J 491 " --> pdb=" O ALA J 487 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL J 498 " --> pdb=" O LYS J 494 " (cutoff:3.500A) Processing helix chain 'J' and resid 508 through 511 removed outlier: 3.738A pdb=" N TRP J 511 " --> pdb=" O ARG J 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 508 through 511' Processing helix chain 'J' and resid 521 through 525 Processing helix chain 'J' and resid 538 through 561 removed outlier: 3.964A pdb=" N ASP J 542 " --> pdb=" O SER J 538 " (cutoff:3.500A) Processing helix chain 'J' and resid 563 through 583 Processing helix chain 'J' and resid 602 through 608 Processing helix chain 'J' and resid 612 through 618 removed outlier: 3.907A pdb=" N ASN J 617 " --> pdb=" O ARG J 613 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU J 618 " --> pdb=" O PHE J 614 " (cutoff:3.500A) Processing helix chain 'J' and resid 646 through 653 removed outlier: 3.522A pdb=" N PHE J 653 " --> pdb=" O ALA J 649 " (cutoff:3.500A) Processing helix chain 'J' and resid 653 through 664 removed outlier: 3.569A pdb=" N LYS J 664 " --> pdb=" O LYS J 660 " (cutoff:3.500A) Processing helix chain 'J' and resid 669 through 678 Processing helix chain 'J' and resid 679 through 683 removed outlier: 3.621A pdb=" N ASP J 682 " --> pdb=" O ARG J 679 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE J 683 " --> pdb=" O GLN J 680 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 679 through 683' Processing helix chain 'J' and resid 684 through 695 Processing helix chain 'J' and resid 709 through 711 No H-bonds generated for 'chain 'J' and resid 709 through 711' Processing helix chain 'J' and resid 729 through 734 removed outlier: 4.243A pdb=" N GLU J 734 " --> pdb=" O LEU J 731 " (cutoff:3.500A) Processing helix chain 'J' and resid 752 through 763 Processing helix chain 'J' and resid 782 through 793 Processing helix chain 'J' and resid 810 through 822 removed outlier: 4.460A pdb=" N ALA J 814 " --> pdb=" O GLU J 810 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 841 Processing helix chain 'J' and resid 845 through 855 Processing helix chain 'J' and resid 876 through 890 Processing helix chain 'J' and resid 893 through 899 Processing helix chain 'J' and resid 907 through 923 Processing helix chain 'J' and resid 924 through 946 removed outlier: 3.650A pdb=" N GLY J 946 " --> pdb=" O SER J 942 " (cutoff:3.500A) Processing helix chain 'J' and resid 959 through 980 Processing helix chain 'J' and resid 984 through 1015 removed outlier: 3.588A pdb=" N GLU J1001 " --> pdb=" O THR J 997 " (cutoff:3.500A) Processing helix chain 'J' and resid 1018 through 1026 Processing helix chain 'J' and resid 1031 through 1040 Processing helix chain 'J' and resid 1066 through 1102 removed outlier: 3.956A pdb=" N HIS J1075 " --> pdb=" O PHE J1071 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY J1076 " --> pdb=" O ILE J1072 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA J1089 " --> pdb=" O ALA J1085 " (cutoff:3.500A) Processing helix chain 'J' and resid 1136 through 1145 Processing helix chain 'J' and resid 1167 through 1181 Processing helix chain 'J' and resid 1190 through 1194 Processing helix chain 'J' and resid 1201 through 1206 Processing helix chain 'J' and resid 1220 through 1231 removed outlier: 3.658A pdb=" N VAL J1224 " --> pdb=" O ALA J1220 " (cutoff:3.500A) Processing helix chain 'J' and resid 1232 through 1236 Processing helix chain 'J' and resid 1256 through 1264 Processing helix chain 'J' and resid 1331 through 1339 Processing helix chain 'J' and resid 1340 through 1359 removed outlier: 3.724A pdb=" N VAL J1355 " --> pdb=" O GLU J1351 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR J1356 " --> pdb=" O ILE J1352 " (cutoff:3.500A) Processing helix chain 'J' and resid 1364 through 1376 removed outlier: 4.549A pdb=" N ILE J1368 " --> pdb=" O HIS J1364 " (cutoff:3.500A) Processing helix chain 'J' and resid 1395 through 1407 Processing helix chain 'J' and resid 1423 through 1430 Processing helix chain 'J' and resid 1433 through 1441 removed outlier: 4.089A pdb=" N ALA J1437 " --> pdb=" O SER J1433 " (cutoff:3.500A) Processing helix chain 'J' and resid 1442 through 1453 removed outlier: 3.567A pdb=" N VAL J1446 " --> pdb=" O ASN J1442 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA J1453 " --> pdb=" O GLU J1449 " (cutoff:3.500A) Processing helix chain 'J' and resid 1461 through 1469 removed outlier: 4.080A pdb=" N ASN J1465 " --> pdb=" O GLY J1461 " (cutoff:3.500A) Processing helix chain 'J' and resid 1474 through 1477 Processing helix chain 'J' and resid 1478 through 1483 removed outlier: 4.640A pdb=" N PHE J1483 " --> pdb=" O ASP J1479 " (cutoff:3.500A) Processing helix chain 'J' and resid 1489 through 1503 Processing helix chain 'K' and resid 5 through 12 removed outlier: 3.525A pdb=" N MET K 12 " --> pdb=" O LYS K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 33 Processing helix chain 'K' and resid 52 through 56 Processing helix chain 'K' and resid 59 through 70 removed outlier: 4.047A pdb=" N THR K 70 " --> pdb=" O LYS K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 90 removed outlier: 4.019A pdb=" N LEU K 85 " --> pdb=" O PRO K 81 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU K 90 " --> pdb=" O GLN K 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 10 through 16 removed outlier: 3.513A pdb=" N TYR G 20 " --> pdb=" O GLN G 16 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TYR G 20 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR G 201 " --> pdb=" O TYR G 20 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLU G 22 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE G 199 " --> pdb=" O GLU G 22 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL G 24 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU G 197 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLU G 26 " --> pdb=" O LEU G 195 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU G 195 " --> pdb=" O GLU G 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 96 through 103 removed outlier: 7.636A pdb=" N ASN G 139 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ILE G 58 " --> pdb=" O ASN G 139 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU G 141 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL G 56 " --> pdb=" O GLU G 141 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG G 143 " --> pdb=" O THR G 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'G' and resid 150 through 151 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 16 removed outlier: 3.608A pdb=" N TYR H 20 " --> pdb=" O GLN H 16 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N TYR H 20 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR H 201 " --> pdb=" O TYR H 20 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLU H 22 " --> pdb=" O ILE H 199 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE H 199 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL H 24 " --> pdb=" O LEU H 197 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU H 197 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLU H 26 " --> pdb=" O LEU H 195 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LEU H 195 " --> pdb=" O GLU H 26 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU H 192 " --> pdb=" O THR H 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 96 through 103 removed outlier: 7.588A pdb=" N ASN H 139 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE H 58 " --> pdb=" O ASN H 139 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU H 141 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL H 56 " --> pdb=" O GLU H 141 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG H 143 " --> pdb=" O THR H 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA8, first strand: chain 'H' and resid 108 through 110 Processing sheet with id=AA9, first strand: chain 'H' and resid 150 through 151 Processing sheet with id=AB1, first strand: chain 'I' and resid 2 through 5 removed outlier: 6.208A pdb=" N GLU I 2 " --> pdb=" O ARG I 900 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE I 902 " --> pdb=" O GLU I 2 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LYS I 4 " --> pdb=" O ILE I 902 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 65 through 72 removed outlier: 5.146A pdb=" N LEU I 66 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE I 101 " --> pdb=" O LEU I 66 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N PHE I 68 " --> pdb=" O GLN I 99 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN I 99 " --> pdb=" O PHE I 68 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU I 70 " --> pdb=" O ARG I 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 65 through 72 removed outlier: 5.146A pdb=" N LEU I 66 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE I 101 " --> pdb=" O LEU I 66 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N PHE I 68 " --> pdb=" O GLN I 99 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN I 99 " --> pdb=" O PHE I 68 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU I 70 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLY I 116 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA I 96 " --> pdb=" O PHE I 114 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE I 114 " --> pdb=" O ALA I 96 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AB5, first strand: chain 'I' and resid 331 through 334 removed outlier: 6.588A pdb=" N SER I 138 " --> pdb=" O SER I 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 145 through 150 removed outlier: 6.125A pdb=" N TYR I 158 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL I 176 " --> pdb=" O TYR I 158 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP I 173 " --> pdb=" O LYS I 185 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS I 185 " --> pdb=" O ASP I 173 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 460 through 461 removed outlier: 5.544A pdb=" N GLU I 482 " --> pdb=" O ARG I 473 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL I 475 " --> pdb=" O THR I 480 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR I 480 " --> pdb=" O VAL I 475 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 460 through 461 Processing sheet with id=AB9, first strand: chain 'I' and resid 513 through 516 Processing sheet with id=AC1, first strand: chain 'I' and resid 595 through 596 removed outlier: 6.488A pdb=" N LEU I 595 " --> pdb=" O LEU I 655 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 620 through 624 removed outlier: 5.760A pdb=" N ARG I 614 " --> pdb=" O VAL I 603 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL I 603 " --> pdb=" O ARG I 614 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 629 through 630 Processing sheet with id=AC4, first strand: chain 'I' and resid 971 through 972 removed outlier: 7.330A pdb=" N ILE I 688 " --> pdb=" O ALA I 850 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE I 852 " --> pdb=" O ILE I 688 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE I 690 " --> pdb=" O ILE I 852 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N VAL I 869 " --> pdb=" O ASN I 671 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU I 673 " --> pdb=" O VAL I 869 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU I 871 " --> pdb=" O LEU I 673 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA I 675 " --> pdb=" O LEU I 871 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL I 988 " --> pdb=" O ILE I 676 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 701 through 713 removed outlier: 7.611A pdb=" N ARG I 820 " --> pdb=" O ARG I 807 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG I 807 " --> pdb=" O ARG I 820 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL I 822 " --> pdb=" O ARG I 805 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ARG I 805 " --> pdb=" O VAL I 822 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG I 824 " --> pdb=" O THR I 803 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR I 803 " --> pdb=" O ARG I 824 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR I 826 " --> pdb=" O VAL I 801 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 721 through 722 Processing sheet with id=AC7, first strand: chain 'I' and resid 754 through 756 removed outlier: 6.827A pdb=" N LEU I 790 " --> pdb=" O LEU I 755 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 1108 through 1109 removed outlier: 4.170A pdb=" N THR I1101 " --> pdb=" O VAL I1109 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN I1100 " --> pdb=" O ARG J 9 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS J 7 " --> pdb=" O LEU I1102 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE J 10 " --> pdb=" O LYS J1455 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 91 through 100 removed outlier: 3.566A pdb=" N LEU J 95 " --> pdb=" O GLU J 515 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU J 515 " --> pdb=" O LEU J 95 " (cutoff:3.500A) removed outlier: 11.403A pdb=" N THR J 97 " --> pdb=" O ILE J 513 " (cutoff:3.500A) removed outlier: 10.876A pdb=" N ILE J 513 " --> pdb=" O THR J 97 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 132 through 134 removed outlier: 3.539A pdb=" N LEU J 153 " --> pdb=" O ILE J 133 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 167 through 170 removed outlier: 3.642A pdb=" N GLU J 183 " --> pdb=" O ALA J 203 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 399 through 402 Processing sheet with id=AD4, first strand: chain 'J' and resid 420 through 422 removed outlier: 7.598A pdb=" N VAL J 427 " --> pdb=" O LEU J 421 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 528 through 529 Processing sheet with id=AD6, first strand: chain 'J' and resid 626 through 633 removed outlier: 7.661A pdb=" N ILE J 726 " --> pdb=" O ARG J 628 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL J 630 " --> pdb=" O ILE J 726 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU J 728 " --> pdb=" O VAL J 630 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL J 632 " --> pdb=" O LEU J 728 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 842 through 843 removed outlier: 7.183A pdb=" N PHE J 843 " --> pdb=" O ARG J 867 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 1118 through 1121 Processing sheet with id=AD9, first strand: chain 'J' and resid 1123 through 1124 removed outlier: 3.811A pdb=" N ARG J1133 " --> pdb=" O GLN J1124 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 1153 through 1154 Processing sheet with id=AE2, first strand: chain 'J' and resid 1300 through 1305 Processing sheet with id=AE3, first strand: chain 'J' and resid 1392 through 1394 removed outlier: 4.580A pdb=" N TYR J1378 " --> pdb=" O LEU J1420 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 1485 through 1488 939 hydrogen bonds defined for protein. 2631 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.65 Time building geometry restraints manager: 6.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7616 1.34 - 1.46: 2951 1.46 - 1.58: 12793 1.58 - 1.70: 2 1.70 - 1.82: 115 Bond restraints: 23477 Sorted by residual: bond pdb=" CB PRO J 39 " pdb=" CG PRO J 39 " ideal model delta sigma weight residual 1.492 1.609 -0.117 5.00e-02 4.00e+02 5.47e+00 bond pdb=" CB PRO G 9 " pdb=" CG PRO G 9 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 4.03e+00 bond pdb=" CG GLN K 29 " pdb=" CD GLN K 29 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.58e+00 bond pdb=" C ASP I 857 " pdb=" N MET I 858 " ideal model delta sigma weight residual 1.339 1.262 0.077 5.57e-02 3.22e+02 1.92e+00 bond pdb=" C ILE I 852 " pdb=" N LEU I 853 " ideal model delta sigma weight residual 1.331 1.296 0.035 2.83e-02 1.25e+03 1.54e+00 ... (remaining 23472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 31184 2.20 - 4.40: 489 4.40 - 6.60: 67 6.60 - 8.80: 9 8.80 - 11.00: 6 Bond angle restraints: 31755 Sorted by residual: angle pdb=" CA PRO J 39 " pdb=" N PRO J 39 " pdb=" CD PRO J 39 " ideal model delta sigma weight residual 112.00 104.87 7.13 1.40e+00 5.10e-01 2.60e+01 angle pdb=" N VAL I 254 " pdb=" CA VAL I 254 " pdb=" C VAL I 254 " ideal model delta sigma weight residual 113.53 108.55 4.98 9.80e-01 1.04e+00 2.58e+01 angle pdb=" C HIS I 117 " pdb=" N ILE I 118 " pdb=" CA ILE I 118 " ideal model delta sigma weight residual 123.43 118.45 4.98 1.10e+00 8.26e-01 2.05e+01 angle pdb=" CA PRO G 9 " pdb=" N PRO G 9 " pdb=" CD PRO G 9 " ideal model delta sigma weight residual 112.00 105.97 6.03 1.40e+00 5.10e-01 1.85e+01 angle pdb=" N GLN K 29 " pdb=" CA GLN K 29 " pdb=" CB GLN K 29 " ideal model delta sigma weight residual 110.16 116.23 -6.07 1.48e+00 4.57e-01 1.68e+01 ... (remaining 31750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 13199 17.82 - 35.64: 1065 35.64 - 53.45: 145 53.45 - 71.27: 37 71.27 - 89.09: 14 Dihedral angle restraints: 14460 sinusoidal: 6068 harmonic: 8392 Sorted by residual: dihedral pdb=" CA GLU J1109 " pdb=" C GLU J1109 " pdb=" N ALA J1110 " pdb=" CA ALA J1110 " ideal model delta harmonic sigma weight residual 180.00 142.36 37.64 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CA ASP J 136 " pdb=" C ASP J 136 " pdb=" N PRO J 137 " pdb=" CA PRO J 137 " ideal model delta harmonic sigma weight residual -180.00 -149.93 -30.07 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA VAL I1081 " pdb=" C VAL I1081 " pdb=" N PRO I1082 " pdb=" CA PRO I1082 " ideal model delta harmonic sigma weight residual 180.00 -150.85 -29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 14457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2871 0.056 - 0.113: 644 0.113 - 0.169: 74 0.169 - 0.226: 0 0.226 - 0.282: 1 Chirality restraints: 3590 Sorted by residual: chirality pdb=" CB ILE I 163 " pdb=" CA ILE I 163 " pdb=" CG1 ILE I 163 " pdb=" CG2 ILE I 163 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE I 21 " pdb=" CA ILE I 21 " pdb=" CG1 ILE I 21 " pdb=" CG2 ILE I 21 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CA ILE G 58 " pdb=" N ILE G 58 " pdb=" C ILE G 58 " pdb=" CB ILE G 58 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 3587 not shown) Planarity restraints: 4170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 38 " 0.081 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO J 39 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO J 39 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO J 39 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 8 " -0.056 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO G 9 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO G 9 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 9 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 309 " 0.027 2.00e-02 2.50e+03 1.97e-02 7.78e+00 pdb=" CG TYR I 309 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR I 309 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR I 309 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR I 309 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR I 309 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR I 309 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR I 309 " 0.003 2.00e-02 2.50e+03 ... (remaining 4167 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 331 2.62 - 3.19: 21194 3.19 - 3.76: 36116 3.76 - 4.33: 49649 4.33 - 4.90: 80215 Nonbonded interactions: 187505 Sorted by model distance: nonbonded pdb=" OD1 ASP J 741 " pdb="MG MG J1603 " model vdw 2.046 2.170 nonbonded pdb=" OD1 ASP J 739 " pdb="MG MG J1603 " model vdw 2.072 2.170 nonbonded pdb=" OH TYR J1378 " pdb=" O SER J1430 " model vdw 2.099 3.040 nonbonded pdb=" O ALA I1116 " pdb=" OH TYR J 23 " model vdw 2.107 3.040 nonbonded pdb=" OG SER I 525 " pdb=" OE1 GLU I 528 " model vdw 2.112 3.040 ... (remaining 187500 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' selection = chain 'H' } 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 55.510 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 0.004 0.117 23481 Z= 0.180 Angle : 0.699 11.000 31761 Z= 0.365 Chirality : 0.046 0.282 3590 Planarity : 0.005 0.118 4170 Dihedral : 13.144 89.088 9064 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.08 % Allowed : 0.24 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.16), residues: 2905 helix: 0.34 (0.17), residues: 959 sheet: -0.53 (0.25), residues: 424 loop : -1.16 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP J 21 HIS 0.014 0.001 HIS K 33 PHE 0.035 0.002 PHE J 754 TYR 0.047 0.002 TYR I 309 ARG 0.005 0.000 ARG I1031 Details of bonding type rmsd hydrogen bonds : bond 0.15025 ( 934) hydrogen bonds : angle 6.64817 ( 2631) metal coordination : bond 0.01218 ( 4) metal coordination : angle 4.83554 ( 6) covalent geometry : bond 0.00410 (23477) covalent geometry : angle 0.69600 (31755) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 123 MET cc_start: 0.8658 (mpp) cc_final: 0.8167 (mpp) REVERT: I 580 MET cc_start: 0.8804 (mtm) cc_final: 0.8476 (mtm) REVERT: I 880 MET cc_start: 0.7716 (mpp) cc_final: 0.7434 (mpp) REVERT: I 1041 GLU cc_start: 0.8717 (tt0) cc_final: 0.8411 (tp30) REVERT: I 1052 MET cc_start: 0.8698 (ttm) cc_final: 0.8451 (ttm) REVERT: I 1067 TYR cc_start: 0.9144 (t80) cc_final: 0.8925 (t80) REVERT: I 1111 ILE cc_start: 0.9092 (mp) cc_final: 0.8561 (tt) REVERT: J 21 TRP cc_start: 0.7918 (m-10) cc_final: 0.7144 (m-10) REVERT: J 41 ARG cc_start: 0.8695 (tpm170) cc_final: 0.8332 (ptp-170) REVERT: J 456 MET cc_start: 0.6130 (mmm) cc_final: 0.5410 (tpt) REVERT: J 573 MET cc_start: 0.5980 (ttp) cc_final: 0.5469 (tpp) REVERT: J 661 MET cc_start: 0.8420 (ppp) cc_final: 0.8033 (ppp) REVERT: K 52 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7623 (mm-30) outliers start: 2 outliers final: 0 residues processed: 161 average time/residue: 0.3191 time to fit residues: 84.1323 Evaluate side-chains 117 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 244 optimal weight: 0.0270 chunk 219 optimal weight: 30.0000 chunk 121 optimal weight: 0.0170 chunk 74 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 226 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 262 optimal weight: 4.9990 overall best weight: 1.3880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 212 ASN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 617 ASN ** J1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.079540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.054544 restraints weight = 88148.204| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 4.65 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23481 Z= 0.149 Angle : 0.646 15.693 31761 Z= 0.321 Chirality : 0.045 0.197 3590 Planarity : 0.005 0.073 4170 Dihedral : 5.198 36.917 3237 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.56 % Allowed : 7.33 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.16), residues: 2905 helix: 0.42 (0.17), residues: 991 sheet: -0.49 (0.26), residues: 404 loop : -1.00 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J1398 HIS 0.008 0.001 HIS I 999 PHE 0.026 0.001 PHE J 806 TYR 0.027 0.002 TYR J1207 ARG 0.006 0.000 ARG I 274 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 934) hydrogen bonds : angle 5.39158 ( 2631) metal coordination : bond 0.00866 ( 4) metal coordination : angle 3.89419 ( 6) covalent geometry : bond 0.00341 (23477) covalent geometry : angle 0.64425 (31755) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 2.435 Fit side-chains revert: symmetry clash REVERT: G 123 MET cc_start: 0.8684 (mpp) cc_final: 0.8153 (mpp) REVERT: I 1 MET cc_start: 0.7221 (tmm) cc_final: 0.6898 (ttp) REVERT: I 158 TYR cc_start: 0.5485 (OUTLIER) cc_final: 0.4682 (p90) REVERT: I 580 MET cc_start: 0.8749 (mtm) cc_final: 0.8546 (mtm) REVERT: I 880 MET cc_start: 0.7820 (mpp) cc_final: 0.7600 (mpp) REVERT: I 1041 GLU cc_start: 0.8741 (tt0) cc_final: 0.8233 (pt0) REVERT: I 1111 ILE cc_start: 0.9018 (mp) cc_final: 0.8592 (tt) REVERT: J 41 ARG cc_start: 0.8927 (tpm170) cc_final: 0.8518 (ptp-170) REVERT: J 512 MET cc_start: 0.8743 (tmm) cc_final: 0.8488 (tmm) REVERT: K 44 GLU cc_start: 0.8996 (tp30) cc_final: 0.8038 (pm20) REVERT: K 52 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7565 (mm-30) outliers start: 14 outliers final: 5 residues processed: 143 average time/residue: 0.2979 time to fit residues: 72.9553 Evaluate side-chains 124 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 202 TYR Chi-restraints excluded: chain I residue 227 PHE Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain J residue 829 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 226 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 283 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1093 GLN ** J1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.077579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.052542 restraints weight = 88479.056| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 4.63 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 23481 Z= 0.217 Angle : 0.664 14.728 31761 Z= 0.331 Chirality : 0.045 0.162 3590 Planarity : 0.005 0.063 4170 Dihedral : 5.236 39.301 3237 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.17 % Allowed : 11.63 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2905 helix: 0.44 (0.17), residues: 996 sheet: -0.52 (0.26), residues: 421 loop : -1.06 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP J 21 HIS 0.009 0.001 HIS I 889 PHE 0.039 0.002 PHE J 806 TYR 0.030 0.002 TYR J1207 ARG 0.005 0.000 ARG I 274 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 934) hydrogen bonds : angle 5.27645 ( 2631) metal coordination : bond 0.01388 ( 4) metal coordination : angle 4.12989 ( 6) covalent geometry : bond 0.00497 (23477) covalent geometry : angle 0.66156 (31755) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 2.442 Fit side-chains REVERT: G 123 MET cc_start: 0.8737 (mpp) cc_final: 0.8228 (mpp) REVERT: H 7 LYS cc_start: 0.7813 (pttp) cc_final: 0.7519 (pttp) REVERT: I 158 TYR cc_start: 0.5775 (OUTLIER) cc_final: 0.4821 (p90) REVERT: I 275 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.8413 (m-10) REVERT: I 880 MET cc_start: 0.7861 (mpp) cc_final: 0.7576 (mpp) REVERT: I 1041 GLU cc_start: 0.8821 (tt0) cc_final: 0.8464 (tp30) REVERT: I 1083 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6849 (tp30) REVERT: I 1111 ILE cc_start: 0.9051 (mp) cc_final: 0.8657 (tt) REVERT: J 21 TRP cc_start: 0.8221 (m-10) cc_final: 0.7480 (m-10) REVERT: J 41 ARG cc_start: 0.8901 (tpm170) cc_final: 0.8503 (ptp-170) REVERT: J 512 MET cc_start: 0.8690 (tmm) cc_final: 0.8461 (tmm) REVERT: J 924 MET cc_start: 0.9184 (mmm) cc_final: 0.8897 (mmp) REVERT: K 29 GLN cc_start: 0.9468 (mp10) cc_final: 0.9075 (mp10) REVERT: K 74 VAL cc_start: 0.9171 (t) cc_final: 0.8743 (m) outliers start: 29 outliers final: 10 residues processed: 142 average time/residue: 0.2919 time to fit residues: 70.6124 Evaluate side-chains 123 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 202 TYR Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain I residue 997 LEU Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1483 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 5 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 247 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 169 optimal weight: 0.0870 chunk 41 optimal weight: 3.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 31 GLN ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1075 HIS ** J1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.077363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.052251 restraints weight = 89082.909| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 4.66 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 23481 Z= 0.176 Angle : 0.622 15.475 31761 Z= 0.308 Chirality : 0.044 0.212 3590 Planarity : 0.004 0.070 4170 Dihedral : 5.133 39.600 3237 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.25 % Allowed : 14.01 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 2905 helix: 0.58 (0.17), residues: 998 sheet: -0.55 (0.26), residues: 422 loop : -1.03 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J1398 HIS 0.006 0.001 HIS I 889 PHE 0.032 0.002 PHE J 806 TYR 0.029 0.002 TYR J1207 ARG 0.004 0.000 ARG I 274 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 934) hydrogen bonds : angle 5.10383 ( 2631) metal coordination : bond 0.01016 ( 4) metal coordination : angle 4.15667 ( 6) covalent geometry : bond 0.00405 (23477) covalent geometry : angle 0.61991 (31755) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 123 MET cc_start: 0.8760 (mpp) cc_final: 0.8141 (mpp) REVERT: H 1 MET cc_start: 0.8949 (ppp) cc_final: 0.8134 (ppp) REVERT: I 158 TYR cc_start: 0.5956 (OUTLIER) cc_final: 0.5081 (p90) REVERT: I 275 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.8382 (m-10) REVERT: I 880 MET cc_start: 0.7847 (mpp) cc_final: 0.7510 (mpp) REVERT: I 1041 GLU cc_start: 0.8793 (tt0) cc_final: 0.8434 (tp30) REVERT: I 1059 ASP cc_start: 0.7250 (OUTLIER) cc_final: 0.6917 (t0) REVERT: I 1111 ILE cc_start: 0.9055 (mp) cc_final: 0.8665 (tt) REVERT: J 21 TRP cc_start: 0.8270 (m-10) cc_final: 0.7548 (m-10) REVERT: J 41 ARG cc_start: 0.8874 (tpm170) cc_final: 0.8475 (ptp-170) REVERT: J 512 MET cc_start: 0.8694 (tmm) cc_final: 0.8386 (tmm) REVERT: J 625 TYR cc_start: 0.8242 (m-80) cc_final: 0.8001 (m-80) REVERT: J 657 LEU cc_start: 0.9500 (mm) cc_final: 0.9195 (mm) REVERT: J 661 MET cc_start: 0.9400 (ptp) cc_final: 0.8809 (ptp) REVERT: K 44 GLU cc_start: 0.8939 (tp30) cc_final: 0.8015 (pm20) REVERT: K 74 VAL cc_start: 0.9166 (t) cc_final: 0.8748 (m) outliers start: 31 outliers final: 11 residues processed: 152 average time/residue: 0.3119 time to fit residues: 80.1718 Evaluate side-chains 126 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 202 TYR Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 963 LEU Chi-restraints excluded: chain I residue 997 LEU Chi-restraints excluded: chain I residue 1059 ASP Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 1483 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 170 optimal weight: 50.0000 chunk 54 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 46 optimal weight: 0.0870 chunk 184 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 22 GLN ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.077917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.052854 restraints weight = 88286.028| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 4.65 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23481 Z= 0.134 Angle : 0.596 14.587 31761 Z= 0.294 Chirality : 0.044 0.361 3590 Planarity : 0.004 0.069 4170 Dihedral : 4.995 39.173 3237 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.61 % Allowed : 15.30 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2905 helix: 0.68 (0.17), residues: 997 sheet: -0.41 (0.26), residues: 412 loop : -0.95 (0.17), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J1398 HIS 0.004 0.001 HIS J1364 PHE 0.022 0.001 PHE J 806 TYR 0.026 0.001 TYR J1207 ARG 0.007 0.000 ARG K 32 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 934) hydrogen bonds : angle 4.97897 ( 2631) metal coordination : bond 0.00613 ( 4) metal coordination : angle 4.11431 ( 6) covalent geometry : bond 0.00311 (23477) covalent geometry : angle 0.59303 (31755) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 3.129 Fit side-chains revert: symmetry clash REVERT: G 123 MET cc_start: 0.8765 (mpp) cc_final: 0.8148 (mpp) REVERT: H 1 MET cc_start: 0.8876 (ppp) cc_final: 0.7945 (ppp) REVERT: H 7 LYS cc_start: 0.7891 (pttp) cc_final: 0.7457 (pttp) REVERT: I 158 TYR cc_start: 0.6079 (OUTLIER) cc_final: 0.5220 (p90) REVERT: I 275 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8323 (m-10) REVERT: I 532 MET cc_start: 0.8593 (ttt) cc_final: 0.8263 (ttt) REVERT: I 731 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8401 (mm-30) REVERT: I 880 MET cc_start: 0.7868 (mpp) cc_final: 0.7556 (mpp) REVERT: I 1005 MET cc_start: 0.7413 (mtt) cc_final: 0.7141 (mtm) REVERT: I 1041 GLU cc_start: 0.8857 (tt0) cc_final: 0.8552 (tp30) REVERT: I 1059 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6932 (t0) REVERT: I 1081 VAL cc_start: 0.7948 (OUTLIER) cc_final: 0.7656 (m) REVERT: I 1085 PHE cc_start: 0.8344 (t80) cc_final: 0.8129 (t80) REVERT: I 1111 ILE cc_start: 0.9055 (mp) cc_final: 0.8743 (tp) REVERT: J 21 TRP cc_start: 0.8247 (m-10) cc_final: 0.7572 (m-10) REVERT: J 41 ARG cc_start: 0.8874 (tpm170) cc_final: 0.8474 (ptp-170) REVERT: J 512 MET cc_start: 0.8708 (tmm) cc_final: 0.8396 (tmm) REVERT: J 657 LEU cc_start: 0.9473 (mm) cc_final: 0.9217 (mm) REVERT: J 661 MET cc_start: 0.9327 (ptp) cc_final: 0.9106 (ptt) REVERT: K 44 GLU cc_start: 0.8929 (tp30) cc_final: 0.7993 (pm20) REVERT: K 74 VAL cc_start: 0.9181 (t) cc_final: 0.8828 (m) outliers start: 40 outliers final: 20 residues processed: 159 average time/residue: 0.3085 time to fit residues: 85.6416 Evaluate side-chains 140 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 202 TYR Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 963 LEU Chi-restraints excluded: chain I residue 997 LEU Chi-restraints excluded: chain I residue 999 HIS Chi-restraints excluded: chain I residue 1059 ASP Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1081 VAL Chi-restraints excluded: chain J residue 648 MET Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1219 GLU Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain K residue 40 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 37 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 chunk 216 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 284 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 117 HIS ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 575 GLN I 728 HIS J1227 GLN ** J1364 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 = 0.3748 r_free = 0.3748 target = 0.074582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.049665 restraints weight = 89714.615| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 4.61 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.167 23481 Z= 0.348 Angle : 0.776 13.852 31761 Z= 0.388 Chirality : 0.049 0.311 3590 Planarity : 0.006 0.070 4170 Dihedral : 5.490 41.860 3237 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.54 % Allowed : 15.66 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 2905 helix: 0.35 (0.17), residues: 978 sheet: -0.69 (0.26), residues: 418 loop : -1.26 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP J1398 HIS 0.009 0.002 HIS I 406 PHE 0.030 0.002 PHE J 806 TYR 0.034 0.002 TYR J1207 ARG 0.013 0.001 ARG K 32 Details of bonding type rmsd hydrogen bonds : bond 0.04731 ( 934) hydrogen bonds : angle 5.42634 ( 2631) metal coordination : bond 0.02046 ( 4) metal coordination : angle 5.07595 ( 6) covalent geometry : bond 0.00796 (23477) covalent geometry : angle 0.77264 (31755) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 119 time to evaluate : 2.858 Fit side-chains revert: symmetry clash REVERT: G 123 MET cc_start: 0.8810 (mpp) cc_final: 0.8236 (mpp) REVERT: H 1 MET cc_start: 0.8928 (ppp) cc_final: 0.7899 (ppp) REVERT: H 183 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8411 (t0) REVERT: I 158 TYR cc_start: 0.6587 (OUTLIER) cc_final: 0.5833 (p90) REVERT: I 275 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8457 (m-10) REVERT: I 348 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7948 (mp) REVERT: I 880 MET cc_start: 0.7842 (mpp) cc_final: 0.7490 (mpp) REVERT: I 944 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9136 (mm) REVERT: I 1005 MET cc_start: 0.7250 (mtt) cc_final: 0.7006 (mtm) REVERT: I 1041 GLU cc_start: 0.8954 (tt0) cc_final: 0.8678 (tp30) REVERT: I 1059 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6842 (t0) REVERT: I 1081 VAL cc_start: 0.8097 (OUTLIER) cc_final: 0.7794 (m) REVERT: I 1111 ILE cc_start: 0.9087 (mp) cc_final: 0.8815 (tp) REVERT: J 21 TRP cc_start: 0.8349 (m-10) cc_final: 0.7537 (m-10) REVERT: J 41 ARG cc_start: 0.8785 (tpm170) cc_final: 0.8376 (ptp-170) REVERT: J 512 MET cc_start: 0.8757 (tmm) cc_final: 0.8430 (tmm) REVERT: J 796 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8460 (ptp-170) REVERT: K 29 GLN cc_start: 0.9545 (mt0) cc_final: 0.9015 (mp10) REVERT: K 31 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9224 (mm) REVERT: K 44 GLU cc_start: 0.8900 (tp30) cc_final: 0.8023 (pm20) REVERT: K 74 VAL cc_start: 0.9200 (t) cc_final: 0.8892 (m) outliers start: 63 outliers final: 37 residues processed: 177 average time/residue: 0.3177 time to fit residues: 95.5184 Evaluate side-chains 155 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 109 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 183 ASP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 175 GLU Chi-restraints excluded: chain I residue 227 PHE Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 321 GLU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 569 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 668 LEU Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 944 LEU Chi-restraints excluded: chain I residue 963 LEU Chi-restraints excluded: chain I residue 997 LEU Chi-restraints excluded: chain I residue 1059 ASP Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1081 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 648 MET Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 796 ARG Chi-restraints excluded: chain J residue 827 ILE Chi-restraints excluded: chain J residue 836 VAL Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 873 LEU Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1435 LEU Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 40 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 33 optimal weight: 10.0000 chunk 233 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 chunk 219 optimal weight: 0.4980 chunk 183 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 210 optimal weight: 0.7980 chunk 265 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 102 HIS ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.077141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.052175 restraints weight = 88359.622| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 4.63 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23481 Z= 0.127 Angle : 0.623 12.896 31761 Z= 0.308 Chirality : 0.045 0.404 3590 Planarity : 0.005 0.072 4170 Dihedral : 5.126 41.420 3237 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.85 % Allowed : 16.75 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 2905 helix: 0.63 (0.17), residues: 983 sheet: -0.61 (0.26), residues: 404 loop : -1.07 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J1398 HIS 0.007 0.001 HIS I 999 PHE 0.026 0.001 PHE J 806 TYR 0.028 0.001 TYR J1207 ARG 0.008 0.000 ARG K 32 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 934) hydrogen bonds : angle 5.02099 ( 2631) metal coordination : bond 0.00428 ( 4) metal coordination : angle 4.31127 ( 6) covalent geometry : bond 0.00294 (23477) covalent geometry : angle 0.62014 (31755) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 123 time to evaluate : 2.560 Fit side-chains REVERT: G 123 MET cc_start: 0.8808 (mpp) cc_final: 0.8218 (mpp) REVERT: H 1 MET cc_start: 0.8891 (ppp) cc_final: 0.7818 (ppp) REVERT: H 7 LYS cc_start: 0.7768 (pttp) cc_final: 0.7492 (pttp) REVERT: I 102 HIS cc_start: 0.5335 (OUTLIER) cc_final: 0.5134 (m-70) REVERT: I 158 TYR cc_start: 0.6608 (OUTLIER) cc_final: 0.6111 (p90) REVERT: I 275 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.8332 (m-10) REVERT: I 731 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8349 (mm-30) REVERT: I 880 MET cc_start: 0.7786 (mpp) cc_final: 0.7419 (mpp) REVERT: I 1005 MET cc_start: 0.7227 (mtt) cc_final: 0.6969 (mtm) REVERT: I 1059 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6828 (t0) REVERT: I 1097 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8230 (mm) REVERT: I 1111 ILE cc_start: 0.9103 (mp) cc_final: 0.8717 (tt) REVERT: J 21 TRP cc_start: 0.8242 (m-10) cc_final: 0.7552 (m-10) REVERT: J 41 ARG cc_start: 0.8809 (tpm170) cc_final: 0.8415 (ptp-170) REVERT: J 512 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8383 (tmm) REVERT: J 573 MET cc_start: 0.5802 (ttp) cc_final: 0.5251 (tpp) REVERT: J 657 LEU cc_start: 0.9466 (mm) cc_final: 0.9250 (mm) REVERT: K 31 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9174 (mm) REVERT: K 44 GLU cc_start: 0.8884 (tp30) cc_final: 0.7960 (pm20) REVERT: K 74 VAL cc_start: 0.9207 (t) cc_final: 0.8855 (m) outliers start: 46 outliers final: 25 residues processed: 163 average time/residue: 0.3014 time to fit residues: 83.4071 Evaluate side-chains 151 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 102 HIS Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 175 GLU Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 668 LEU Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 997 LEU Chi-restraints excluded: chain I residue 1059 ASP Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1097 LEU Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 512 MET Chi-restraints excluded: chain J residue 648 MET Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 836 VAL Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 895 VAL Chi-restraints excluded: chain J residue 992 ILE Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain K residue 31 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 114 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 253 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 254 optimal weight: 0.7980 chunk 230 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.077085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.052224 restraints weight = 87771.960| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 4.60 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 23481 Z= 0.134 Angle : 0.605 11.001 31761 Z= 0.301 Chirality : 0.045 0.454 3590 Planarity : 0.004 0.074 4170 Dihedral : 5.006 40.248 3237 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.17 % Allowed : 16.51 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2905 helix: 0.70 (0.17), residues: 985 sheet: -0.53 (0.26), residues: 407 loop : -1.05 (0.16), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP J1398 HIS 0.014 0.001 HIS I 102 PHE 0.027 0.001 PHE I1085 TYR 0.028 0.001 TYR J 128 ARG 0.008 0.000 ARG K 32 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 934) hydrogen bonds : angle 4.95602 ( 2631) metal coordination : bond 0.00531 ( 4) metal coordination : angle 4.19450 ( 6) covalent geometry : bond 0.00314 (23477) covalent geometry : angle 0.60186 (31755) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 123 time to evaluate : 2.599 Fit side-chains revert: symmetry clash REVERT: G 123 MET cc_start: 0.8807 (mpp) cc_final: 0.8239 (mpp) REVERT: H 1 MET cc_start: 0.8871 (ppp) cc_final: 0.7854 (ppp) REVERT: I 1 MET cc_start: 0.7960 (tpp) cc_final: 0.7676 (tmm) REVERT: I 158 TYR cc_start: 0.6759 (OUTLIER) cc_final: 0.6186 (p90) REVERT: I 275 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.8319 (m-10) REVERT: I 880 MET cc_start: 0.7876 (mpp) cc_final: 0.7530 (mpp) REVERT: I 1005 MET cc_start: 0.7274 (mtt) cc_final: 0.7017 (mtm) REVERT: I 1041 GLU cc_start: 0.9175 (tp30) cc_final: 0.8964 (tp30) REVERT: I 1059 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6847 (t0) REVERT: I 1097 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8194 (mm) REVERT: I 1111 ILE cc_start: 0.9123 (mp) cc_final: 0.8658 (tt) REVERT: J 21 TRP cc_start: 0.8265 (m-10) cc_final: 0.7639 (m-10) REVERT: J 41 ARG cc_start: 0.8793 (tpm170) cc_final: 0.8409 (ptp-170) REVERT: J 512 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8356 (tmm) REVERT: J 573 MET cc_start: 0.5774 (ttp) cc_final: 0.5232 (tpp) REVERT: J 911 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9123 (mm) REVERT: K 31 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9191 (mm) REVERT: K 44 GLU cc_start: 0.8802 (tp30) cc_final: 0.7957 (pm20) REVERT: K 74 VAL cc_start: 0.9190 (t) cc_final: 0.8846 (m) outliers start: 54 outliers final: 33 residues processed: 167 average time/residue: 0.2958 time to fit residues: 84.1553 Evaluate side-chains 158 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 175 GLU Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 321 GLU Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 668 LEU Chi-restraints excluded: chain I residue 800 VAL Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 963 LEU Chi-restraints excluded: chain I residue 997 LEU Chi-restraints excluded: chain I residue 1059 ASP Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1097 LEU Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 512 MET Chi-restraints excluded: chain J residue 648 MET Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 836 VAL Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 895 VAL Chi-restraints excluded: chain J residue 911 LEU Chi-restraints excluded: chain J residue 992 ILE Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1459 LEU Chi-restraints excluded: chain J residue 1468 LEU Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 40 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 176 optimal weight: 20.0000 chunk 129 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 221 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 47 optimal weight: 0.0370 chunk 248 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 102 HIS ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.078133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.053317 restraints weight = 87538.661| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 4.63 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23481 Z= 0.111 Angle : 0.608 14.395 31761 Z= 0.297 Chirality : 0.045 0.507 3590 Planarity : 0.004 0.074 4170 Dihedral : 4.848 38.487 3237 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.65 % Allowed : 17.11 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2905 helix: 0.77 (0.17), residues: 991 sheet: -0.39 (0.27), residues: 397 loop : -0.95 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J1398 HIS 0.004 0.001 HIS J1364 PHE 0.030 0.001 PHE J1440 TYR 0.025 0.001 TYR J1207 ARG 0.008 0.000 ARG K 32 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 934) hydrogen bonds : angle 4.83144 ( 2631) metal coordination : bond 0.00220 ( 4) metal coordination : angle 3.98548 ( 6) covalent geometry : bond 0.00259 (23477) covalent geometry : angle 0.60538 (31755) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 2.581 Fit side-chains revert: symmetry clash REVERT: G 123 MET cc_start: 0.8837 (mpp) cc_final: 0.8265 (mpp) REVERT: I 1 MET cc_start: 0.7827 (tpp) cc_final: 0.7517 (tmm) REVERT: I 158 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6815 (p90) REVERT: I 275 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.8297 (m-10) REVERT: I 731 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8354 (mm-30) REVERT: I 880 MET cc_start: 0.7835 (mpp) cc_final: 0.7501 (mpp) REVERT: I 1005 MET cc_start: 0.7314 (mtt) cc_final: 0.7041 (mtm) REVERT: I 1041 GLU cc_start: 0.9159 (tp30) cc_final: 0.8912 (tp30) REVERT: I 1059 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6815 (t0) REVERT: I 1111 ILE cc_start: 0.9091 (mp) cc_final: 0.8646 (tt) REVERT: J 21 TRP cc_start: 0.8279 (m-10) cc_final: 0.7670 (m-10) REVERT: J 41 ARG cc_start: 0.8785 (tpm170) cc_final: 0.8384 (ptp-170) REVERT: J 512 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8300 (tmm) REVERT: J 911 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9137 (mm) REVERT: K 31 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9167 (mm) REVERT: K 44 GLU cc_start: 0.8804 (tp30) cc_final: 0.7937 (pm20) REVERT: K 74 VAL cc_start: 0.9182 (t) cc_final: 0.8845 (m) outliers start: 41 outliers final: 29 residues processed: 159 average time/residue: 0.2953 time to fit residues: 80.5355 Evaluate side-chains 154 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 668 LEU Chi-restraints excluded: chain I residue 800 VAL Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 997 LEU Chi-restraints excluded: chain I residue 1059 ASP Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 512 MET Chi-restraints excluded: chain J residue 648 MET Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 827 ILE Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 836 VAL Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 895 VAL Chi-restraints excluded: chain J residue 911 LEU Chi-restraints excluded: chain J residue 992 ILE Chi-restraints excluded: chain J residue 1044 LEU Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1219 GLU Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain K residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 234 optimal weight: 0.6980 chunk 117 optimal weight: 0.4980 chunk 283 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 219 optimal weight: 0.0570 chunk 192 optimal weight: 0.4980 chunk 282 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 25 optimal weight: 0.0050 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.3512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 556 ASN I 575 GLN I 728 HIS I1018 GLN J 617 ASN ** J1364 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 = 0.3836 r_free = 0.3836 target = 0.078746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.054051 restraints weight = 87919.079| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 4.61 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 23481 Z= 0.105 Angle : 0.608 13.153 31761 Z= 0.295 Chirality : 0.045 0.507 3590 Planarity : 0.004 0.075 4170 Dihedral : 4.745 37.211 3237 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.65 % Allowed : 17.11 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2905 helix: 0.78 (0.17), residues: 997 sheet: -0.30 (0.27), residues: 398 loop : -0.93 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP J1398 HIS 0.004 0.001 HIS J1364 PHE 0.032 0.001 PHE J1440 TYR 0.024 0.001 TYR J1207 ARG 0.008 0.000 ARG K 32 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 934) hydrogen bonds : angle 4.77526 ( 2631) metal coordination : bond 0.00173 ( 4) metal coordination : angle 4.00317 ( 6) covalent geometry : bond 0.00244 (23477) covalent geometry : angle 0.60565 (31755) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 123 MET cc_start: 0.8818 (mpp) cc_final: 0.8288 (mpp) REVERT: H 1 MET cc_start: 0.8771 (ppp) cc_final: 0.8068 (ppp) REVERT: I 1 MET cc_start: 0.7786 (tpp) cc_final: 0.7451 (tmm) REVERT: I 158 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.6974 (p90) REVERT: I 221 LEU cc_start: 0.9101 (pp) cc_final: 0.8870 (mp) REVERT: I 275 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.8317 (m-10) REVERT: I 340 MET cc_start: 0.8612 (tmm) cc_final: 0.8372 (tmm) REVERT: I 731 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8379 (mm-30) REVERT: I 880 MET cc_start: 0.7792 (mpp) cc_final: 0.7523 (mpp) REVERT: I 1059 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.6906 (t0) REVERT: I 1111 ILE cc_start: 0.9096 (mp) cc_final: 0.8690 (tt) REVERT: J 21 TRP cc_start: 0.8277 (m-10) cc_final: 0.7678 (m-10) REVERT: J 41 ARG cc_start: 0.8759 (tpm170) cc_final: 0.8358 (ptp-170) REVERT: J 512 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8296 (tmm) REVERT: J 573 MET cc_start: 0.5619 (ttp) cc_final: 0.4966 (tpp) REVERT: J 924 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8711 (mmp) REVERT: K 31 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9183 (mm) REVERT: K 66 LYS cc_start: 0.8747 (ptpt) cc_final: 0.8480 (pttt) REVERT: K 74 VAL cc_start: 0.9192 (t) cc_final: 0.8858 (m) outliers start: 41 outliers final: 27 residues processed: 162 average time/residue: 0.3076 time to fit residues: 85.1781 Evaluate side-chains 154 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 668 LEU Chi-restraints excluded: chain I residue 800 VAL Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 997 LEU Chi-restraints excluded: chain I residue 1059 ASP Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 512 MET Chi-restraints excluded: chain J residue 745 MET Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 827 ILE Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 895 VAL Chi-restraints excluded: chain J residue 911 LEU Chi-restraints excluded: chain J residue 924 MET Chi-restraints excluded: chain J residue 992 ILE Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1219 GLU Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain K residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 224 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 258 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 211 optimal weight: 0.0270 chunk 253 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 264 optimal weight: 8.9990 chunk 284 optimal weight: 7.9990 chunk 160 optimal weight: 0.9980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 575 GLN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.078605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.053858 restraints weight = 87232.561| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 4.64 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23481 Z= 0.111 Angle : 0.610 13.105 31761 Z= 0.295 Chirality : 0.045 0.539 3590 Planarity : 0.004 0.075 4170 Dihedral : 4.677 36.919 3237 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.57 % Allowed : 17.63 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.16), residues: 2905 helix: 0.79 (0.17), residues: 998 sheet: -0.28 (0.26), residues: 408 loop : -0.93 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP J1398 HIS 0.004 0.001 HIS J1364 PHE 0.032 0.001 PHE J1440 TYR 0.024 0.001 TYR J1207 ARG 0.008 0.000 ARG K 32 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 934) hydrogen bonds : angle 4.73284 ( 2631) metal coordination : bond 0.00286 ( 4) metal coordination : angle 3.92038 ( 6) covalent geometry : bond 0.00263 (23477) covalent geometry : angle 0.60728 (31755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9989.48 seconds wall clock time: 173 minutes 57.66 seconds (10437.66 seconds total)