Starting phenix.real_space_refine on Mon Feb 19 13:20:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asw_15623/02_2024/8asw_15623_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asw_15623/02_2024/8asw_15623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asw_15623/02_2024/8asw_15623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asw_15623/02_2024/8asw_15623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asw_15623/02_2024/8asw_15623_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asw_15623/02_2024/8asw_15623_updated.pdb" } resolution = 3.96 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 Fe 4 7.16 5 P 73 5.49 5 S 100 5.16 5 C 15403 2.51 5 N 4219 2.21 5 O 4982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 114": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 700": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "A GLU 1180": "OE1" <-> "OE2" Residue "A GLU 1181": "OE1" <-> "OE2" Residue "A GLU 1190": "OE1" <-> "OE2" Residue "A GLU 1237": "OE1" <-> "OE2" Residue "A GLU 1238": "OE1" <-> "OE2" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "A GLU 1309": "OE1" <-> "OE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B GLU 716": "OE1" <-> "OE2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "C GLU 430": "OE1" <-> "OE2" Residue "C GLU 523": "OE1" <-> "OE2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "C TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1085": "OE1" <-> "OE2" Residue "D GLU 1337": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24781 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1255, 10014 Classifications: {'peptide': 1255} Link IDs: {'PTRANS': 41, 'TRANS': 1213} Chain breaks: 1 Chain: "B" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6177 Classifications: {'peptide': 772} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 746} Chain breaks: 1 Chain: "C" Number of atoms: 4236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4236 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 503} Chain breaks: 1 Chain: "D" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2769 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 9, 'TRANS': 333} Chain: "X" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1559 Classifications: {'RNA': 73} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 27, 'rna3p_pyr': 27} Link IDs: {'rna2p': 19, 'rna3p': 53} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'5AD': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17020 SG CYS C 121 101.938 65.799 107.346 1.00 54.66 S ATOM 16995 SG CYS C 118 106.716 63.440 108.105 1.00 58.89 S ATOM 16920 SG CYS C 108 101.260 59.927 108.980 1.00 47.95 S Time building chain proxies: 14.01, per 1000 atoms: 0.57 Number of scatterers: 24781 At special positions: 0 Unit cell: (174.96, 150.66, 165.24, 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) Fe 4 26.01 S 100 16.00 P 73 15.00 O 4982 8.00 N 4219 7.00 C 15403 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.10 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 601 " pdb="FE2 SF4 C 601 " - pdb=" NE2 HIS C 110 " pdb="FE1 SF4 C 601 " - pdb=" SG CYS C 121 " pdb="FE4 SF4 C 601 " - pdb=" SG CYS C 108 " pdb="FE2 SF4 C 601 " - pdb=" SG CYS C 118 " Number of angles added : 9 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5482 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 32 sheets defined 26.4% alpha, 20.8% beta 18 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 14.82 Creating SS restraints... Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 520 through 523 No H-bonds generated for 'chain 'A' and resid 520 through 523' Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 632 through 635 No H-bonds generated for 'chain 'A' and resid 632 through 635' Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 773 through 777 Processing helix chain 'A' and resid 780 through 793 removed outlier: 5.618A pdb=" N GLU A 788 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL A 789 " --> pdb=" O GLU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 803 Processing helix chain 'A' and resid 838 through 845 removed outlier: 3.839A pdb=" N LYS A 845 " --> pdb=" O TYR A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 867 Processing helix chain 'A' and resid 870 through 875 Processing helix chain 'A' and resid 877 through 886 Processing helix chain 'A' and resid 892 through 901 Processing helix chain 'A' and resid 907 through 918 Processing helix chain 'A' and resid 921 through 930 Processing helix chain 'A' and resid 935 through 943 removed outlier: 4.350A pdb=" N LYS A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 959 Proline residue: A 953 - end of helix Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 977 through 987 removed outlier: 4.538A pdb=" N GLU A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE A 987 " --> pdb=" O HIS A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1004 Processing helix chain 'A' and resid 1007 through 1013 Processing helix chain 'A' and resid 1018 through 1035 Processing helix chain 'A' and resid 1039 through 1048 removed outlier: 4.329A pdb=" N MET A1047 " --> pdb=" O VAL A1043 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A1048 " --> pdb=" O ALA A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1060 Processing helix chain 'A' and resid 1064 through 1074 Processing helix chain 'A' and resid 1079 through 1093 removed outlier: 3.539A pdb=" N ALA A1083 " --> pdb=" O VAL A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1105 Processing helix chain 'A' and resid 1110 through 1119 Processing helix chain 'A' and resid 1124 through 1132 Processing helix chain 'A' and resid 1137 through 1141 Processing helix chain 'A' and resid 1143 through 1171 Processing helix chain 'A' and resid 1260 through 1282 removed outlier: 4.562A pdb=" N ARG A1265 " --> pdb=" O ARG A1261 " (cutoff:3.500A) Proline residue: A1271 - end of helix Processing helix chain 'A' and resid 1286 through 1302 Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 539 through 545 Processing helix chain 'B' and resid 664 through 666 No H-bonds generated for 'chain 'B' and resid 664 through 666' Processing helix chain 'B' and resid 747 through 749 No H-bonds generated for 'chain 'B' and resid 747 through 749' Processing helix chain 'C' and resid 20 through 38 Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.661A pdb=" N TYR C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 removed outlier: 3.736A pdb=" N SER C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 85 removed outlier: 4.168A pdb=" N TYR C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) Proline residue: C 83 - end of helix Processing helix chain 'C' and resid 89 through 92 No H-bonds generated for 'chain 'C' and resid 89 through 92' Processing helix chain 'C' and resid 109 through 114 removed outlier: 3.866A pdb=" N THR C 114 " --> pdb=" O ILE C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 153 through 166 Processing helix chain 'C' and resid 188 through 203 Processing helix chain 'C' and resid 210 through 219 removed outlier: 3.939A pdb=" N GLN C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 261 through 266 Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 302 through 313 Processing helix chain 'C' and resid 338 through 341 No H-bonds generated for 'chain 'C' and resid 338 through 341' Processing helix chain 'C' and resid 351 through 364 removed outlier: 3.597A pdb=" N LEU C 364 " --> pdb=" O ARG C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 392 through 403 Processing helix chain 'C' and resid 415 through 418 No H-bonds generated for 'chain 'C' and resid 415 through 418' Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 535 through 537 No H-bonds generated for 'chain 'C' and resid 535 through 537' Processing helix chain 'C' and resid 540 through 542 No H-bonds generated for 'chain 'C' and resid 540 through 542' Processing helix chain 'D' and resid 1020 through 1034 Processing helix chain 'D' and resid 1039 through 1044 Processing helix chain 'D' and resid 1052 through 1061 removed outlier: 4.051A pdb=" N SER D1060 " --> pdb=" O GLY D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1064 through 1074 Processing helix chain 'D' and resid 1079 through 1093 removed outlier: 3.536A pdb=" N SER D1089 " --> pdb=" O GLU D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1096 through 1105 Processing helix chain 'D' and resid 1111 through 1118 Processing helix chain 'D' and resid 1123 through 1133 removed outlier: 4.097A pdb=" N ALA D1133 " --> pdb=" O VAL D1129 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1142 Processing helix chain 'D' and resid 1144 through 1168 Processing helix chain 'D' and resid 1215 through 1217 No H-bonds generated for 'chain 'D' and resid 1215 through 1217' Processing helix chain 'D' and resid 1228 through 1230 No H-bonds generated for 'chain 'D' and resid 1228 through 1230' Processing helix chain 'D' and resid 1252 through 1282 Proline residue: D1271 - end of helix Processing helix chain 'D' and resid 1286 through 1304 Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 Processing sheet with id= B, first strand: chain 'A' and resid 46 through 49 removed outlier: 7.199A pdb=" N VAL A 62 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLN A 75 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N VAL A 84 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 97 through 103 removed outlier: 6.706A pdb=" N VAL A 112 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE A 100 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL A 110 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N HIS A 102 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN A 108 " --> pdb=" O HIS A 102 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 118 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY A 139 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR A 120 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE A 137 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR A 122 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE A 135 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 145 through 150 removed outlier: 6.950A pdb=" N VAL A 160 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA A 148 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA A 158 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TRP A 150 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N THR A 156 " --> pdb=" O TRP A 150 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER A 170 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 252 through 255 Processing sheet with id= F, first strand: chain 'A' and resid 317 through 321 Processing sheet with id= G, first strand: chain 'A' and resid 357 through 362 removed outlier: 7.083A pdb=" N VAL A 372 " --> pdb=" O GLU A 358 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL A 360 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA A 370 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG A 376 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 391 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR A 381 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU A 389 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 441 through 446 Processing sheet with id= I, first strand: chain 'A' and resid 478 through 480 removed outlier: 6.308A pdb=" N ALA A 499 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE A 514 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 569 through 572 removed outlier: 3.762A pdb=" N SER A 551 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASP A 546 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU A 530 " --> pdb=" O ASP A 546 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 576 through 581 removed outlier: 6.748A pdb=" N GLU A 591 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU A 579 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL A 589 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLN A 599 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU A 608 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 618 through 624 removed outlier: 4.213A pdb=" N ALA A 661 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ALA A 655 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 666 through 670 removed outlier: 4.087A pdb=" N SER A 666 " --> pdb=" O THR A 677 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 736 through 739 removed outlier: 5.820A pdb=" N GLN A 730 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU A 717 " --> pdb=" O GLN A 730 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 20 through 25 removed outlier: 3.529A pdb=" N ILE A 22 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 425 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASP A 423 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 21 through 24 Processing sheet with id= Q, first strand: chain 'B' and resid 62 through 68 removed outlier: 6.582A pdb=" N ALA B 77 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B 65 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 75 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N PHE B 67 " --> pdb=" O PHE B 73 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE B 73 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN B 98 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS B 87 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N CYS B 96 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 107 through 113 removed outlier: 6.399A pdb=" N GLY B 120 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU B 110 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER B 118 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA B 112 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ARG B 130 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU B 140 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 153 through 160 removed outlier: 6.968A pdb=" N GLY B 171 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU B 156 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA B 169 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU B 158 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU B 167 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LYS B 160 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS B 165 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER B 181 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL B 194 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 205 through 210 removed outlier: 7.004A pdb=" N GLY B 224 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU B 208 " --> pdb=" O CYS B 222 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N CYS B 222 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N PHE B 210 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU B 220 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ARG B 234 " --> pdb=" O PHE B 273 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N PHE B 273 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG B 236 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE B 271 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 284 through 288 removed outlier: 6.919A pdb=" N ALA B 299 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU B 287 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 297 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU B 309 " --> pdb=" O CYS B 319 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N CYS B 319 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 344 through 349 removed outlier: 3.724A pdb=" N MET B 352 " --> pdb=" O HIS B 349 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 391 through 393 removed outlier: 6.587A pdb=" N ALA B 413 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLU B 431 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TRP B 415 " --> pdb=" O TRP B 429 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TRP B 429 " --> pdb=" O TRP B 415 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 444 through 447 removed outlier: 3.512A pdb=" N GLU B 552 " --> pdb=" O SER B 464 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 587 through 591 Processing sheet with id= Z, first strand: chain 'B' and resid 609 through 614 removed outlier: 7.086A pdb=" N VAL B 624 " --> pdb=" O THR B 610 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU B 612 " --> pdb=" O LEU B 622 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B 622 " --> pdb=" O LEU B 612 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLU B 634 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU B 644 " --> pdb=" O GLU B 634 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 656 through 661 removed outlier: 6.904A pdb=" N ALA B 673 " --> pdb=" O TRP B 657 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA B 659 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL B 671 " --> pdb=" O ALA B 659 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TRP B 661 " --> pdb=" O VAL B 669 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL B 669 " --> pdb=" O TRP B 661 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG B 683 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LEU B 694 " --> pdb=" O ARG B 683 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN B 685 " --> pdb=" O TYR B 692 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N TYR B 692 " --> pdb=" O GLN B 685 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 704 through 709 removed outlier: 6.580A pdb=" N GLY B 723 " --> pdb=" O THR B 705 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE B 707 " --> pdb=" O SER B 721 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N SER B 721 " --> pdb=" O ILE B 707 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE B 709 " --> pdb=" O LEU B 719 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 719 " --> pdb=" O ILE B 709 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N SER B 733 " --> pdb=" O LEU B 741 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU B 741 " --> pdb=" O SER B 733 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 5 through 12 removed outlier: 6.593A pdb=" N ILE B 782 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE B 10 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR B 780 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER B 779 " --> pdb=" O SER B 775 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.976A pdb=" N LYS C 173 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL C 99 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLU C 175 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL C 101 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL C 177 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS C 223 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR C 176 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL C 225 " --> pdb=" O TYR C 176 " (cutoff:3.500A) removed outlier: 12.363A pdb=" N LEU C 178 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 10.213A pdb=" N ILE C 227 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ARG C 251 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR C 231 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU C 253 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS C 289 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE C 254 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL C 291 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY C 323 " --> pdb=" O SER C 292 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N MET C 294 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LYS C 325 " --> pdb=" O MET C 294 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG C 370 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE C 326 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N TYR C 372 " --> pdb=" O ILE C 326 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'C' and resid 429 through 438 removed outlier: 4.294A pdb=" N TRP C 442 " --> pdb=" O LYS C 464 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP C 450 " --> pdb=" O LEU C 456 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU C 456 " --> pdb=" O ASP C 450 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU C 485 " --> pdb=" O ARG C 461 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 480 through 483 removed outlier: 6.818A pdb=" N LYS C 528 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL C 483 " --> pdb=" O LYS C 528 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N SER C 530 " --> pdb=" O VAL C 483 " (cutoff:3.500A) 753 hydrogen bonds defined for protein. 2133 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 12.10 Time building geometry restraints manager: 11.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 10913 1.43 - 1.64: 14354 1.64 - 1.85: 149 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 25428 Sorted by residual: bond pdb=" N ILE A 770 " pdb=" CA ILE A 770 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.27e+00 bond pdb=" N ARG A 769 " pdb=" CA ARG A 769 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.93e+00 bond pdb=" N ASN A 771 " pdb=" CA ASN A 771 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.66e+00 bond pdb=" N LEU A 772 " pdb=" CA LEU A 772 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.82e+00 bond pdb=" N TYR C 489 " pdb=" CA TYR C 489 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.06e-02 8.90e+03 4.82e+00 ... (remaining 25423 not shown) Histogram of bond angle deviations from ideal: 73.44 - 85.56: 12 85.56 - 97.67: 1 97.67 - 109.78: 4111 109.78 - 121.90: 25208 121.90 - 134.01: 5436 Bond angle restraints: 34768 Sorted by residual: angle pdb=" C ARG A 350 " pdb=" N LEU A 351 " pdb=" CA LEU A 351 " ideal model delta sigma weight residual 120.68 128.70 -8.02 1.52e+00 4.33e-01 2.78e+01 angle pdb=" N ILE A 804 " pdb=" CA ILE A 804 " pdb=" C ILE A 804 " ideal model delta sigma weight residual 111.91 107.24 4.67 8.90e-01 1.26e+00 2.75e+01 angle pdb=" C ASN A1306 " pdb=" CA ASN A1306 " pdb=" CB ASN A1306 " ideal model delta sigma weight residual 115.79 110.61 5.18 1.19e+00 7.06e-01 1.90e+01 angle pdb=" CB MET C 184 " pdb=" CG MET C 184 " pdb=" SD MET C 184 " ideal model delta sigma weight residual 112.70 125.04 -12.34 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C ASP A 773 " pdb=" N ILE A 774 " pdb=" CA ILE A 774 " ideal model delta sigma weight residual 121.97 115.00 6.97 1.80e+00 3.09e-01 1.50e+01 ... (remaining 34763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.29: 14642 33.29 - 66.58: 767 66.58 - 99.86: 110 99.86 - 133.15: 4 133.15 - 166.44: 4 Dihedral angle restraints: 15527 sinusoidal: 7031 harmonic: 8496 Sorted by residual: dihedral pdb=" C4' A X 7 " pdb=" C3' A X 7 " pdb=" C2' A X 7 " pdb=" C1' A X 7 " ideal model delta sinusoidal sigma weight residual -35.00 32.54 -67.54 1 8.00e+00 1.56e-02 9.27e+01 dihedral pdb=" C5' A X 7 " pdb=" C4' A X 7 " pdb=" C3' A X 7 " pdb=" O3' A X 7 " ideal model delta sinusoidal sigma weight residual 147.00 85.63 61.37 1 8.00e+00 1.56e-02 7.81e+01 dihedral pdb=" O4' A X 7 " pdb=" C2' A X 7 " pdb=" C1' A X 7 " pdb=" C3' A X 7 " ideal model delta sinusoidal sigma weight residual -35.00 22.82 -57.82 1 8.00e+00 1.56e-02 7.01e+01 ... (remaining 15524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3228 0.056 - 0.112: 631 0.112 - 0.169: 75 0.169 - 0.225: 4 0.225 - 0.281: 3 Chirality restraints: 3941 Sorted by residual: chirality pdb=" C3' A X 7 " pdb=" C4' A X 7 " pdb=" O3' A X 7 " pdb=" C2' A X 7 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB VAL A1197 " pdb=" CA VAL A1197 " pdb=" CG1 VAL A1197 " pdb=" CG2 VAL A1197 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C3' U X 65 " pdb=" C4' U X 65 " pdb=" O3' U X 65 " pdb=" C2' U X 65 " both_signs ideal model delta sigma weight residual False -2.48 -2.24 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 3938 not shown) Planarity restraints: 4195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 768 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" C HIS A 768 " 0.049 2.00e-02 2.50e+03 pdb=" O HIS A 768 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG A 769 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D1285 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C MET D1285 " -0.039 2.00e-02 2.50e+03 pdb=" O MET D1285 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG D1286 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 488 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C VAL C 488 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL C 488 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR C 489 " 0.013 2.00e-02 2.50e+03 ... (remaining 4192 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 599 2.63 - 3.20: 23796 3.20 - 3.76: 40456 3.76 - 4.33: 55529 4.33 - 4.90: 88991 Nonbonded interactions: 209371 Sorted by model distance: nonbonded pdb=" O2' U X 65 " pdb=" OP1 U X 66 " model vdw 2.061 2.440 nonbonded pdb=" OG1 THR A 665 " pdb=" OG1 THR A 677 " model vdw 2.100 2.440 nonbonded pdb=" OD1 ASP A1005 " pdb=" OH TYR A1007 " model vdw 2.111 2.440 nonbonded pdb=" OE2 GLU A1181 " pdb=" OG SER A1202 " model vdw 2.112 2.440 nonbonded pdb=" OG SER C 292 " pdb=" OH TYR C 313 " model vdw 2.116 2.440 ... (remaining 209366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 15.800 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 85.760 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 : 0.005 0.042 25428 Z= 0.339 Angle : 0.752 12.336 34768 Z= 0.422 Chirality : 0.044 0.281 3941 Planarity : 0.004 0.057 4195 Dihedral : 19.806 166.439 10045 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.51 % Favored : 89.25 % Rotamer: Outliers : 0.71 % Allowed : 28.59 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.15), residues: 2883 helix: 0.02 (0.18), residues: 789 sheet: -1.33 (0.20), residues: 683 loop : -2.36 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 308 HIS 0.007 0.001 HIS C 110 PHE 0.016 0.002 PHE C 319 TYR 0.025 0.002 TYR C 216 ARG 0.005 0.001 ARG C 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1328 TYR cc_start: 0.0718 (OUTLIER) cc_final: 0.0394 (t80) outliers start: 18 outliers final: 8 residues processed: 119 average time/residue: 0.3620 time to fit residues: 71.6783 Evaluate side-chains 110 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1328 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 0.0170 chunk 150 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 267 optimal weight: 0.4980 overall best weight: 1.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 142 HIS ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN D1166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.0602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25428 Z= 0.188 Angle : 0.579 8.793 34768 Z= 0.299 Chirality : 0.042 0.226 3941 Planarity : 0.004 0.049 4195 Dihedral : 15.984 166.537 4378 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.46 % Favored : 91.36 % Rotamer: Outliers : 3.61 % Allowed : 26.67 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.15), residues: 2883 helix: 0.20 (0.19), residues: 785 sheet: -1.19 (0.20), residues: 670 loop : -2.28 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 308 HIS 0.006 0.001 HIS A1290 PHE 0.013 0.001 PHE A 285 TYR 0.021 0.001 TYR C 216 ARG 0.005 0.000 ARG A1286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 112 time to evaluate : 3.021 Fit side-chains revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7727 (p0) cc_final: 0.7214 (p0) REVERT: A 1037 MET cc_start: 0.7686 (tpt) cc_final: 0.7048 (tpt) REVERT: B 614 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.7030 (t80) REVERT: C 68 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7430 (t70) REVERT: C 553 MET cc_start: 0.8480 (mmm) cc_final: 0.8261 (mmt) REVERT: D 1328 TYR cc_start: 0.0943 (OUTLIER) cc_final: 0.0552 (t80) outliers start: 92 outliers final: 52 residues processed: 196 average time/residue: 0.3251 time to fit residues: 108.7366 Evaluate side-chains 159 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 104 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 614 PHE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1233 ASN Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 289 optimal weight: 10.0000 chunk 239 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.0569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25428 Z= 0.314 Angle : 0.620 9.190 34768 Z= 0.320 Chirality : 0.043 0.218 3941 Planarity : 0.004 0.047 4195 Dihedral : 15.842 166.296 4371 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.09 % Favored : 89.73 % Rotamer: Outliers : 5.69 % Allowed : 26.47 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.15), residues: 2883 helix: 0.09 (0.18), residues: 790 sheet: -1.32 (0.20), residues: 672 loop : -2.31 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 308 HIS 0.008 0.001 HIS C 110 PHE 0.017 0.002 PHE D1296 TYR 0.017 0.002 TYR C 136 ARG 0.005 0.000 ARG A1286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 102 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7767 (p0) cc_final: 0.7252 (p0) REVERT: A 169 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8240 (pp) REVERT: A 588 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8541 (tt) REVERT: A 842 TYR cc_start: 0.6845 (t80) cc_final: 0.6562 (t80) REVERT: B 614 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.6989 (t80) REVERT: B 676 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7482 (m-30) REVERT: B 713 MET cc_start: 0.4829 (tpp) cc_final: 0.3219 (ttp) REVERT: B 781 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7339 (mtt-85) REVERT: C 68 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7337 (t0) REVERT: C 338 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.6721 (t80) REVERT: D 1253 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.6125 (tp30) REVERT: D 1328 TYR cc_start: 0.1121 (OUTLIER) cc_final: 0.0674 (t80) outliers start: 145 outliers final: 96 residues processed: 239 average time/residue: 0.3107 time to fit residues: 126.0778 Evaluate side-chains 202 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 97 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 682 ASN Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1008 LYS Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1232 LYS Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 614 PHE Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 676 ASP Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 781 ARG Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1167 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1233 ASN Chi-restraints excluded: chain D residue 1253 GLU Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Chi-restraints excluded: chain D residue 1348 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 265 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 269 optimal weight: 9.9990 chunk 285 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 255 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 142 HIS ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25428 Z= 0.239 Angle : 0.593 9.369 34768 Z= 0.306 Chirality : 0.042 0.215 3941 Planarity : 0.004 0.046 4195 Dihedral : 15.743 166.370 4371 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.09 % Favored : 90.74 % Rotamer: Outliers : 5.65 % Allowed : 27.10 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.15), residues: 2883 helix: 0.05 (0.18), residues: 797 sheet: -1.23 (0.20), residues: 668 loop : -2.34 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 308 HIS 0.007 0.001 HIS A1290 PHE 0.015 0.001 PHE D1296 TYR 0.016 0.001 TYR C 120 ARG 0.004 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 107 time to evaluate : 3.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7782 (p0) cc_final: 0.7270 (p0) REVERT: A 115 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7363 (mm110) REVERT: A 169 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8236 (pp) REVERT: A 588 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8485 (tt) REVERT: A 842 TYR cc_start: 0.6869 (t80) cc_final: 0.6554 (t80) REVERT: B 614 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.7018 (t80) REVERT: B 676 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7508 (m-30) REVERT: B 713 MET cc_start: 0.4664 (tpp) cc_final: 0.3068 (ttp) REVERT: C 68 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7407 (t70) REVERT: D 1328 TYR cc_start: 0.1234 (OUTLIER) cc_final: 0.0707 (t80) outliers start: 144 outliers final: 105 residues processed: 241 average time/residue: 0.3289 time to fit residues: 134.2396 Evaluate side-chains 215 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 103 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 682 ASN Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1232 LYS Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 614 PHE Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 676 ASP Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1143 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1218 THR Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1233 ASN Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Chi-restraints excluded: chain D residue 1348 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 212 optimal weight: 1.9990 chunk 117 optimal weight: 0.2980 chunk 243 optimal weight: 3.9990 chunk 197 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 255 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25428 Z= 0.203 Angle : 0.580 10.330 34768 Z= 0.297 Chirality : 0.042 0.214 3941 Planarity : 0.004 0.049 4195 Dihedral : 15.583 166.564 4371 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.40 % Favored : 90.43 % Rotamer: Outliers : 5.57 % Allowed : 27.33 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.15), residues: 2883 helix: 0.11 (0.18), residues: 791 sheet: -1.16 (0.20), residues: 667 loop : -2.31 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 308 HIS 0.007 0.001 HIS A1290 PHE 0.029 0.001 PHE D1296 TYR 0.015 0.001 TYR C 136 ARG 0.006 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 107 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7791 (p0) cc_final: 0.7296 (p0) REVERT: A 115 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7387 (mm110) REVERT: A 169 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8278 (pp) REVERT: A 428 MET cc_start: 0.7446 (mmt) cc_final: 0.7034 (mmp) REVERT: A 588 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8515 (tt) REVERT: A 842 TYR cc_start: 0.6915 (t80) cc_final: 0.6545 (t80) REVERT: B 614 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7030 (t80) REVERT: B 650 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7787 (ttpt) REVERT: B 676 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: B 713 MET cc_start: 0.4613 (tpp) cc_final: 0.3027 (ttp) REVERT: C 68 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7405 (t70) REVERT: C 338 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.6652 (t80) REVERT: C 553 MET cc_start: 0.8474 (mmm) cc_final: 0.8250 (mmm) REVERT: D 1328 TYR cc_start: 0.1340 (OUTLIER) cc_final: 0.0777 (t80) outliers start: 142 outliers final: 107 residues processed: 238 average time/residue: 0.3234 time to fit residues: 129.2207 Evaluate side-chains 218 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 102 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1008 LYS Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1232 LYS Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 614 PHE Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 676 ASP Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1143 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1167 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1233 ASN Chi-restraints excluded: chain D residue 1272 ASP Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 0.9990 chunk 256 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 285 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25428 Z= 0.240 Angle : 0.590 10.252 34768 Z= 0.304 Chirality : 0.042 0.212 3941 Planarity : 0.004 0.049 4195 Dihedral : 15.552 166.407 4369 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.54 % Favored : 90.29 % Rotamer: Outliers : 6.35 % Allowed : 27.06 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.15), residues: 2883 helix: 0.05 (0.18), residues: 798 sheet: -1.26 (0.20), residues: 671 loop : -2.30 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 308 HIS 0.008 0.001 HIS C 110 PHE 0.016 0.001 PHE D1075 TYR 0.016 0.001 TYR C 136 ARG 0.006 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 101 time to evaluate : 3.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7815 (p0) cc_final: 0.7317 (p0) REVERT: A 115 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7351 (mm110) REVERT: A 169 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8232 (pp) REVERT: A 355 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6727 (mm-30) REVERT: A 588 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8515 (tt) REVERT: A 1280 LEU cc_start: 0.7487 (tt) cc_final: 0.6768 (tp) REVERT: B 306 MET cc_start: 0.7290 (ptm) cc_final: 0.7065 (ptm) REVERT: B 614 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.7021 (t80) REVERT: B 650 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7806 (ttpt) REVERT: B 676 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7493 (m-30) REVERT: B 713 MET cc_start: 0.4596 (tpp) cc_final: 0.3031 (ttp) REVERT: C 68 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7386 (t0) REVERT: C 225 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8835 (t) REVERT: C 338 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.6657 (t80) REVERT: C 553 MET cc_start: 0.8473 (mmm) cc_final: 0.8233 (mmt) REVERT: D 1328 TYR cc_start: 0.1326 (OUTLIER) cc_final: 0.0708 (t80) outliers start: 162 outliers final: 131 residues processed: 253 average time/residue: 0.3221 time to fit residues: 138.5342 Evaluate side-chains 242 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 100 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1008 LYS Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1232 LYS Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 553 LYS Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 614 PHE Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 676 ASP Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1143 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1167 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1233 ASN Chi-restraints excluded: chain D residue 1272 ASP Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Chi-restraints excluded: chain D residue 1348 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 40.0000 chunk 32 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 284 optimal weight: 6.9990 chunk 177 optimal weight: 0.4980 chunk 173 optimal weight: 0.0030 chunk 131 optimal weight: 0.8980 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 GLN A 891 ASN ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25428 Z= 0.153 Angle : 0.552 11.173 34768 Z= 0.283 Chirality : 0.041 0.213 3941 Planarity : 0.003 0.048 4195 Dihedral : 15.402 166.965 4369 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.12 % Favored : 91.71 % Rotamer: Outliers : 5.14 % Allowed : 28.24 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.16), residues: 2883 helix: 0.21 (0.18), residues: 801 sheet: -1.00 (0.20), residues: 662 loop : -2.22 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 308 HIS 0.006 0.001 HIS A1290 PHE 0.026 0.001 PHE D1296 TYR 0.011 0.001 TYR B 219 ARG 0.005 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 112 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7768 (p0) cc_final: 0.7263 (p0) REVERT: A 169 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8241 (pp) REVERT: A 428 MET cc_start: 0.7414 (mmt) cc_final: 0.7026 (mmp) REVERT: A 508 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8208 (mmpt) REVERT: A 588 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8496 (tt) REVERT: A 842 TYR cc_start: 0.6921 (t80) cc_final: 0.6512 (t80) REVERT: A 1280 LEU cc_start: 0.7327 (tt) cc_final: 0.6823 (tp) REVERT: B 614 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7040 (t80) REVERT: B 676 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7393 (m-30) REVERT: B 713 MET cc_start: 0.4390 (tpp) cc_final: 0.2800 (ttp) REVERT: C 225 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8769 (t) REVERT: C 338 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.6597 (t80) REVERT: D 1014 TYR cc_start: 0.1732 (m-80) cc_final: 0.1248 (m-80) REVERT: D 1328 TYR cc_start: 0.1396 (OUTLIER) cc_final: 0.0792 (t80) outliers start: 131 outliers final: 106 residues processed: 232 average time/residue: 0.3186 time to fit residues: 125.3389 Evaluate side-chains 217 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 103 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 891 ASN Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1008 LYS Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1232 LYS Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 553 LYS Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 614 PHE Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 676 ASP Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1143 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1167 SER Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1272 ASP Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1299 VAL Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Chi-restraints excluded: chain D residue 1348 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 193 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 223 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 GLN ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25428 Z= 0.213 Angle : 0.575 11.256 34768 Z= 0.295 Chirality : 0.041 0.213 3941 Planarity : 0.004 0.050 4195 Dihedral : 15.399 166.707 4369 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.33 % Favored : 90.50 % Rotamer: Outliers : 5.33 % Allowed : 28.24 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.16), residues: 2883 helix: 0.20 (0.18), residues: 798 sheet: -1.05 (0.20), residues: 668 loop : -2.22 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 308 HIS 0.008 0.001 HIS C 110 PHE 0.020 0.001 PHE D1296 TYR 0.013 0.001 TYR C 136 ARG 0.004 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 104 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7779 (p0) cc_final: 0.7279 (p0) REVERT: A 169 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8268 (pp) REVERT: A 428 MET cc_start: 0.7423 (mmt) cc_final: 0.6990 (mmp) REVERT: A 508 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8200 (mmpt) REVERT: A 588 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8518 (tt) REVERT: A 1280 LEU cc_start: 0.7387 (tt) cc_final: 0.6846 (tp) REVERT: B 306 MET cc_start: 0.7150 (ptm) cc_final: 0.6947 (ptm) REVERT: B 614 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7004 (t80) REVERT: B 676 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: C 68 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7317 (t70) REVERT: C 338 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.6631 (t80) REVERT: D 1328 TYR cc_start: 0.1429 (OUTLIER) cc_final: 0.0613 (t80) outliers start: 136 outliers final: 116 residues processed: 229 average time/residue: 0.3011 time to fit residues: 117.9328 Evaluate side-chains 226 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 102 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1008 LYS Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1232 LYS Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 614 PHE Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 676 ASP Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1143 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1167 SER Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1272 ASP Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 239 optimal weight: 0.8980 chunk 250 optimal weight: 0.9980 chunk 173 optimal weight: 7.9990 chunk 280 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25428 Z= 0.238 Angle : 0.590 11.503 34768 Z= 0.303 Chirality : 0.042 0.212 3941 Planarity : 0.004 0.051 4195 Dihedral : 15.412 166.257 4369 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.57 % Favored : 90.25 % Rotamer: Outliers : 5.53 % Allowed : 28.12 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.15), residues: 2883 helix: 0.14 (0.18), residues: 797 sheet: -1.08 (0.20), residues: 667 loop : -2.24 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 308 HIS 0.008 0.001 HIS C 110 PHE 0.021 0.001 PHE D1296 TYR 0.014 0.001 TYR C 136 ARG 0.004 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 105 time to evaluate : 3.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7779 (p0) cc_final: 0.7273 (p0) REVERT: A 169 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8272 (pp) REVERT: A 355 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6712 (mm-30) REVERT: A 428 MET cc_start: 0.7444 (mmt) cc_final: 0.7024 (mmp) REVERT: A 508 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8199 (mmpt) REVERT: A 588 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8528 (tt) REVERT: A 1280 LEU cc_start: 0.7420 (tt) cc_final: 0.7000 (tp) REVERT: B 614 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.6989 (t80) REVERT: B 676 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: B 713 MET cc_start: 0.4907 (mmt) cc_final: 0.3857 (ttp) REVERT: C 288 TYR cc_start: 0.8867 (m-10) cc_final: 0.8620 (m-10) REVERT: C 338 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.7292 (t80) REVERT: D 1328 TYR cc_start: 0.1467 (OUTLIER) cc_final: 0.0715 (t80) outliers start: 141 outliers final: 126 residues processed: 236 average time/residue: 0.3199 time to fit residues: 128.6014 Evaluate side-chains 236 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 102 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1008 LYS Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1232 LYS Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 553 LYS Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 614 PHE Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 676 ASP Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1143 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1167 SER Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1233 ASN Chi-restraints excluded: chain D residue 1272 ASP Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1299 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Chi-restraints excluded: chain D residue 1348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 293 optimal weight: 20.0000 chunk 270 optimal weight: 9.9990 chunk 234 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 25428 Z= 0.411 Angle : 0.701 11.121 34768 Z= 0.361 Chirality : 0.044 0.213 3941 Planarity : 0.004 0.050 4195 Dihedral : 15.660 164.951 4369 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.34 % Favored : 88.48 % Rotamer: Outliers : 6.00 % Allowed : 27.73 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.15), residues: 2883 helix: -0.22 (0.18), residues: 798 sheet: -1.37 (0.20), residues: 679 loop : -2.44 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 682 HIS 0.008 0.001 HIS C 110 PHE 0.023 0.002 PHE D1296 TYR 0.018 0.002 TYR A 951 ARG 0.006 0.001 ARG C 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 98 time to evaluate : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7814 (p0) cc_final: 0.7304 (p0) REVERT: A 115 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7368 (mm110) REVERT: A 169 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8206 (pp) REVERT: A 355 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6821 (mm-30) REVERT: A 508 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8265 (mmpt) REVERT: A 588 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8504 (tt) REVERT: A 815 THR cc_start: 0.6656 (OUTLIER) cc_final: 0.6393 (t) REVERT: A 1280 LEU cc_start: 0.7650 (tt) cc_final: 0.7235 (tp) REVERT: B 614 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.6960 (t80) REVERT: B 650 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7901 (ttpt) REVERT: B 676 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: C 68 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7350 (t70) REVERT: C 288 TYR cc_start: 0.8962 (m-10) cc_final: 0.8749 (m-10) REVERT: C 338 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.7467 (t80) REVERT: D 1328 TYR cc_start: 0.1413 (OUTLIER) cc_final: 0.0474 (t80) outliers start: 153 outliers final: 127 residues processed: 244 average time/residue: 0.3002 time to fit residues: 125.0920 Evaluate side-chains 234 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 95 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 916 CYS Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 990 ASP Chi-restraints excluded: chain A residue 1008 LYS Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1232 LYS Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 614 PHE Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 676 ASP Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 338 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain D residue 1097 VAL Chi-restraints excluded: chain D residue 1108 ASP Chi-restraints excluded: chain D residue 1143 VAL Chi-restraints excluded: chain D residue 1151 PHE Chi-restraints excluded: chain D residue 1167 SER Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1212 THR Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1233 ASN Chi-restraints excluded: chain D residue 1272 ASP Chi-restraints excluded: chain D residue 1290 HIS Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1299 VAL Chi-restraints excluded: chain D residue 1317 ASP Chi-restraints excluded: chain D residue 1327 VAL Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1347 VAL Chi-restraints excluded: chain D residue 1348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 234 optimal weight: 0.1980 chunk 98 optimal weight: 9.9990 chunk 240 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** 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 = 0.085263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.066761 restraints weight = 108777.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.066699 restraints weight = 77116.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.066902 restraints weight = 62115.116| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25428 Z= 0.157 Angle : 0.587 12.025 34768 Z= 0.299 Chirality : 0.042 0.216 3941 Planarity : 0.003 0.052 4195 Dihedral : 15.418 166.204 4369 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.98 % Favored : 91.85 % Rotamer: Outliers : 4.31 % Allowed : 29.45 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.15), residues: 2883 helix: 0.08 (0.18), residues: 795 sheet: -1.11 (0.20), residues: 665 loop : -2.23 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 308 HIS 0.006 0.001 HIS A1290 PHE 0.020 0.001 PHE D1296 TYR 0.011 0.001 TYR C 120 ARG 0.004 0.000 ARG A1286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4170.45 seconds wall clock time: 78 minutes 33.98 seconds (4713.98 seconds total)