Starting phenix.real_space_refine on Mon Jun 16 22:25:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b62_44235/06_2025/9b62_44235.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b62_44235/06_2025/9b62_44235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b62_44235/06_2025/9b62_44235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b62_44235/06_2025/9b62_44235.map" model { file = "/net/cci-nas-00/data/ceres_data/9b62_44235/06_2025/9b62_44235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b62_44235/06_2025/9b62_44235.cif" } resolution = 2.9 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= 0.005 sd= 1.201 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 P 6 5.49 5 Mg 2 5.21 5 S 102 5.16 5 C 12327 2.51 5 N 3268 2.21 5 O 3582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19287 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8380 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 35, 'TRANS': 997} Chain breaks: 1 Chain: "B" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1405 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain: "C" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1251 Classifications: {'peptide': 156} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 139} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 630 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2026 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 9, 'TRANS': 242} Chain breaks: 3 Chain: "F" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "G" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3886 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 500} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.23, per 1000 atoms: 0.63 Number of scatterers: 19287 At special positions: 0 Unit cell: (120.405, 136.363, 179.157, 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) S 102 16.00 P 6 15.00 Mg 2 11.99 O 3582 8.00 N 3268 7.00 C 12327 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.58 Conformation dependent library (CDL) restraints added in 2.3 seconds 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 8 sheets defined 60.3% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 9 through 15 Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 40 through 55 removed outlier: 3.530A pdb=" N ARG A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 61 removed outlier: 3.614A pdb=" N THR A 61 " --> pdb=" O ASP A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 61' Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.850A pdb=" N GLU A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 91 removed outlier: 3.640A pdb=" N LYS A 76 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP A 91 " --> pdb=" O ILE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 115 Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 125 through 146 Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 148 through 157 Processing helix chain 'A' and resid 160 through 180 Processing helix chain 'A' and resid 187 through 201 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.593A pdb=" N ARG A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 245 through 254 removed outlier: 3.739A pdb=" N PHE A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 280 through 295 removed outlier: 3.592A pdb=" N THR A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 312 through 340 removed outlier: 6.436A pdb=" N GLN A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 358 Processing helix chain 'A' and resid 362 through 384 removed outlier: 3.715A pdb=" N TYR A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 423 removed outlier: 4.029A pdb=" N LEU A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 4.561A pdb=" N PHE A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LYS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 416 " --> pdb=" O MET A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 468 Processing helix chain 'A' and resid 468 through 485 removed outlier: 3.818A pdb=" N THR A 472 " --> pdb=" O ASP A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 504 removed outlier: 3.716A pdb=" N ILE A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 531 removed outlier: 3.572A pdb=" N GLU A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 550 Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 558 through 573 removed outlier: 3.557A pdb=" N LEU A 562 " --> pdb=" O HIS A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 595 Processing helix chain 'A' and resid 596 through 601 removed outlier: 4.205A pdb=" N VAL A 600 " --> pdb=" O ARG A 596 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN A 601 " --> pdb=" O ARG A 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 596 through 601' Processing helix chain 'A' and resid 609 through 617 removed outlier: 3.534A pdb=" N GLU A 613 " --> pdb=" O PRO A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 642 removed outlier: 3.615A pdb=" N MET A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 658 Processing helix chain 'A' and resid 658 through 675 removed outlier: 3.502A pdb=" N ASN A 662 " --> pdb=" O MET A 658 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 674 " --> pdb=" O GLN A 670 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 681 through 703 Processing helix chain 'A' and resid 706 through 736 removed outlier: 5.458A pdb=" N LEU A 715 " --> pdb=" O GLY A 711 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ASP A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 741 Processing helix chain 'A' and resid 742 through 765 removed outlier: 3.520A pdb=" N ARG A 765 " --> pdb=" O GLY A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 776 through 784 removed outlier: 4.144A pdb=" N LEU A 780 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 781 " --> pdb=" O VAL A 777 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A 782 " --> pdb=" O PRO A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 791 Processing helix chain 'A' and resid 792 through 796 removed outlier: 3.603A pdb=" N ARG A 796 " --> pdb=" O PRO A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 812 removed outlier: 4.305A pdb=" N LEU A 801 " --> pdb=" O GLU A 797 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 802 " --> pdb=" O PRO A 798 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 805 " --> pdb=" O LEU A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 816 removed outlier: 3.725A pdb=" N THR A 816 " --> pdb=" O GLY A 813 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 813 through 816' Processing helix chain 'A' and resid 818 through 835 removed outlier: 5.341A pdb=" N GLU A 828 " --> pdb=" O ASP A 824 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N CYS A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 859 Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 867 through 882 removed outlier: 3.614A pdb=" N PHE A 882 " --> pdb=" O ILE A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 907 removed outlier: 3.798A pdb=" N GLU A 907 " --> pdb=" O ASN A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 931 removed outlier: 4.331A pdb=" N GLN A 912 " --> pdb=" O GLU A 908 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N SER A 913 " --> pdb=" O ALA A 909 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N CYS A 920 " --> pdb=" O GLN A 916 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ASP A 921 " --> pdb=" O THR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 937 removed outlier: 3.832A pdb=" N THR A 936 " --> pdb=" O THR A 933 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ALA A 937 " --> pdb=" O SER A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 955 Processing helix chain 'A' and resid 969 through 986 removed outlier: 3.739A pdb=" N GLN A 975 " --> pdb=" O GLN A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1004 Processing helix chain 'A' and resid 1007 through 1022 Processing helix chain 'A' and resid 1034 through 1052 Processing helix chain 'B' and resid 22 through 33 removed outlier: 3.592A pdb=" N HIS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 94 through 100 removed outlier: 3.763A pdb=" N TYR B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 110 Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 138 through 143 removed outlier: 3.859A pdb=" N LYS B 142 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 170 Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 108 through 121 removed outlier: 4.311A pdb=" N ASN C 121 " --> pdb=" O GLN C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 140 removed outlier: 3.637A pdb=" N TYR C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 155 Processing helix chain 'D' and resid 44 through 55 removed outlier: 3.712A pdb=" N SER D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLN D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 81 removed outlier: 4.123A pdb=" N LEU D 80 " --> pdb=" O THR D 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 2641 through 2652 Processing helix chain 'E' and resid 2656 through 2663 removed outlier: 3.528A pdb=" N CYS E2659 " --> pdb=" O THR E2656 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR E2660 " --> pdb=" O PHE E2657 " (cutoff:3.500A) Processing helix chain 'E' and resid 2676 through 2685 removed outlier: 3.533A pdb=" N LEU E2684 " --> pdb=" O ALA E2680 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN E2685 " --> pdb=" O VAL E2681 " (cutoff:3.500A) Processing helix chain 'E' and resid 2849 through 2857 Processing helix chain 'E' and resid 3026 through 3048 removed outlier: 3.713A pdb=" N ALA E3030 " --> pdb=" O THR E3026 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN E3048 " --> pdb=" O LEU E3044 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 32 Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 76 through 81 removed outlier: 4.116A pdb=" N TYR F 80 " --> pdb=" O ARG F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 99 removed outlier: 3.525A pdb=" N TYR F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 112 removed outlier: 3.805A pdb=" N VAL F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 removed outlier: 3.709A pdb=" N LYS F 141 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS F 142 " --> pdb=" O PHE F 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 137 through 142' Processing helix chain 'F' and resid 158 through 170 Processing helix chain 'F' and resid 190 through 205 removed outlier: 4.378A pdb=" N ALA F 195 " --> pdb=" O PRO F 191 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN F 196 " --> pdb=" O ALA F 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 15 removed outlier: 3.569A pdb=" N LYS G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 37 No H-bonds generated for 'chain 'G' and resid 35 through 37' Processing helix chain 'G' and resid 38 through 47 Processing helix chain 'G' and resid 62 through 74 Processing helix chain 'G' and resid 95 through 111 removed outlier: 3.520A pdb=" N ALA G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 138 removed outlier: 4.268A pdb=" N ALA G 134 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU G 135 " --> pdb=" O GLY G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 142 removed outlier: 3.570A pdb=" N PHE G 142 " --> pdb=" O SER G 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 139 through 142' Processing helix chain 'G' and resid 154 through 177 removed outlier: 3.866A pdb=" N GLY G 158 " --> pdb=" O MET G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 207 removed outlier: 3.541A pdb=" N VAL G 206 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE G 207 " --> pdb=" O ALA G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 235 removed outlier: 4.004A pdb=" N ALA G 227 " --> pdb=" O PRO G 223 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL G 234 " --> pdb=" O GLN G 230 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN G 235 " --> pdb=" O ALA G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 263 removed outlier: 3.967A pdb=" N THR G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 290 Processing helix chain 'G' and resid 306 through 319 removed outlier: 4.038A pdb=" N ASP G 319 " --> pdb=" O GLU G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 347 removed outlier: 3.503A pdb=" N GLU G 339 " --> pdb=" O GLU G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 440 removed outlier: 3.637A pdb=" N PHE G 440 " --> pdb=" O THR G 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 442 through 449 removed outlier: 3.769A pdb=" N LEU G 447 " --> pdb=" O PRO G 443 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU G 449 " --> pdb=" O LYS G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 461 removed outlier: 3.586A pdb=" N ILE G 457 " --> pdb=" O SER G 453 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA G 458 " --> pdb=" O SER G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 465 through 479 removed outlier: 4.254A pdb=" N VAL G 479 " --> pdb=" O LYS G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 483 through 503 Processing helix chain 'G' and resid 508 through 520 Processing helix chain 'G' and resid 535 through 547 removed outlier: 3.850A pdb=" N GLN G 547 " --> pdb=" O ASN G 543 " (cutoff:3.500A) Processing helix chain 'G' and resid 555 through 564 Processing helix chain 'G' and resid 567 through 572 removed outlier: 3.614A pdb=" N SER G 572 " --> pdb=" O SER G 568 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 587 removed outlier: 3.526A pdb=" N VAL G 587 " --> pdb=" O THR G 583 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 430 through 434 Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 54 removed outlier: 6.890A pdb=" N PHE B 11 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N TRP B 64 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU B 13 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR B 66 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU B 15 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N CYS B 85 " --> pdb=" O GLN B 10 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS B 12 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE B 87 " --> pdb=" O LYS B 12 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B 14 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N MET B 89 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 16 " --> pdb=" O MET B 89 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ASP B 91 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA B 86 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N CYS B 120 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE B 88 " --> pdb=" O CYS B 120 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASN B 122 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE B 90 " --> pdb=" O ASN B 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 25 through 30 removed outlier: 5.795A pdb=" N ASN C 40 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 62 through 65 removed outlier: 4.203A pdb=" N ASP D 86 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N GLU D 33 " --> pdb=" O GLU E2637 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU E2637 " --> pdb=" O GLU D 33 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N HIS D 35 " --> pdb=" O VAL E2635 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU E2633 " --> pdb=" O LYS D 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 2981 through 2986 removed outlier: 6.930A pdb=" N VAL E2981 " --> pdb=" O ARG E2975 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ARG E2975 " --> pdb=" O VAL E2981 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E2983 " --> pdb=" O MET E2973 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG E2974 " --> pdb=" O ASP E2957 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP E2957 " --> pdb=" O ARG E2974 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU E2940 " --> pdb=" O ARG E2953 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL E2955 " --> pdb=" O ALA E2938 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA E2938 " --> pdb=" O VAL E2955 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASP E2957 " --> pdb=" O GLU E2936 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLU E2936 " --> pdb=" O ASP E2957 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS E2959 " --> pdb=" O PHE E2934 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE E2934 " --> pdb=" O LYS E2959 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU E2961 " --> pdb=" O ILE E2932 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE E2932 " --> pdb=" O LEU E2961 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N HIS E2963 " --> pdb=" O GLU E2930 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N GLU E2930 " --> pdb=" O HIS E2963 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLN E3019 " --> pdb=" O TRP E2943 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 45 through 54 removed outlier: 6.626A pdb=" N PHE F 11 " --> pdb=" O ASN F 62 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N TRP F 64 " --> pdb=" O PHE F 11 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU F 13 " --> pdb=" O TRP F 64 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR F 66 " --> pdb=" O LEU F 13 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU F 15 " --> pdb=" O THR F 66 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N CYS F 85 " --> pdb=" O GLN F 10 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS F 12 " --> pdb=" O CYS F 85 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ILE F 87 " --> pdb=" O LYS F 12 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL F 14 " --> pdb=" O ILE F 87 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N MET F 89 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL F 16 " --> pdb=" O MET F 89 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N ASP F 91 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA F 86 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N CYS F 120 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE F 88 " --> pdb=" O CYS F 120 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASN F 122 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE F 90 " --> pdb=" O ASN F 122 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN F 145 " --> pdb=" O ILE F 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 23 through 24 removed outlier: 6.827A pdb=" N LEU G 23 " --> pdb=" O ARG G 55 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU G 54 " --> pdb=" O HIS G 83 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS G 82 " --> pdb=" O ASP G 118 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE G 185 " --> pdb=" O HIS G 214 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL G 213 " --> pdb=" O ASN G 242 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE G 269 " --> pdb=" O ASN G 299 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU G 298 " --> pdb=" O ASP G 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 31 through 32 1018 hydrogen bonds defined for protein. 2976 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.72 Time building geometry restraints manager: 5.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6284 1.34 - 1.46: 3180 1.46 - 1.57: 10041 1.57 - 1.69: 10 1.69 - 1.81: 162 Bond restraints: 19677 Sorted by residual: bond pdb=" CG PRO A 427 " pdb=" CD PRO A 427 " ideal model delta sigma weight residual 1.503 1.478 0.025 3.40e-02 8.65e+02 5.44e-01 bond pdb=" CG PRO A 842 " pdb=" CD PRO A 842 " ideal model delta sigma weight residual 1.503 1.479 0.024 3.40e-02 8.65e+02 5.07e-01 bond pdb=" C2' GTP F 301 " pdb=" C3' GTP F 301 " ideal model delta sigma weight residual 1.524 1.510 0.014 2.00e-02 2.50e+03 4.65e-01 bond pdb=" CB PRO A 143 " pdb=" CG PRO A 143 " ideal model delta sigma weight residual 1.492 1.525 -0.033 5.00e-02 4.00e+02 4.43e-01 bond pdb=" CG PRO G 216 " pdb=" CD PRO G 216 " ideal model delta sigma weight residual 1.503 1.481 0.022 3.40e-02 8.65e+02 4.16e-01 ... (remaining 19672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 26044 1.14 - 2.29: 429 2.29 - 3.43: 105 3.43 - 4.57: 41 4.57 - 5.72: 8 Bond angle restraints: 26627 Sorted by residual: angle pdb=" N LYS A 124 " pdb=" CA LYS A 124 " pdb=" CB LYS A 124 " ideal model delta sigma weight residual 113.65 109.90 3.75 1.47e+00 4.63e-01 6.52e+00 angle pdb=" N SER G 278 " pdb=" CA SER G 278 " pdb=" CB SER G 278 " ideal model delta sigma weight residual 113.65 110.05 3.60 1.47e+00 4.63e-01 6.01e+00 angle pdb=" N VAL G 479 " pdb=" CA VAL G 479 " pdb=" C VAL G 479 " ideal model delta sigma weight residual 112.29 110.11 2.18 9.40e-01 1.13e+00 5.40e+00 angle pdb=" CA TRP A 762 " pdb=" CB TRP A 762 " pdb=" CG TRP A 762 " ideal model delta sigma weight residual 113.60 109.83 3.77 1.90e+00 2.77e-01 3.94e+00 angle pdb=" N VAL A 676 " pdb=" CA VAL A 676 " pdb=" C VAL A 676 " ideal model delta sigma weight residual 113.07 110.40 2.67 1.36e+00 5.41e-01 3.86e+00 ... (remaining 26622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.71: 11788 31.71 - 63.42: 110 63.42 - 95.13: 8 95.13 - 126.83: 3 126.83 - 158.54: 4 Dihedral angle restraints: 11913 sinusoidal: 4872 harmonic: 7041 Sorted by residual: dihedral pdb=" C8 GTP B 301 " pdb=" C1' GTP B 301 " pdb=" N9 GTP B 301 " pdb=" O4' GTP B 301 " ideal model delta sinusoidal sigma weight residual 104.59 -53.95 158.54 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" O5' GTP B 301 " pdb=" O3A GTP B 301 " pdb=" PA GTP B 301 " pdb=" PB GTP B 301 " ideal model delta sinusoidal sigma weight residual 274.12 118.87 155.25 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O5' GTP F 301 " pdb=" O3A GTP F 301 " pdb=" PA GTP F 301 " pdb=" PB GTP F 301 " ideal model delta sinusoidal sigma weight residual 274.12 126.11 148.02 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 11910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1869 0.027 - 0.055: 769 0.055 - 0.082: 210 0.082 - 0.110: 114 0.110 - 0.137: 44 Chirality restraints: 3006 Sorted by residual: chirality pdb=" CA ILE B 88 " pdb=" N ILE B 88 " pdb=" C ILE B 88 " pdb=" CB ILE B 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE C 45 " pdb=" N ILE C 45 " pdb=" C ILE C 45 " pdb=" CB ILE C 45 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE B 59 " pdb=" N ILE B 59 " pdb=" C ILE B 59 " pdb=" CB ILE B 59 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 3003 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 96 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO G 97 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO G 97 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 97 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 76 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.65e+00 pdb=" C ARG B 76 " 0.022 2.00e-02 2.50e+03 pdb=" O ARG B 76 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP B 77 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 83 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO C 84 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 84 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 84 " -0.018 5.00e-02 4.00e+02 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 86 2.46 - 3.07: 13878 3.07 - 3.68: 27694 3.68 - 4.29: 43349 4.29 - 4.90: 73471 Nonbonded interactions: 158478 Sorted by model distance: nonbonded pdb=" O1B GTP F 301 " pdb="MG MG F 302 " model vdw 1.851 2.170 nonbonded pdb=" OG1 THR B 24 " pdb="MG MG B 302 " model vdw 1.858 2.170 nonbonded pdb=" O3G GTP F 301 " pdb="MG MG F 302 " model vdw 1.888 2.170 nonbonded pdb=" OG1 THR B 42 " pdb="MG MG B 302 " model vdw 1.899 2.170 nonbonded pdb=" O1B GTP B 301 " pdb="MG MG B 302 " model vdw 1.913 2.170 ... (remaining 158473 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 44.200 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 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:13.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.003 0.115 19678 Z= 0.144 Angle : 0.440 5.716 26627 Z= 0.231 Chirality : 0.037 0.137 3006 Planarity : 0.003 0.054 3405 Dihedral : 10.589 158.542 7337 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.62 % Allowed : 2.70 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.28 (0.18), residues: 2390 helix: 2.07 (0.15), residues: 1255 sheet: -0.80 (0.36), residues: 229 loop : -0.41 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 762 HIS 0.004 0.001 HIS A1014 PHE 0.017 0.001 PHE A 882 TYR 0.014 0.001 TYR A 657 ARG 0.003 0.000 ARG A 845 Details of bonding type rmsd hydrogen bonds : bond 0.14499 ( 1018) hydrogen bonds : angle 5.85941 ( 2976) covalent geometry : bond 0.00275 (19677) covalent geometry : angle 0.44044 (26627) Misc. bond : bond 0.11486 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 245 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 HIS cc_start: 0.7011 (m-70) cc_final: 0.6458 (t-170) REVERT: A 647 GLN cc_start: 0.7375 (mm-40) cc_final: 0.7016 (tp40) REVERT: B 171 ASP cc_start: 0.7693 (t70) cc_final: 0.7480 (t70) REVERT: B 175 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6999 (mm-30) REVERT: D 48 LYS cc_start: 0.8030 (tttt) cc_final: 0.7198 (mmmt) REVERT: D 82 MET cc_start: 0.4376 (mtt) cc_final: 0.3669 (ttt) REVERT: E 2942 ARG cc_start: 0.8006 (ttp-110) cc_final: 0.7718 (ttp-110) outliers start: 13 outliers final: 4 residues processed: 255 average time/residue: 1.3929 time to fit residues: 400.6173 Evaluate side-chains 156 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 152 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain F residue 30 HIS Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain G residue 101 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 chunk 72 optimal weight: 0.0020 chunk 113 optimal weight: 0.2980 chunk 138 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 overall best weight: 1.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 704 HIS A 993 GLN B 48 HIS ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN E2857 ASN E2967 ASN E3043 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.112588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.086107 restraints weight = 34472.930| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.20 r_work: 0.3161 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19678 Z= 0.164 Angle : 0.580 8.365 26627 Z= 0.298 Chirality : 0.042 0.203 3006 Planarity : 0.004 0.080 3405 Dihedral : 8.657 160.931 2596 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.56 % Allowed : 8.35 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.23 (0.18), residues: 2390 helix: 1.97 (0.15), residues: 1278 sheet: -0.73 (0.36), residues: 219 loop : -0.45 (0.22), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 762 HIS 0.008 0.001 HIS G 544 PHE 0.020 0.002 PHE A 882 TYR 0.017 0.002 TYR A 657 ARG 0.006 0.001 ARG A 845 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 1018) hydrogen bonds : angle 4.55037 ( 2976) covalent geometry : bond 0.00394 (19677) covalent geometry : angle 0.58016 (26627) Misc. bond : bond 0.00228 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.7206 (m) cc_final: 0.6854 (m) REVERT: A 354 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8669 (mmp) REVERT: A 362 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: A 509 HIS cc_start: 0.7412 (m-70) cc_final: 0.6260 (t-170) REVERT: A 514 LYS cc_start: 0.8087 (tttt) cc_final: 0.7544 (ttmm) REVERT: A 647 GLN cc_start: 0.7501 (mm-40) cc_final: 0.6826 (tp40) REVERT: B 134 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8460 (pttp) REVERT: B 171 ASP cc_start: 0.8003 (t70) cc_final: 0.7622 (t70) REVERT: B 175 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7337 (mm-30) REVERT: D 48 LYS cc_start: 0.7936 (tttt) cc_final: 0.6940 (mmmt) REVERT: D 91 TYR cc_start: 0.6487 (m-80) cc_final: 0.6262 (m-10) REVERT: E 2964 THR cc_start: 0.8753 (p) cc_final: 0.8419 (m) REVERT: G 488 MET cc_start: 0.7564 (mmm) cc_final: 0.7119 (mmp) outliers start: 33 outliers final: 13 residues processed: 190 average time/residue: 1.3701 time to fit residues: 295.3353 Evaluate side-chains 166 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 338 CYS Chi-restraints excluded: chain G residue 463 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 12 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 201 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 856 ASN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2967 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.111641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.084891 restraints weight = 34053.523| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.21 r_work: 0.3140 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19678 Z= 0.207 Angle : 0.583 7.933 26627 Z= 0.299 Chirality : 0.043 0.160 3006 Planarity : 0.005 0.072 3405 Dihedral : 8.652 161.718 2594 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.42 % Allowed : 9.06 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.94 (0.17), residues: 2390 helix: 1.74 (0.14), residues: 1283 sheet: -0.88 (0.35), residues: 230 loop : -0.57 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 762 HIS 0.011 0.001 HIS G 544 PHE 0.023 0.002 PHE A 882 TYR 0.037 0.002 TYR E3010 ARG 0.006 0.001 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.04749 ( 1018) hydrogen bonds : angle 4.48932 ( 2976) covalent geometry : bond 0.00512 (19677) covalent geometry : angle 0.58272 (26627) Misc. bond : bond 0.00188 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 159 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.6998 (m) cc_final: 0.6512 (m) REVERT: A 351 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8868 (mt) REVERT: A 354 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8811 (mmp) REVERT: A 509 HIS cc_start: 0.7482 (m-70) cc_final: 0.6211 (t-90) REVERT: A 514 LYS cc_start: 0.8229 (tttt) cc_final: 0.7708 (ttmm) REVERT: A 647 GLN cc_start: 0.7557 (mm-40) cc_final: 0.6833 (tp40) REVERT: B 134 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8481 (pttp) REVERT: B 171 ASP cc_start: 0.8084 (t70) cc_final: 0.7622 (t70) REVERT: B 175 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7537 (mm-30) REVERT: D 48 LYS cc_start: 0.7906 (tttt) cc_final: 0.6809 (mmtp) REVERT: D 75 HIS cc_start: 0.6238 (OUTLIER) cc_final: 0.5807 (m170) REVERT: D 82 MET cc_start: 0.4387 (mtt) cc_final: 0.2975 (ttt) REVERT: E 3009 ASP cc_start: 0.8362 (t0) cc_final: 0.8149 (t0) REVERT: G 213 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8914 (p) REVERT: G 488 MET cc_start: 0.7716 (mmm) cc_final: 0.7368 (tmm) outliers start: 51 outliers final: 22 residues processed: 194 average time/residue: 1.2450 time to fit residues: 275.2468 Evaluate side-chains 166 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 2635 VAL Chi-restraints excluded: chain E residue 2940 LEU Chi-restraints excluded: chain E residue 2955 VAL Chi-restraints excluded: chain E residue 2990 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 338 CYS Chi-restraints excluded: chain G residue 463 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 68 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 321 ASN A 601 GLN B 103 ASN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2967 ASN F 55 ASN F 205 GLN G 150 ASN ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.111330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.084506 restraints weight = 34623.161| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.33 r_work: 0.3143 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19678 Z= 0.197 Angle : 0.570 8.226 26627 Z= 0.293 Chirality : 0.043 0.185 3006 Planarity : 0.004 0.065 3405 Dihedral : 8.666 161.852 2594 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.28 % Allowed : 10.05 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.81 (0.17), residues: 2390 helix: 1.62 (0.14), residues: 1303 sheet: -0.76 (0.36), residues: 219 loop : -0.75 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 762 HIS 0.009 0.001 HIS G 544 PHE 0.023 0.002 PHE A 882 TYR 0.039 0.002 TYR E3010 ARG 0.005 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 1018) hydrogen bonds : angle 4.45774 ( 2976) covalent geometry : bond 0.00488 (19677) covalent geometry : angle 0.57003 (26627) Misc. bond : bond 0.00166 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.6970 (m) cc_final: 0.6475 (m) REVERT: A 351 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8821 (mt) REVERT: A 509 HIS cc_start: 0.7420 (m-70) cc_final: 0.6125 (t-90) REVERT: A 514 LYS cc_start: 0.8145 (tttt) cc_final: 0.7601 (ttmm) REVERT: A 647 GLN cc_start: 0.7521 (mm-40) cc_final: 0.6787 (tt0) REVERT: A 738 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7409 (ptt) REVERT: B 171 ASP cc_start: 0.8073 (t70) cc_final: 0.7595 (t70) REVERT: B 175 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7502 (mm-30) REVERT: D 48 LYS cc_start: 0.7899 (tttt) cc_final: 0.6733 (mmtp) REVERT: D 75 HIS cc_start: 0.6269 (OUTLIER) cc_final: 0.5885 (m170) REVERT: D 82 MET cc_start: 0.4430 (mtt) cc_final: 0.2984 (ttt) REVERT: E 2931 GLU cc_start: 0.7509 (mp0) cc_final: 0.7307 (mp0) REVERT: E 3009 ASP cc_start: 0.8336 (t70) cc_final: 0.8097 (t0) REVERT: E 3043 ASN cc_start: 0.9091 (m-40) cc_final: 0.8848 (t0) REVERT: G 143 THR cc_start: 0.9185 (p) cc_final: 0.8881 (t) REVERT: G 213 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8927 (p) outliers start: 48 outliers final: 27 residues processed: 187 average time/residue: 1.5474 time to fit residues: 332.9580 Evaluate side-chains 177 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 2940 LEU Chi-restraints excluded: chain E residue 2947 VAL Chi-restraints excluded: chain E residue 2955 VAL Chi-restraints excluded: chain E residue 2990 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 338 CYS Chi-restraints excluded: chain G residue 463 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 130 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 223 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 193 HIS A 601 GLN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN E2967 ASN F 114 ASN ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.112908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.085992 restraints weight = 34313.488| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.30 r_work: 0.3167 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19678 Z= 0.124 Angle : 0.515 8.622 26627 Z= 0.265 Chirality : 0.041 0.242 3006 Planarity : 0.004 0.059 3405 Dihedral : 8.550 161.412 2594 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.99 % Allowed : 10.67 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.03 (0.18), residues: 2390 helix: 1.87 (0.14), residues: 1296 sheet: -0.66 (0.35), residues: 228 loop : -0.74 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 762 HIS 0.009 0.001 HIS G 544 PHE 0.017 0.001 PHE D 36 TYR 0.030 0.001 TYR E3010 ARG 0.004 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 1018) hydrogen bonds : angle 4.29036 ( 2976) covalent geometry : bond 0.00290 (19677) covalent geometry : angle 0.51455 (26627) Misc. bond : bond 0.00124 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 3.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.7064 (m) cc_final: 0.6506 (m) REVERT: A 122 LYS cc_start: 0.7581 (mmmt) cc_final: 0.7318 (mmpt) REVERT: A 351 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8749 (mt) REVERT: A 509 HIS cc_start: 0.7368 (m-70) cc_final: 0.6046 (t-90) REVERT: A 647 GLN cc_start: 0.7471 (mm-40) cc_final: 0.6747 (tt0) REVERT: A 738 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7354 (ptt) REVERT: B 171 ASP cc_start: 0.8061 (t70) cc_final: 0.7610 (t70) REVERT: B 175 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7507 (mm-30) REVERT: D 48 LYS cc_start: 0.7892 (tttt) cc_final: 0.6578 (mmtp) REVERT: D 75 HIS cc_start: 0.6334 (OUTLIER) cc_final: 0.5924 (m170) REVERT: D 82 MET cc_start: 0.4451 (mtt) cc_final: 0.3025 (ttt) REVERT: E 2931 GLU cc_start: 0.7514 (mp0) cc_final: 0.7210 (mp0) REVERT: E 3009 ASP cc_start: 0.8304 (t70) cc_final: 0.8050 (t0) REVERT: E 3010 TYR cc_start: 0.8457 (t80) cc_final: 0.8243 (t80) REVERT: E 3043 ASN cc_start: 0.9130 (m-40) cc_final: 0.8887 (t0) REVERT: G 143 THR cc_start: 0.9138 (p) cc_final: 0.8862 (t) REVERT: G 213 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8892 (p) outliers start: 42 outliers final: 18 residues processed: 188 average time/residue: 1.4144 time to fit residues: 306.7704 Evaluate side-chains 166 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 2635 VAL Chi-restraints excluded: chain E residue 2947 VAL Chi-restraints excluded: chain E residue 2990 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 327 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 231 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 chunk 177 optimal weight: 0.3980 chunk 11 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 601 GLN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.112738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.085284 restraints weight = 34346.271| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.43 r_work: 0.3159 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19678 Z= 0.136 Angle : 0.522 9.317 26627 Z= 0.267 Chirality : 0.041 0.277 3006 Planarity : 0.004 0.059 3405 Dihedral : 8.499 161.355 2592 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.37 % Allowed : 10.72 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.06 (0.18), residues: 2390 helix: 1.89 (0.14), residues: 1302 sheet: -0.57 (0.36), residues: 226 loop : -0.76 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 762 HIS 0.007 0.001 HIS G 544 PHE 0.018 0.001 PHE A 882 TYR 0.023 0.001 TYR E3010 ARG 0.003 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 1018) hydrogen bonds : angle 4.24901 ( 2976) covalent geometry : bond 0.00326 (19677) covalent geometry : angle 0.52204 (26627) Misc. bond : bond 0.00118 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 157 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.7323 (m) cc_final: 0.6768 (m) REVERT: A 351 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8634 (mt) REVERT: A 509 HIS cc_start: 0.7266 (m-70) cc_final: 0.6084 (t-170) REVERT: A 647 GLN cc_start: 0.7420 (mm-40) cc_final: 0.6758 (tt0) REVERT: A 738 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7251 (ptt) REVERT: B 34 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6581 (pp20) REVERT: B 171 ASP cc_start: 0.7977 (t70) cc_final: 0.7549 (t70) REVERT: B 175 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7301 (mm-30) REVERT: D 48 LYS cc_start: 0.7927 (tttt) cc_final: 0.6658 (mmtp) REVERT: D 75 HIS cc_start: 0.6320 (OUTLIER) cc_final: 0.5974 (m170) REVERT: D 82 MET cc_start: 0.4398 (mtt) cc_final: 0.2963 (ttt) REVERT: E 2931 GLU cc_start: 0.7411 (mp0) cc_final: 0.7196 (mp0) REVERT: E 3009 ASP cc_start: 0.8174 (t70) cc_final: 0.7913 (t0) REVERT: E 3043 ASN cc_start: 0.9138 (m-40) cc_final: 0.8905 (t0) REVERT: F 114 ASN cc_start: 0.8265 (p0) cc_final: 0.8041 (p0) REVERT: G 143 THR cc_start: 0.9081 (p) cc_final: 0.8811 (t) REVERT: G 213 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8786 (p) outliers start: 50 outliers final: 25 residues processed: 189 average time/residue: 1.2968 time to fit residues: 282.9097 Evaluate side-chains 179 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 2635 VAL Chi-restraints excluded: chain E residue 2641 THR Chi-restraints excluded: chain E residue 2940 LEU Chi-restraints excluded: chain E residue 2947 VAL Chi-restraints excluded: chain E residue 2955 VAL Chi-restraints excluded: chain E residue 2990 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 327 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 116 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 0.1980 chunk 96 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 229 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 310 ASN A 601 GLN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2967 ASN F 205 GLN ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.113239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.086323 restraints weight = 33936.187| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.34 r_work: 0.3185 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19678 Z= 0.123 Angle : 0.513 8.898 26627 Z= 0.263 Chirality : 0.040 0.150 3006 Planarity : 0.004 0.057 3405 Dihedral : 8.448 161.421 2592 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.23 % Allowed : 11.14 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.15 (0.18), residues: 2390 helix: 1.99 (0.14), residues: 1296 sheet: -0.55 (0.37), residues: 216 loop : -0.75 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 762 HIS 0.006 0.001 HIS G 544 PHE 0.017 0.001 PHE A 882 TYR 0.025 0.001 TYR E3010 ARG 0.006 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 1018) hydrogen bonds : angle 4.19168 ( 2976) covalent geometry : bond 0.00289 (19677) covalent geometry : angle 0.51325 (26627) Misc. bond : bond 0.00098 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.7133 (m) cc_final: 0.6466 (m) REVERT: A 351 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8623 (mt) REVERT: A 354 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8781 (mmp) REVERT: A 509 HIS cc_start: 0.7320 (m-70) cc_final: 0.6026 (t-90) REVERT: A 647 GLN cc_start: 0.7462 (mm-40) cc_final: 0.6719 (tt0) REVERT: A 738 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7363 (ptt) REVERT: A 753 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7976 (mtp85) REVERT: B 34 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6794 (pp20) REVERT: B 175 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7448 (mm-30) REVERT: D 48 LYS cc_start: 0.7966 (tttt) cc_final: 0.6836 (mmtp) REVERT: D 75 HIS cc_start: 0.6369 (OUTLIER) cc_final: 0.6089 (m170) REVERT: D 82 MET cc_start: 0.4460 (mtt) cc_final: 0.2985 (ttt) REVERT: E 2931 GLU cc_start: 0.7512 (mp0) cc_final: 0.7155 (mp0) REVERT: E 3009 ASP cc_start: 0.8261 (t70) cc_final: 0.7976 (t0) REVERT: E 3043 ASN cc_start: 0.9099 (m-40) cc_final: 0.8892 (t0) REVERT: F 56 ARG cc_start: 0.9089 (mtp85) cc_final: 0.8826 (mtp85) REVERT: F 114 ASN cc_start: 0.8350 (p0) cc_final: 0.8147 (p0) REVERT: F 205 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8059 (mp10) REVERT: G 143 THR cc_start: 0.9163 (p) cc_final: 0.8898 (t) REVERT: G 213 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8881 (p) outliers start: 47 outliers final: 23 residues processed: 198 average time/residue: 1.3219 time to fit residues: 300.9084 Evaluate side-chains 176 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 2635 VAL Chi-restraints excluded: chain E residue 2641 THR Chi-restraints excluded: chain E residue 2940 LEU Chi-restraints excluded: chain E residue 2947 VAL Chi-restraints excluded: chain E residue 2955 VAL Chi-restraints excluded: chain E residue 2990 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 327 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 49 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 86 optimal weight: 0.0670 chunk 222 optimal weight: 0.9980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 72 ASN A 310 ASN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.113062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.086313 restraints weight = 34120.141| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.33 r_work: 0.3166 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19678 Z= 0.131 Angle : 0.517 8.730 26627 Z= 0.264 Chirality : 0.041 0.215 3006 Planarity : 0.004 0.057 3405 Dihedral : 8.433 161.431 2592 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.90 % Allowed : 11.62 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.16 (0.18), residues: 2390 helix: 1.97 (0.14), residues: 1303 sheet: -0.47 (0.36), residues: 226 loop : -0.74 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 762 HIS 0.006 0.001 HIS G 544 PHE 0.018 0.001 PHE A 882 TYR 0.025 0.001 TYR D 51 ARG 0.002 0.000 ARG A 845 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 1018) hydrogen bonds : angle 4.17766 ( 2976) covalent geometry : bond 0.00314 (19677) covalent geometry : angle 0.51709 (26627) Misc. bond : bond 0.00103 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.7336 (m) cc_final: 0.6705 (m) REVERT: A 351 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8567 (mt) REVERT: A 509 HIS cc_start: 0.7231 (m-70) cc_final: 0.6062 (t-170) REVERT: A 647 GLN cc_start: 0.7391 (mm-40) cc_final: 0.6712 (tt0) REVERT: A 738 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7296 (ptt) REVERT: A 753 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7794 (mtp85) REVERT: B 175 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7305 (mm-30) REVERT: D 48 LYS cc_start: 0.7946 (tttt) cc_final: 0.6765 (mttm) REVERT: D 75 HIS cc_start: 0.6366 (OUTLIER) cc_final: 0.6093 (m170) REVERT: D 82 MET cc_start: 0.4397 (mtt) cc_final: 0.2964 (ttt) REVERT: E 2931 GLU cc_start: 0.7445 (mp0) cc_final: 0.7102 (mp0) REVERT: E 3009 ASP cc_start: 0.8073 (t70) cc_final: 0.7791 (t0) REVERT: E 3043 ASN cc_start: 0.9130 (m-40) cc_final: 0.8925 (t0) REVERT: F 114 ASN cc_start: 0.8273 (p0) cc_final: 0.8042 (p0) REVERT: F 205 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: G 143 THR cc_start: 0.9109 (p) cc_final: 0.8847 (t) REVERT: G 213 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8779 (p) REVERT: G 348 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7426 (t80) outliers start: 40 outliers final: 25 residues processed: 178 average time/residue: 1.2149 time to fit residues: 247.8897 Evaluate side-chains 179 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 2635 VAL Chi-restraints excluded: chain E residue 2641 THR Chi-restraints excluded: chain E residue 2940 LEU Chi-restraints excluded: chain E residue 2947 VAL Chi-restraints excluded: chain E residue 2955 VAL Chi-restraints excluded: chain E residue 2990 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 348 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 37 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 210 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** E2662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3000 ASN F 205 GLN ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.113192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.086254 restraints weight = 34267.687| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.30 r_work: 0.3166 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 19678 Z= 0.128 Angle : 0.515 9.213 26627 Z= 0.263 Chirality : 0.040 0.188 3006 Planarity : 0.004 0.057 3405 Dihedral : 8.404 161.375 2592 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.71 % Allowed : 11.76 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.20 (0.18), residues: 2390 helix: 2.00 (0.14), residues: 1303 sheet: -0.43 (0.36), residues: 226 loop : -0.73 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 762 HIS 0.006 0.001 HIS G 544 PHE 0.018 0.001 PHE A 882 TYR 0.018 0.001 TYR A 657 ARG 0.003 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 1018) hydrogen bonds : angle 4.13724 ( 2976) covalent geometry : bond 0.00306 (19677) covalent geometry : angle 0.51548 (26627) Misc. bond : bond 0.00098 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.7344 (m) cc_final: 0.6709 (m) REVERT: A 351 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8558 (mt) REVERT: A 509 HIS cc_start: 0.7225 (m-70) cc_final: 0.6072 (t-170) REVERT: A 647 GLN cc_start: 0.7378 (mm-40) cc_final: 0.6706 (tt0) REVERT: A 738 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7291 (ptt) REVERT: A 753 ARG cc_start: 0.8078 (mtt180) cc_final: 0.7786 (mtp85) REVERT: B 175 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7301 (mm-30) REVERT: D 48 LYS cc_start: 0.8020 (tttt) cc_final: 0.6768 (mmtp) REVERT: D 75 HIS cc_start: 0.6393 (OUTLIER) cc_final: 0.6085 (m170) REVERT: D 82 MET cc_start: 0.4350 (mtt) cc_final: 0.2925 (ttt) REVERT: E 2931 GLU cc_start: 0.7477 (mp0) cc_final: 0.7144 (mp0) REVERT: E 3009 ASP cc_start: 0.8072 (t70) cc_final: 0.7792 (t0) REVERT: F 114 ASN cc_start: 0.8281 (p0) cc_final: 0.8071 (p0) REVERT: F 205 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7309 (mp10) REVERT: G 143 THR cc_start: 0.9122 (p) cc_final: 0.8881 (t) REVERT: G 213 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8767 (p) REVERT: G 317 MET cc_start: 0.8033 (tpp) cc_final: 0.7812 (tpt) outliers start: 36 outliers final: 26 residues processed: 176 average time/residue: 1.2045 time to fit residues: 243.5322 Evaluate side-chains 177 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 2635 VAL Chi-restraints excluded: chain E residue 2641 THR Chi-restraints excluded: chain E residue 2940 LEU Chi-restraints excluded: chain E residue 2947 VAL Chi-restraints excluded: chain E residue 2955 VAL Chi-restraints excluded: chain E residue 2990 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 327 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 205 optimal weight: 2.9990 chunk 17 optimal weight: 0.0770 chunk 200 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 72 ASN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** E2662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2949 GLN E2967 ASN E3000 ASN ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.113650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.086372 restraints weight = 34064.695| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.36 r_work: 0.3186 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19678 Z= 0.113 Angle : 0.510 9.507 26627 Z= 0.260 Chirality : 0.040 0.168 3006 Planarity : 0.004 0.056 3405 Dihedral : 8.374 161.353 2592 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.47 % Allowed : 12.14 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.24 (0.18), residues: 2390 helix: 2.05 (0.14), residues: 1303 sheet: -0.47 (0.37), residues: 211 loop : -0.73 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 762 HIS 0.006 0.001 HIS G 544 PHE 0.016 0.001 PHE A 882 TYR 0.017 0.001 TYR A 657 ARG 0.003 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 1018) hydrogen bonds : angle 4.10147 ( 2976) covalent geometry : bond 0.00265 (19677) covalent geometry : angle 0.50960 (26627) Misc. bond : bond 0.00084 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.7075 (m) cc_final: 0.6442 (m) REVERT: A 351 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8578 (mt) REVERT: A 509 HIS cc_start: 0.7280 (m-70) cc_final: 0.5973 (t-170) REVERT: A 647 GLN cc_start: 0.7420 (mm-40) cc_final: 0.6686 (tt0) REVERT: A 738 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7364 (ptt) REVERT: A 753 ARG cc_start: 0.8317 (mtt180) cc_final: 0.7968 (mtp85) REVERT: B 175 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7467 (mm-30) REVERT: D 48 LYS cc_start: 0.7997 (tttt) cc_final: 0.6733 (mmtp) REVERT: D 75 HIS cc_start: 0.6422 (OUTLIER) cc_final: 0.6109 (m170) REVERT: D 82 MET cc_start: 0.4413 (mtt) cc_final: 0.2936 (ttt) REVERT: E 2931 GLU cc_start: 0.7588 (mp0) cc_final: 0.7238 (mp0) REVERT: E 3009 ASP cc_start: 0.8196 (t70) cc_final: 0.7927 (t0) REVERT: G 143 THR cc_start: 0.9203 (p) cc_final: 0.8953 (t) REVERT: G 213 VAL cc_start: 0.9124 (OUTLIER) cc_final: 0.8872 (p) outliers start: 31 outliers final: 25 residues processed: 172 average time/residue: 1.2227 time to fit residues: 243.1901 Evaluate side-chains 174 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 2635 VAL Chi-restraints excluded: chain E residue 2641 THR Chi-restraints excluded: chain E residue 2940 LEU Chi-restraints excluded: chain E residue 2947 VAL Chi-restraints excluded: chain E residue 2955 VAL Chi-restraints excluded: chain E residue 2990 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 35 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 151 optimal weight: 0.0770 chunk 189 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** E2662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3000 ASN F 114 ASN ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.113042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.085809 restraints weight = 34334.566| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.34 r_work: 0.3172 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19678 Z= 0.135 Angle : 0.524 10.948 26627 Z= 0.267 Chirality : 0.041 0.184 3006 Planarity : 0.004 0.057 3405 Dihedral : 8.383 161.410 2592 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.75 % Allowed : 12.00 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.19 (0.18), residues: 2390 helix: 2.00 (0.14), residues: 1304 sheet: -0.64 (0.35), residues: 238 loop : -0.68 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 762 HIS 0.006 0.001 HIS G 544 PHE 0.018 0.001 PHE A 882 TYR 0.019 0.001 TYR A 657 ARG 0.003 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 1018) hydrogen bonds : angle 4.11934 ( 2976) covalent geometry : bond 0.00325 (19677) covalent geometry : angle 0.52394 (26627) Misc. bond : bond 0.00100 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13672.26 seconds wall clock time: 239 minutes 44.06 seconds (14384.06 seconds total)