Starting phenix.real_space_refine on Tue Nov 19 10:14:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b62_44235/11_2024/9b62_44235.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b62_44235/11_2024/9b62_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b62_44235/11_2024/9b62_44235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b62_44235/11_2024/9b62_44235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b62_44235/11_2024/9b62_44235.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b62_44235/11_2024/9b62_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-5513/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: 9.14, per 1000 atoms: 0.47 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=0, symmetry=0 Time building additional restraints: 4.68 Conformation dependent library (CDL) restraints added in 2.9 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: 1.99 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: 6.83 Time building geometry restraints manager: 5.46 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: 1.32 - 2.03: 7 2.03 - 2.75: 2625 2.75 - 3.47: 27747 3.47 - 4.18: 44210 4.18 - 4.90: 83893 Nonbonded interactions: 158482 Sorted by model distance: nonbonded pdb=" C GLY D 97 " pdb=" NZ LYS G 524 " model vdw 1.315 3.350 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 ... (remaining 158477 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: 20.310 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 5.010 Set scattering table: 0.000 Process input model: 38.260 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.090 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:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.810 ------------------------------------------------------------------------------- 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 0.033 19677 Z= 0.181 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 : 1.315 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 *********************** 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 : 2.300 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: 1.4005 time to fit residues: 402.7854 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 : 2.346 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19677 Z= 0.266 Angle : 0.578 8.019 26627 Z= 0.297 Chirality : 0.042 0.210 3006 Planarity : 0.004 0.082 3405 Dihedral : 8.653 160.826 2596 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.47 % Allowed : 8.39 % Favored : 90.14 % 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: 1.25 (0.18), residues: 2390 helix: 1.99 (0.15), residues: 1278 sheet: -0.71 (0.36), residues: 219 loop : -0.43 (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 0.019 0.002 PHE A 882 TYR 0.017 0.002 TYR A 657 ARG 0.006 0.000 ARG A 845 *********************** 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 192 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: A 509 HIS cc_start: 0.7049 (m-70) cc_final: 0.6528 (t-170) REVERT: A 514 LYS cc_start: 0.7962 (tttt) cc_final: 0.7528 (ttmm) REVERT: A 647 GLN cc_start: 0.7270 (mm-40) cc_final: 0.6944 (tp40) REVERT: A 659 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8167 (tp) REVERT: B 134 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8281 (pttp) REVERT: B 171 ASP cc_start: 0.7680 (t70) cc_final: 0.7435 (t70) REVERT: B 175 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7082 (mm-30) REVERT: D 48 LYS cc_start: 0.8004 (tttt) cc_final: 0.7084 (mmmt) REVERT: D 85 GLU cc_start: 0.5110 (tp30) cc_final: 0.4888 (tp30) REVERT: D 91 TYR cc_start: 0.6005 (m-80) cc_final: 0.5794 (m-10) REVERT: E 2663 ARG cc_start: 0.5521 (OUTLIER) cc_final: 0.5249 (mtp-110) REVERT: E 2964 THR cc_start: 0.8465 (p) cc_final: 0.7989 (m) outliers start: 31 outliers final: 12 residues processed: 183 average time/residue: 1.4458 time to fit residues: 299.9708 Evaluate side-chains 162 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 134 LYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 2663 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 94 SER 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 120 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 179 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 216 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 214 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 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 193 HIS A 856 ASN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2967 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19677 Z= 0.217 Angle : 0.531 8.297 26627 Z= 0.273 Chirality : 0.041 0.157 3006 Planarity : 0.004 0.071 3405 Dihedral : 8.548 161.211 2594 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.04 % Allowed : 9.15 % Favored : 88.81 % 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: 1.14 (0.18), residues: 2390 helix: 1.87 (0.14), residues: 1301 sheet: -0.69 (0.36), residues: 223 loop : -0.53 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 762 HIS 0.011 0.001 HIS G 544 PHE 0.017 0.001 PHE A 882 TYR 0.038 0.002 TYR E3010 ARG 0.005 0.000 ARG A 44 *********************** 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 208 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 HIS cc_start: 0.7010 (m-70) cc_final: 0.6492 (t-170) REVERT: A 514 LYS cc_start: 0.7917 (tttt) cc_final: 0.7503 (ttmm) REVERT: A 647 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6932 (tp40) REVERT: A 659 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8168 (tp) REVERT: B 171 ASP cc_start: 0.7669 (t70) cc_final: 0.7420 (t70) REVERT: B 175 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7087 (mm-30) REVERT: D 48 LYS cc_start: 0.7959 (tttt) cc_final: 0.6949 (mmtp) REVERT: D 75 HIS cc_start: 0.5718 (m170) cc_final: 0.5295 (m170) REVERT: D 82 MET cc_start: 0.3959 (mtt) cc_final: 0.3070 (ttt) REVERT: G 213 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8627 (p) outliers start: 43 outliers final: 14 residues processed: 195 average time/residue: 1.2974 time to fit residues: 288.9695 Evaluate side-chains 163 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 974 LEU 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 95 THR Chi-restraints excluded: chain F residue 16 VAL 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 213 VAL Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 338 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 103 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 217 optimal weight: 0.7980 chunk 230 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 205 optimal weight: 0.2980 chunk 61 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 81 GLN A 601 GLN B 103 ASN ** C 40 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19677 Z= 0.159 Angle : 0.496 9.655 26627 Z= 0.254 Chirality : 0.040 0.167 3006 Planarity : 0.004 0.062 3405 Dihedral : 8.433 160.991 2592 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.80 % Allowed : 10.15 % Favored : 88.05 % 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: 1.27 (0.18), residues: 2390 helix: 2.02 (0.14), residues: 1305 sheet: -0.45 (0.36), residues: 220 loop : -0.62 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 762 HIS 0.010 0.001 HIS G 544 PHE 0.015 0.001 PHE G 132 TYR 0.034 0.001 TYR E3010 ARG 0.004 0.000 ARG A 44 *********************** 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 197 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 HIS cc_start: 0.6967 (m-70) cc_final: 0.6439 (t-170) REVERT: A 647 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6930 (tt0) REVERT: A 659 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8125 (tp) REVERT: A 738 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6589 (ptt) REVERT: B 158 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: B 175 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7095 (mm-30) REVERT: D 48 LYS cc_start: 0.7977 (tttt) cc_final: 0.6845 (mmtp) REVERT: D 75 HIS cc_start: 0.5707 (OUTLIER) cc_final: 0.5349 (m170) REVERT: D 82 MET cc_start: 0.4013 (mtt) cc_final: 0.3059 (ttt) REVERT: G 143 THR cc_start: 0.8767 (p) cc_final: 0.8558 (t) outliers start: 38 outliers final: 16 residues processed: 184 average time/residue: 1.3590 time to fit residues: 285.3783 Evaluate side-chains 161 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 GLU 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 974 LEU Chi-restraints excluded: chain B residue 158 GLU 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 2947 VAL Chi-restraints excluded: chain E residue 2955 VAL Chi-restraints excluded: chain E residue 2990 THR Chi-restraints excluded: chain F residue 81 ILE 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 327 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 94 optimal weight: 0.0570 chunk 196 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.9700 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19677 Z= 0.213 Angle : 0.519 8.547 26627 Z= 0.265 Chirality : 0.041 0.289 3006 Planarity : 0.004 0.060 3405 Dihedral : 8.369 161.345 2590 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.94 % Allowed : 10.53 % Favored : 87.53 % 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: 1.23 (0.18), residues: 2390 helix: 2.00 (0.14), residues: 1305 sheet: -0.46 (0.36), residues: 221 loop : -0.67 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 762 HIS 0.007 0.001 HIS G 544 PHE 0.019 0.001 PHE A 882 TYR 0.026 0.001 TYR E3010 ARG 0.005 0.000 ARG A 44 *********************** 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 197 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 2.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 HIS cc_start: 0.6977 (m-70) cc_final: 0.6444 (t-170) REVERT: A 647 GLN cc_start: 0.7211 (mm-40) cc_final: 0.6945 (tt0) REVERT: A 659 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8118 (tp) REVERT: A 738 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6611 (ptt) REVERT: B 158 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: B 175 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7088 (mm-30) REVERT: D 48 LYS cc_start: 0.8003 (tttt) cc_final: 0.6850 (mmtp) REVERT: D 75 HIS cc_start: 0.5827 (OUTLIER) cc_final: 0.5492 (m170) REVERT: D 82 MET cc_start: 0.3994 (mtt) cc_final: 0.3046 (ttt) REVERT: G 213 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8598 (p) outliers start: 41 outliers final: 19 residues processed: 180 average time/residue: 1.3415 time to fit residues: 277.1094 Evaluate side-chains 168 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 974 LEU Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 158 GLU 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 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 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 77 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 191 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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** ** E2662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2967 ASN F 205 GLN G 150 ASN ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19677 Z= 0.226 Angle : 0.522 8.701 26627 Z= 0.268 Chirality : 0.041 0.151 3006 Planarity : 0.004 0.059 3405 Dihedral : 8.378 161.531 2590 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.99 % Allowed : 10.81 % Favored : 87.20 % 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: 1.98 (0.14), residues: 1302 sheet: -0.47 (0.36), residues: 226 loop : -0.69 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 762 HIS 0.007 0.001 HIS G 544 PHE 0.020 0.001 PHE A 882 TYR 0.024 0.001 TYR E3010 ARG 0.004 0.000 ARG A 44 *********************** 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 195 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 HIS cc_start: 0.6986 (m-70) cc_final: 0.6456 (t-170) REVERT: A 647 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6949 (tt0) REVERT: A 659 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8155 (tp) REVERT: A 738 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6637 (ptt) REVERT: B 158 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: B 175 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7084 (mm-30) REVERT: D 48 LYS cc_start: 0.8061 (tttt) cc_final: 0.6937 (mmtp) REVERT: D 82 MET cc_start: 0.4002 (mtt) cc_final: 0.3058 (ttt) REVERT: G 213 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8590 (p) outliers start: 42 outliers final: 24 residues processed: 182 average time/residue: 1.1254 time to fit residues: 234.7376 Evaluate side-chains 172 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 974 LEU Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain D residue 26 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 168 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS ** E2662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19677 Z= 0.183 Angle : 0.504 8.596 26627 Z= 0.259 Chirality : 0.040 0.206 3006 Planarity : 0.004 0.057 3405 Dihedral : 8.336 161.574 2590 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.13 % Allowed : 11.00 % Favored : 86.87 % 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: 1.25 (0.18), residues: 2390 helix: 2.03 (0.14), residues: 1306 sheet: -0.44 (0.36), residues: 226 loop : -0.69 (0.21), residues: 858 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 0.017 0.001 PHE A 882 TYR 0.016 0.001 TYR A 657 ARG 0.005 0.000 ARG A 44 *********************** 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 196 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 HIS cc_start: 0.6964 (m-70) cc_final: 0.6429 (t-170) REVERT: A 647 GLN cc_start: 0.7175 (mm-40) cc_final: 0.6925 (tt0) REVERT: A 659 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8122 (tp) REVERT: A 738 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6621 (ptt) REVERT: B 158 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: B 175 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7078 (mm-30) REVERT: D 48 LYS cc_start: 0.8042 (tttt) cc_final: 0.6841 (mmtp) REVERT: D 82 MET cc_start: 0.3950 (mtt) cc_final: 0.3047 (ttt) REVERT: F 205 GLN cc_start: 0.8103 (mt0) cc_final: 0.7828 (mp10) REVERT: G 213 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8573 (p) outliers start: 45 outliers final: 27 residues processed: 183 average time/residue: 0.9832 time to fit residues: 207.5446 Evaluate side-chains 176 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 1.586 ------------------------------------------------------------------------------- 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 362 GLU Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 659 LEU 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 974 LEU Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain D residue 26 VAL 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 Chi-restraints excluded: chain G residue 356 SER Chi-restraints excluded: chain G residue 433 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 113 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 180 optimal weight: 0.0170 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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** D 75 HIS ** E2662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 ASN ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 19677 Z= 0.167 Angle : 0.495 8.953 26627 Z= 0.255 Chirality : 0.039 0.181 3006 Planarity : 0.004 0.057 3405 Dihedral : 8.264 161.172 2590 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.99 % Allowed : 11.33 % Favored : 86.68 % 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: 1.32 (0.18), residues: 2390 helix: 2.10 (0.14), residues: 1308 sheet: -0.36 (0.36), residues: 221 loop : -0.69 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 762 HIS 0.006 0.001 HIS A 558 PHE 0.015 0.001 PHE A 882 TYR 0.014 0.001 TYR A 657 ARG 0.005 0.000 ARG A 44 *********************** 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 196 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 HIS cc_start: 0.6955 (m-70) cc_final: 0.6401 (t-170) REVERT: A 647 GLN cc_start: 0.7089 (mm-40) cc_final: 0.6834 (tt0) REVERT: A 659 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7959 (tp) REVERT: A 738 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6602 (ptt) REVERT: B 158 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: B 175 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7070 (mm-30) REVERT: D 48 LYS cc_start: 0.7963 (tttt) cc_final: 0.6895 (mttm) REVERT: D 82 MET cc_start: 0.3881 (mtt) cc_final: 0.3017 (ttt) REVERT: G 213 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8563 (p) outliers start: 42 outliers final: 25 residues processed: 184 average time/residue: 1.2369 time to fit residues: 261.5472 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 : 1.779 ------------------------------------------------------------------------------- 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 362 GLU 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 56 ARG Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain D residue 26 VAL 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 Chi-restraints excluded: chain G residue 433 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 0.7980 chunk 219 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 B 10 GLN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 HIS ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 19677 Z= 0.437 Angle : 0.631 12.305 26627 Z= 0.321 Chirality : 0.045 0.166 3006 Planarity : 0.005 0.060 3405 Dihedral : 8.519 161.947 2590 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.94 % Allowed : 11.57 % 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: 0.86 (0.17), residues: 2390 helix: 1.67 (0.14), residues: 1306 sheet: -0.57 (0.36), residues: 215 loop : -0.80 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 91 HIS 0.006 0.001 HIS G 544 PHE 0.030 0.002 PHE A 882 TYR 0.030 0.002 TYR A 657 ARG 0.006 0.001 ARG B 29 *********************** 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: 41 poor density : 146 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 HIS cc_start: 0.7059 (m-70) cc_final: 0.6528 (t-170) REVERT: A 647 GLN cc_start: 0.7201 (mm-40) cc_final: 0.6905 (tt0) REVERT: A 738 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6703 (ptt) REVERT: B 158 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: B 175 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7055 (mm-30) REVERT: D 48 LYS cc_start: 0.8158 (tttt) cc_final: 0.6963 (mttm) REVERT: D 75 HIS cc_start: 0.5798 (OUTLIER) cc_final: 0.5479 (m170) REVERT: D 82 MET cc_start: 0.4019 (mtt) cc_final: 0.3094 (ttt) REVERT: F 114 ASN cc_start: 0.8010 (p0) cc_final: 0.7752 (p0) REVERT: G 348 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.7100 (t80) outliers start: 41 outliers final: 26 residues processed: 174 average time/residue: 1.2853 time to fit residues: 256.5547 Evaluate side-chains 171 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 2.321 ------------------------------------------------------------------------------- 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 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 43 LEU Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 158 GLU 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 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 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 348 PHE Chi-restraints excluded: chain G residue 433 ASP Chi-restraints excluded: chain G residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 chunk 107 optimal weight: 0.4980 chunk 157 optimal weight: 0.9980 chunk 237 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 145 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 149 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS B 10 GLN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3000 ASN ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19677 Z= 0.179 Angle : 0.515 9.935 26627 Z= 0.265 Chirality : 0.040 0.154 3006 Planarity : 0.004 0.055 3405 Dihedral : 8.363 160.864 2590 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.33 % Allowed : 12.14 % 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: 1.14 (0.18), residues: 2390 helix: 1.96 (0.14), residues: 1307 sheet: -0.54 (0.36), residues: 216 loop : -0.76 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 762 HIS 0.006 0.001 HIS A 558 PHE 0.016 0.001 PHE G 132 TYR 0.020 0.001 TYR A 657 ARG 0.003 0.000 ARG A 44 ********************** 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 177 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 HIS cc_start: 0.6968 (m-70) cc_final: 0.6451 (t-170) REVERT: A 647 GLN cc_start: 0.7096 (mm-40) cc_final: 0.6842 (tt0) REVERT: A 738 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6628 (ptt) REVERT: B 158 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: B 175 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7087 (mm-30) REVERT: D 48 LYS cc_start: 0.8032 (tttt) cc_final: 0.6895 (mttm) REVERT: D 75 HIS cc_start: 0.5831 (OUTLIER) cc_final: 0.5464 (m170) REVERT: D 82 MET cc_start: 0.3880 (mtt) cc_final: 0.3040 (ttt) REVERT: F 114 ASN cc_start: 0.7983 (p0) cc_final: 0.7736 (p0) REVERT: G 213 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8543 (p) REVERT: G 348 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6984 (t80) outliers start: 28 outliers final: 20 residues processed: 170 average time/residue: 1.2547 time to fit residues: 244.6097 Evaluate side-chains 167 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 2.220 ------------------------------------------------------------------------------- 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 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 43 LEU Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain D residue 75 HIS 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 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 348 PHE Chi-restraints excluded: chain G residue 433 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 3.9990 chunk 57 optimal weight: 0.3980 chunk 174 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 189 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** E2967 ASN E3000 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 = 0.3818 r_free = 0.3818 target = 0.113834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.086383 restraints weight = 33974.094| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.35 r_work: 0.3192 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19677 Z= 0.184 Angle : 0.512 9.386 26627 Z= 0.262 Chirality : 0.040 0.148 3006 Planarity : 0.004 0.056 3405 Dihedral : 8.271 161.157 2590 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.33 % Allowed : 12.19 % 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: 1.24 (0.18), residues: 2390 helix: 2.04 (0.14), residues: 1307 sheet: -0.45 (0.37), residues: 211 loop : -0.74 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 762 HIS 0.006 0.001 HIS A 558 PHE 0.017 0.001 PHE A 882 TYR 0.019 0.001 TYR A 657 ARG 0.006 0.000 ARG F 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5863.63 seconds wall clock time: 144 minutes 30.22 seconds (8670.22 seconds total)