Starting phenix.real_space_refine on Sun Aug 24 10:38:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b62_44235/08_2025/9b62_44235.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b62_44235/08_2025/9b62_44235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b62_44235/08_2025/9b62_44235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b62_44235/08_2025/9b62_44235.map" model { file = "/net/cci-nas-00/data/ceres_data/9b62_44235/08_2025/9b62_44235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b62_44235/08_2025/9b62_44235.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.63, per 1000 atoms: 0.24 Number of scatterers: 19287 At special positions: 0 Unit cell: (120.405, 136.363, 179.157, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 6 15.00 Mg 2 11.99 O 3582 8.00 N 3268 7.00 C 12327 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 972.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.76 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: 4.06 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6284 1.34 - 1.46: 3180 1.46 - 1.57: 10041 1.57 - 1.69: 10 1.69 - 1.81: 162 Bond restraints: 19677 Sorted by residual: bond pdb=" CG PRO A 427 " pdb=" CD PRO A 427 " ideal model delta sigma weight residual 1.503 1.478 0.025 3.40e-02 8.65e+02 5.44e-01 bond pdb=" CG PRO A 842 " pdb=" CD PRO A 842 " ideal model delta sigma weight residual 1.503 1.479 0.024 3.40e-02 8.65e+02 5.07e-01 bond pdb=" C2' GTP F 301 " pdb=" C3' GTP F 301 " ideal model delta sigma weight residual 1.524 1.510 0.014 2.00e-02 2.50e+03 4.65e-01 bond pdb=" CB PRO A 143 " pdb=" CG PRO A 143 " ideal model delta sigma weight residual 1.492 1.525 -0.033 5.00e-02 4.00e+02 4.43e-01 bond pdb=" CG PRO G 216 " pdb=" CD PRO G 216 " ideal model delta sigma weight residual 1.503 1.481 0.022 3.40e-02 8.65e+02 4.16e-01 ... (remaining 19672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 26044 1.14 - 2.29: 429 2.29 - 3.43: 105 3.43 - 4.57: 41 4.57 - 5.72: 8 Bond angle restraints: 26627 Sorted by residual: angle pdb=" N LYS A 124 " pdb=" CA LYS A 124 " pdb=" CB LYS A 124 " ideal model delta sigma weight residual 113.65 109.90 3.75 1.47e+00 4.63e-01 6.52e+00 angle pdb=" N SER G 278 " pdb=" CA SER G 278 " pdb=" CB SER G 278 " ideal model delta sigma weight residual 113.65 110.05 3.60 1.47e+00 4.63e-01 6.01e+00 angle pdb=" N VAL G 479 " pdb=" CA VAL G 479 " pdb=" C VAL G 479 " ideal model delta sigma weight residual 112.29 110.11 2.18 9.40e-01 1.13e+00 5.40e+00 angle pdb=" CA TRP A 762 " pdb=" CB TRP A 762 " pdb=" CG TRP A 762 " ideal model delta sigma weight residual 113.60 109.83 3.77 1.90e+00 2.77e-01 3.94e+00 angle pdb=" N VAL A 676 " pdb=" CA VAL A 676 " pdb=" C VAL A 676 " ideal model delta sigma weight residual 113.07 110.40 2.67 1.36e+00 5.41e-01 3.86e+00 ... (remaining 26622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.71: 11788 31.71 - 63.42: 110 63.42 - 95.13: 8 95.13 - 126.83: 3 126.83 - 158.54: 4 Dihedral angle restraints: 11913 sinusoidal: 4872 harmonic: 7041 Sorted by residual: dihedral pdb=" C8 GTP B 301 " pdb=" C1' GTP B 301 " pdb=" N9 GTP B 301 " pdb=" O4' GTP B 301 " ideal model delta sinusoidal sigma weight residual 104.59 -53.95 158.54 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" O5' GTP B 301 " pdb=" O3A GTP B 301 " pdb=" PA GTP B 301 " pdb=" PB GTP B 301 " ideal model delta sinusoidal sigma weight residual 274.12 118.87 155.25 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O5' GTP F 301 " pdb=" O3A GTP F 301 " pdb=" PA GTP F 301 " pdb=" PB GTP F 301 " ideal model delta sinusoidal sigma weight residual 274.12 126.11 148.02 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 11910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1869 0.027 - 0.055: 769 0.055 - 0.082: 210 0.082 - 0.110: 114 0.110 - 0.137: 44 Chirality restraints: 3006 Sorted by residual: chirality pdb=" CA ILE B 88 " pdb=" N ILE B 88 " pdb=" C ILE B 88 " pdb=" CB ILE B 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE C 45 " pdb=" N ILE C 45 " pdb=" C ILE C 45 " pdb=" CB ILE C 45 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE B 59 " pdb=" N ILE B 59 " pdb=" C ILE B 59 " pdb=" CB ILE B 59 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 3003 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 96 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO G 97 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO G 97 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 97 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 76 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.65e+00 pdb=" C ARG B 76 " 0.022 2.00e-02 2.50e+03 pdb=" O ARG B 76 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP B 77 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 83 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO C 84 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 84 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 84 " -0.018 5.00e-02 4.00e+02 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 86 2.46 - 3.07: 13878 3.07 - 3.68: 27694 3.68 - 4.29: 43349 4.29 - 4.90: 73471 Nonbonded interactions: 158478 Sorted by model distance: nonbonded pdb=" O1B GTP F 301 " pdb="MG MG F 302 " model vdw 1.851 2.170 nonbonded pdb=" OG1 THR B 24 " pdb="MG MG B 302 " model vdw 1.858 2.170 nonbonded pdb=" O3G GTP F 301 " pdb="MG MG F 302 " model vdw 1.888 2.170 nonbonded pdb=" OG1 THR B 42 " pdb="MG MG B 302 " model vdw 1.899 2.170 nonbonded pdb=" O1B GTP B 301 " pdb="MG MG B 302 " model vdw 1.913 2.170 ... (remaining 158473 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.390 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:8.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 19678 Z= 0.144 Angle : 0.440 5.716 26627 Z= 0.231 Chirality : 0.037 0.137 3006 Planarity : 0.003 0.054 3405 Dihedral : 10.589 158.542 7337 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.62 % Allowed : 2.70 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 845 TYR 0.014 0.001 TYR A 657 PHE 0.017 0.001 PHE A 882 TRP 0.010 0.001 TRP A 762 HIS 0.004 0.001 HIS A1014 Details of bonding type rmsd covalent geometry : bond 0.00275 (19677) covalent geometry : angle 0.44044 (26627) hydrogen bonds : bond 0.14499 ( 1018) hydrogen bonds : angle 5.85941 ( 2976) Misc. bond : bond 0.11486 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 245 time to evaluate : 0.860 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: 0.7167 time to fit residues: 205.1766 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 : 0.848 ------------------------------------------------------------------------------- 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 216 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.0070 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.113893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.086964 restraints weight = 34253.441| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.25 r_work: 0.3196 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19678 Z= 0.133 Angle : 0.553 8.229 26627 Z= 0.285 Chirality : 0.041 0.208 3006 Planarity : 0.004 0.081 3405 Dihedral : 8.595 160.465 2596 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.42 % Allowed : 8.11 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.18), residues: 2390 helix: 2.05 (0.15), residues: 1286 sheet: -0.67 (0.36), residues: 219 loop : -0.40 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 845 TYR 0.014 0.001 TYR D 51 PHE 0.016 0.001 PHE A 882 TRP 0.015 0.001 TRP A 762 HIS 0.009 0.001 HIS G 544 Details of bonding type rmsd covalent geometry : bond 0.00307 (19677) covalent geometry : angle 0.55336 (26627) hydrogen bonds : bond 0.04336 ( 1018) hydrogen bonds : angle 4.50824 ( 2976) Misc. bond : bond 0.00177 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.6975 (m) cc_final: 0.6588 (m) REVERT: A 354 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8820 (mmp) REVERT: A 509 HIS cc_start: 0.7472 (m-70) cc_final: 0.6185 (t-170) REVERT: A 514 LYS cc_start: 0.8173 (tttt) cc_final: 0.7695 (ttmp) REVERT: A 647 GLN cc_start: 0.7564 (mm-40) cc_final: 0.6823 (tp40) REVERT: B 56 ARG cc_start: 0.7957 (mtp180) cc_final: 0.7728 (mtm180) REVERT: B 175 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7513 (mm-30) REVERT: D 48 LYS cc_start: 0.7917 (tttt) cc_final: 0.6928 (mmmt) REVERT: D 85 GLU cc_start: 0.5312 (tp30) cc_final: 0.5082 (mm-30) REVERT: D 91 TYR cc_start: 0.6597 (m-80) cc_final: 0.6371 (m-10) REVERT: E 2964 THR cc_start: 0.8799 (p) cc_final: 0.8513 (m) outliers start: 30 outliers final: 8 residues processed: 188 average time/residue: 0.6803 time to fit residues: 144.9808 Evaluate side-chains 152 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 96 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 207 GLN A 321 ASN A 601 GLN A 704 HIS A 856 ASN B 10 GLN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2967 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.110292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.083220 restraints weight = 34645.299| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.36 r_work: 0.3109 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 19678 Z= 0.273 Angle : 0.648 8.855 26627 Z= 0.331 Chirality : 0.046 0.178 3006 Planarity : 0.005 0.075 3405 Dihedral : 8.750 161.921 2592 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.47 % Allowed : 9.44 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.17), residues: 2390 helix: 1.54 (0.14), residues: 1287 sheet: -0.81 (0.36), residues: 211 loop : -0.71 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 845 TYR 0.025 0.002 TYR A 657 PHE 0.029 0.002 PHE A 882 TRP 0.010 0.002 TRP B 104 HIS 0.010 0.001 HIS G 544 Details of bonding type rmsd covalent geometry : bond 0.00682 (19677) covalent geometry : angle 0.64822 (26627) hydrogen bonds : bond 0.05375 ( 1018) hydrogen bonds : angle 4.61542 ( 2976) Misc. bond : bond 0.00222 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.7012 (m) cc_final: 0.6536 (m) REVERT: A 351 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8868 (mt) REVERT: A 514 LYS cc_start: 0.8276 (tttt) cc_final: 0.7746 (ttmm) REVERT: A 647 GLN cc_start: 0.7598 (mm-40) cc_final: 0.6867 (tp40) REVERT: B 34 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6916 (pp20) REVERT: B 175 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7559 (mm-30) REVERT: D 48 LYS cc_start: 0.7932 (tttt) cc_final: 0.6820 (mmtp) REVERT: D 75 HIS cc_start: 0.6215 (m170) cc_final: 0.5771 (m170) REVERT: D 82 MET cc_start: 0.4367 (mtt) cc_final: 0.3015 (ttt) REVERT: E 2942 ARG cc_start: 0.8376 (ttp-110) cc_final: 0.7995 (ttp-110) REVERT: E 3009 ASP cc_start: 0.8363 (t0) cc_final: 0.8156 (t0) REVERT: F 56 ARG cc_start: 0.9245 (mtp85) cc_final: 0.8951 (mtp85) REVERT: G 213 VAL cc_start: 0.9207 (OUTLIER) cc_final: 0.8936 (p) REVERT: G 250 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: G 317 MET cc_start: 0.8174 (tpp) cc_final: 0.7876 (tpp) outliers start: 52 outliers final: 23 residues processed: 192 average time/residue: 0.6170 time to fit residues: 134.1422 Evaluate side-chains 168 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 2635 VAL Chi-restraints excluded: chain E residue 2940 LEU Chi-restraints excluded: chain E residue 2955 VAL Chi-restraints excluded: chain E residue 2990 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 338 CYS Chi-restraints excluded: chain G residue 463 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 0.9990 chunk 224 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 155 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 207 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 193 HIS A 601 GLN B 103 ASN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** E2662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2967 ASN F 205 GLN G 33 ASN ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.112874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.085660 restraints weight = 34306.340| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.31 r_work: 0.3165 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19678 Z= 0.124 Angle : 0.520 8.521 26627 Z= 0.268 Chirality : 0.040 0.171 3006 Planarity : 0.004 0.062 3405 Dihedral : 8.579 161.114 2592 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.94 % Allowed : 10.48 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.18), residues: 2390 helix: 1.77 (0.14), residues: 1307 sheet: -0.73 (0.35), residues: 230 loop : -0.73 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 44 TYR 0.038 0.002 TYR E3010 PHE 0.016 0.001 PHE A 882 TRP 0.017 0.001 TRP A 762 HIS 0.009 0.001 HIS G 544 Details of bonding type rmsd covalent geometry : bond 0.00288 (19677) covalent geometry : angle 0.52031 (26627) hydrogen bonds : bond 0.03979 ( 1018) hydrogen bonds : angle 4.34777 ( 2976) Misc. bond : bond 0.00117 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.7021 (m) cc_final: 0.6555 (m) REVERT: A 122 LYS cc_start: 0.7564 (mmmt) cc_final: 0.7285 (mmpt) REVERT: A 351 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8796 (mt) REVERT: A 354 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8798 (mmp) REVERT: A 509 HIS cc_start: 0.7375 (m-70) cc_final: 0.6056 (t-90) REVERT: A 514 LYS cc_start: 0.8098 (tttt) cc_final: 0.7562 (ttmm) REVERT: A 647 GLN cc_start: 0.7485 (mm-40) cc_final: 0.6755 (tt0) REVERT: A 738 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7354 (ptt) REVERT: B 175 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7512 (mm-30) REVERT: D 48 LYS cc_start: 0.7883 (tttt) cc_final: 0.6730 (mmtp) REVERT: D 75 HIS cc_start: 0.6256 (OUTLIER) cc_final: 0.5844 (m170) REVERT: D 82 MET cc_start: 0.4493 (mtt) cc_final: 0.3049 (ttt) REVERT: E 2931 GLU cc_start: 0.7514 (mp0) cc_final: 0.7230 (mp0) REVERT: E 3009 ASP cc_start: 0.8306 (t70) cc_final: 0.8073 (t0) REVERT: E 3043 ASN cc_start: 0.9101 (m-40) cc_final: 0.8832 (t0) REVERT: G 143 THR cc_start: 0.9143 (p) cc_final: 0.8844 (t) REVERT: G 213 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8870 (p) REVERT: G 317 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7764 (tpp) outliers start: 41 outliers final: 15 residues processed: 184 average time/residue: 0.5968 time to fit residues: 125.2999 Evaluate side-chains 169 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 2947 VAL Chi-restraints excluded: chain E residue 2990 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 317 MET 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 49 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 169 optimal weight: 0.0270 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 310 ASN A 601 GLN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN G 150 ASN ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.112707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.085304 restraints weight = 34127.774| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.37 r_work: 0.3148 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19678 Z= 0.135 Angle : 0.528 8.516 26627 Z= 0.270 Chirality : 0.041 0.272 3006 Planarity : 0.004 0.061 3405 Dihedral : 8.516 161.202 2592 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.18 % Allowed : 10.76 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.18), residues: 2390 helix: 1.85 (0.14), residues: 1302 sheet: -0.59 (0.36), residues: 221 loop : -0.73 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 44 TYR 0.040 0.002 TYR E3010 PHE 0.018 0.001 PHE A 882 TRP 0.015 0.001 TRP A 762 HIS 0.008 0.001 HIS G 544 Details of bonding type rmsd covalent geometry : bond 0.00323 (19677) covalent geometry : angle 0.52786 (26627) hydrogen bonds : bond 0.03952 ( 1018) hydrogen bonds : angle 4.28510 ( 2976) Misc. bond : bond 0.00118 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.7358 (m) cc_final: 0.6864 (m) REVERT: A 351 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8685 (mt) REVERT: A 509 HIS cc_start: 0.7246 (m-70) cc_final: 0.6046 (t-90) REVERT: A 647 GLN cc_start: 0.7426 (mm-40) cc_final: 0.6753 (tt0) REVERT: A 738 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7262 (ptt) REVERT: B 175 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7324 (mm-30) REVERT: D 48 LYS cc_start: 0.7925 (tttt) cc_final: 0.6566 (mmtp) REVERT: D 75 HIS cc_start: 0.6278 (OUTLIER) cc_final: 0.5962 (m170) REVERT: D 82 MET cc_start: 0.4395 (mtt) cc_final: 0.2987 (ttt) REVERT: E 2931 GLU cc_start: 0.7423 (mp0) cc_final: 0.7135 (mp0) REVERT: E 3009 ASP cc_start: 0.8169 (t70) cc_final: 0.7891 (t0) REVERT: E 3043 ASN cc_start: 0.9138 (m-40) cc_final: 0.8874 (t0) REVERT: G 143 THR cc_start: 0.9090 (p) cc_final: 0.8804 (t) REVERT: G 213 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8793 (p) outliers start: 46 outliers final: 21 residues processed: 189 average time/residue: 0.5785 time to fit residues: 124.9693 Evaluate side-chains 173 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 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 59 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 2635 VAL Chi-restraints excluded: chain E residue 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 101 ILE 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 177 optimal weight: 2.9990 chunk 80 optimal weight: 0.0070 chunk 110 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 58 optimal weight: 0.0870 chunk 127 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 chunk 135 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 160 optimal weight: 0.3980 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 310 ASN A 601 GLN B 10 GLN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN E2967 ASN ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.114518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087351 restraints weight = 34057.013| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.27 r_work: 0.3199 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 19678 Z= 0.101 Angle : 0.493 8.759 26627 Z= 0.253 Chirality : 0.039 0.152 3006 Planarity : 0.004 0.058 3405 Dihedral : 8.376 160.379 2592 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.94 % Allowed : 11.10 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.18), residues: 2390 helix: 2.03 (0.14), residues: 1304 sheet: -0.53 (0.36), residues: 222 loop : -0.72 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.017 0.001 TYR E3010 PHE 0.013 0.001 PHE G 132 TRP 0.018 0.001 TRP A 762 HIS 0.007 0.001 HIS G 544 Details of bonding type rmsd covalent geometry : bond 0.00224 (19677) covalent geometry : angle 0.49343 (26627) hydrogen bonds : bond 0.03328 ( 1018) hydrogen bonds : angle 4.13867 ( 2976) Misc. bond : bond 0.00075 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.7127 (m) cc_final: 0.6594 (m) REVERT: A 509 HIS cc_start: 0.7296 (m-70) cc_final: 0.5982 (t-170) REVERT: A 647 GLN cc_start: 0.7477 (mm-40) cc_final: 0.6737 (tt0) REVERT: A 738 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7354 (ptt) REVERT: A 753 ARG cc_start: 0.8300 (mtt180) cc_final: 0.7962 (mtp85) REVERT: B 175 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7487 (mm-30) REVERT: D 48 LYS cc_start: 0.7895 (tttt) cc_final: 0.6824 (mmtp) REVERT: D 82 MET cc_start: 0.4431 (mtt) cc_final: 0.2981 (ttt) REVERT: E 2931 GLU cc_start: 0.7458 (mp0) cc_final: 0.7168 (mp0) REVERT: E 3009 ASP cc_start: 0.8216 (t70) cc_final: 0.7924 (t0) REVERT: E 3043 ASN cc_start: 0.9086 (m-40) cc_final: 0.8840 (t0) REVERT: G 143 THR cc_start: 0.9134 (p) cc_final: 0.8869 (t) outliers start: 41 outliers final: 23 residues processed: 189 average time/residue: 0.5943 time to fit residues: 128.0707 Evaluate side-chains 173 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 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 984 SER Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 2641 THR Chi-restraints excluded: chain E residue 2667 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 92 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 G residue 327 ASP Chi-restraints excluded: chain G residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 146 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 F 114 ASN F 205 GLN ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.112558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085472 restraints weight = 34342.547| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.42 r_work: 0.3157 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19678 Z= 0.159 Angle : 0.537 8.721 26627 Z= 0.275 Chirality : 0.041 0.185 3006 Planarity : 0.004 0.058 3405 Dihedral : 8.456 161.754 2592 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.28 % Allowed : 10.81 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.18), residues: 2390 helix: 1.92 (0.14), residues: 1302 sheet: -0.54 (0.36), residues: 223 loop : -0.73 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 44 TYR 0.024 0.002 TYR D 51 PHE 0.022 0.001 PHE A 882 TRP 0.010 0.001 TRP A 762 HIS 0.006 0.001 HIS G 544 Details of bonding type rmsd covalent geometry : bond 0.00390 (19677) covalent geometry : angle 0.53683 (26627) hydrogen bonds : bond 0.04009 ( 1018) hydrogen bonds : angle 4.23224 ( 2976) Misc. bond : bond 0.00127 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.6848 (m) cc_final: 0.6348 (m) REVERT: A 351 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8678 (mt) REVERT: A 354 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8791 (mmp) REVERT: A 509 HIS cc_start: 0.7315 (m-70) cc_final: 0.5997 (t-170) REVERT: A 647 GLN cc_start: 0.7460 (mm-40) cc_final: 0.6732 (tt0) REVERT: A 738 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7395 (ptt) REVERT: A 753 ARG cc_start: 0.8349 (mtt180) cc_final: 0.7996 (mtp85) REVERT: B 175 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7492 (mm-30) REVERT: C 102 ASP cc_start: 0.7125 (t70) cc_final: 0.6734 (m-30) REVERT: D 47 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8126 (mm) REVERT: D 48 LYS cc_start: 0.7932 (tttt) cc_final: 0.6786 (mmtp) REVERT: D 82 MET cc_start: 0.4436 (mtt) cc_final: 0.3011 (ttt) REVERT: E 2931 GLU cc_start: 0.7541 (mp0) cc_final: 0.7196 (mp0) REVERT: E 3009 ASP cc_start: 0.8214 (t70) cc_final: 0.7910 (t0) REVERT: E 3043 ASN cc_start: 0.9106 (m-40) cc_final: 0.8868 (t0) REVERT: F 205 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: G 143 THR cc_start: 0.9213 (p) cc_final: 0.8952 (t) REVERT: G 213 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8899 (p) outliers start: 48 outliers final: 25 residues processed: 186 average time/residue: 0.5832 time to fit residues: 124.0431 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 : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 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 984 SER Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 2641 THR Chi-restraints excluded: chain E residue 2667 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 92 VAL Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 327 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 224 optimal weight: 0.6980 chunk 204 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 D 75 HIS E3000 ASN F 114 ASN ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.113339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.086569 restraints weight = 34060.291| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.35 r_work: 0.3174 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19678 Z= 0.126 Angle : 0.514 9.012 26627 Z= 0.263 Chirality : 0.040 0.211 3006 Planarity : 0.004 0.058 3405 Dihedral : 8.422 161.551 2592 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.94 % Allowed : 11.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.18), residues: 2390 helix: 1.99 (0.14), residues: 1301 sheet: -0.49 (0.36), residues: 226 loop : -0.73 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 44 TYR 0.025 0.001 TYR D 51 PHE 0.018 0.001 PHE A 882 TRP 0.015 0.001 TRP A 762 HIS 0.006 0.001 HIS G 544 Details of bonding type rmsd covalent geometry : bond 0.00302 (19677) covalent geometry : angle 0.51396 (26627) hydrogen bonds : bond 0.03712 ( 1018) hydrogen bonds : angle 4.17866 ( 2976) Misc. bond : bond 0.00100 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.6874 (m) cc_final: 0.6397 (m) REVERT: A 351 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8650 (mt) REVERT: A 354 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8799 (mmp) REVERT: A 362 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7972 (tm-30) REVERT: A 509 HIS cc_start: 0.7317 (m-70) cc_final: 0.5999 (t-170) REVERT: A 647 GLN cc_start: 0.7451 (mm-40) cc_final: 0.6727 (tt0) REVERT: A 738 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7396 (ptt) REVERT: A 753 ARG cc_start: 0.8362 (mtt180) cc_final: 0.8015 (mtp85) REVERT: B 175 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7491 (mm-30) REVERT: C 102 ASP cc_start: 0.7128 (t70) cc_final: 0.6752 (m-30) REVERT: D 48 LYS cc_start: 0.7992 (tttt) cc_final: 0.6782 (mmtp) REVERT: D 82 MET cc_start: 0.4375 (mtt) cc_final: 0.2966 (ttt) REVERT: E 2931 GLU cc_start: 0.7555 (mp0) cc_final: 0.7205 (mp0) REVERT: E 3009 ASP cc_start: 0.8203 (t70) cc_final: 0.7892 (t0) REVERT: E 3043 ASN cc_start: 0.9119 (m-40) cc_final: 0.8886 (t0) REVERT: F 56 ARG cc_start: 0.9126 (mtp85) cc_final: 0.8867 (mtp85) REVERT: F 205 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.8024 (mp10) REVERT: G 143 THR cc_start: 0.9197 (p) cc_final: 0.8936 (t) REVERT: G 213 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8858 (p) outliers start: 41 outliers final: 23 residues processed: 177 average time/residue: 0.6007 time to fit residues: 121.9184 Evaluate side-chains 172 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 2641 THR Chi-restraints excluded: chain E residue 2667 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 92 VAL Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 112 CYS Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 327 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 131 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 chunk 133 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 123 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 223 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 72 ASN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2967 ASN E3000 ASN F 205 GLN ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.113971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.086507 restraints weight = 33839.176| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.43 r_work: 0.3175 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19678 Z= 0.113 Angle : 0.501 9.182 26627 Z= 0.256 Chirality : 0.040 0.172 3006 Planarity : 0.004 0.056 3405 Dihedral : 8.353 161.285 2592 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.56 % Allowed : 11.85 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.18), residues: 2390 helix: 2.05 (0.14), residues: 1304 sheet: -0.42 (0.37), residues: 215 loop : -0.72 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 44 TYR 0.016 0.001 TYR A 657 PHE 0.016 0.001 PHE A 882 TRP 0.017 0.001 TRP A 762 HIS 0.006 0.001 HIS G 544 Details of bonding type rmsd covalent geometry : bond 0.00265 (19677) covalent geometry : angle 0.50130 (26627) hydrogen bonds : bond 0.03484 ( 1018) hydrogen bonds : angle 4.10160 ( 2976) Misc. bond : bond 0.00085 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.7156 (m) cc_final: 0.6716 (m) REVERT: A 351 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8617 (mt) REVERT: A 354 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8663 (mmp) REVERT: A 509 HIS cc_start: 0.7228 (m-70) cc_final: 0.6035 (t-170) REVERT: A 647 GLN cc_start: 0.7363 (mm-40) cc_final: 0.6734 (tt0) REVERT: A 738 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7281 (ptt) REVERT: A 753 ARG cc_start: 0.8118 (mtt180) cc_final: 0.7822 (mtp85) REVERT: B 175 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7329 (mm-30) REVERT: C 102 ASP cc_start: 0.7017 (t70) cc_final: 0.6688 (m-30) REVERT: D 48 LYS cc_start: 0.8081 (tttt) cc_final: 0.6807 (mmtp) REVERT: D 75 HIS cc_start: 0.6209 (OUTLIER) cc_final: 0.5830 (m170) REVERT: D 82 MET cc_start: 0.4283 (mtt) cc_final: 0.2971 (ttt) REVERT: E 2931 GLU cc_start: 0.7423 (mp0) cc_final: 0.7102 (mp0) REVERT: E 3009 ASP cc_start: 0.8038 (t70) cc_final: 0.7750 (t0) REVERT: E 3043 ASN cc_start: 0.9150 (m-40) cc_final: 0.8926 (t0) REVERT: F 56 ARG cc_start: 0.9082 (mtp85) cc_final: 0.8878 (mtp85) REVERT: F 114 ASN cc_start: 0.8208 (p0) cc_final: 0.7983 (p0) REVERT: G 143 THR cc_start: 0.9106 (p) cc_final: 0.8865 (t) REVERT: G 213 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8758 (p) outliers start: 33 outliers final: 23 residues processed: 181 average time/residue: 0.5866 time to fit residues: 121.4861 Evaluate side-chains 175 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 2641 THR Chi-restraints excluded: chain E residue 2667 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 227 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 217 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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** ** E2662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2949 GLN E3000 ASN F 55 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 = 0.3785 r_free = 0.3785 target = 0.111523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.084197 restraints weight = 34318.039| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.33 r_work: 0.3146 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19678 Z= 0.201 Angle : 0.581 11.376 26627 Z= 0.295 Chirality : 0.043 0.175 3006 Planarity : 0.004 0.060 3405 Dihedral : 8.529 161.942 2592 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.71 % Allowed : 11.76 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.17), residues: 2390 helix: 1.80 (0.14), residues: 1307 sheet: -0.61 (0.35), residues: 238 loop : -0.70 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 129 TYR 0.024 0.002 TYR A 657 PHE 0.025 0.002 PHE A 882 TRP 0.007 0.001 TRP B 104 HIS 0.005 0.001 HIS G 544 Details of bonding type rmsd covalent geometry : bond 0.00494 (19677) covalent geometry : angle 0.58071 (26627) hydrogen bonds : bond 0.04452 ( 1018) hydrogen bonds : angle 4.29204 ( 2976) Misc. bond : bond 0.00145 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 CYS cc_start: 0.6831 (m) cc_final: 0.6376 (m) REVERT: A 351 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8733 (mt) REVERT: A 354 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8821 (mmp) REVERT: A 509 HIS cc_start: 0.7349 (m-70) cc_final: 0.6050 (t-170) REVERT: A 647 GLN cc_start: 0.7503 (mm-40) cc_final: 0.6757 (tt0) REVERT: A 738 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7405 (ptt) REVERT: A 753 ARG cc_start: 0.8362 (mtt180) cc_final: 0.8022 (mtp85) REVERT: B 175 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7520 (mm-30) REVERT: D 48 LYS cc_start: 0.8077 (tttt) cc_final: 0.6808 (mmtp) REVERT: D 75 HIS cc_start: 0.6291 (OUTLIER) cc_final: 0.5893 (m170) REVERT: D 82 MET cc_start: 0.4391 (mtt) cc_final: 0.2980 (ttt) REVERT: E 2931 GLU cc_start: 0.7569 (mp0) cc_final: 0.7211 (mp0) REVERT: E 3009 ASP cc_start: 0.8280 (t70) cc_final: 0.7982 (t0) REVERT: E 3043 ASN cc_start: 0.9101 (m-40) cc_final: 0.8881 (t0) REVERT: F 114 ASN cc_start: 0.8398 (p0) cc_final: 0.8179 (p0) REVERT: G 143 THR cc_start: 0.9260 (p) cc_final: 0.9023 (t) REVERT: G 213 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8909 (p) outliers start: 36 outliers final: 24 residues processed: 171 average time/residue: 0.5799 time to fit residues: 113.0343 Evaluate side-chains 171 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 617 ASN Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 2641 THR Chi-restraints excluded: chain E residue 2667 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 E3000 ASN ** G 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.113103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.085682 restraints weight = 34051.616| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.36 r_work: 0.3171 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19678 Z= 0.129 Angle : 0.521 10.040 26627 Z= 0.266 Chirality : 0.040 0.160 3006 Planarity : 0.004 0.055 3405 Dihedral : 8.366 161.290 2590 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.47 % Allowed : 11.95 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.18), residues: 2390 helix: 1.96 (0.14), residues: 1306 sheet: -0.52 (0.36), residues: 216 loop : -0.73 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.019 0.001 TYR A 657 PHE 0.017 0.001 PHE A 882 TRP 0.016 0.001 TRP A 762 HIS 0.006 0.001 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00309 (19677) covalent geometry : angle 0.52063 (26627) hydrogen bonds : bond 0.03709 ( 1018) hydrogen bonds : angle 4.16221 ( 2976) Misc. bond : bond 0.00098 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7034.39 seconds wall clock time: 120 minutes 40.12 seconds (7240.12 seconds total)