Starting phenix.real_space_refine on Mon Oct 26 03:20:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kc0_22803/10_2026/7kc0_22803.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kc0_22803/10_2026/7kc0_22803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kc0_22803/10_2026/7kc0_22803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kc0_22803/10_2026/7kc0_22803.map" model { file = "/net/cci-nas-00/data/ceres_data/7kc0_22803/10_2026/7kc0_22803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kc0_22803/10_2026/7kc0_22803.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7kc0_22803/10_2026/7kc0_22803.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kc0_22803/10_2026/7kc0_22803.cif" } resolution = 3.2 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= 0.000 sd= 0.032 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 1 6.06 5 P 49 5.49 5 Mg 2 5.21 5 S 95 5.16 5 C 12336 2.51 5 N 3232 2.21 5 O 3834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19553 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 430 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1995 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "A" Number of atoms: 8009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 8009 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 963} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3705 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 28, 'TRANS': 434} Chain breaks: 2 Chain: "C" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 905 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain breaks: 2 Chain: "E" Number of atoms: 1987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1987 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain breaks: 3 Chain: "G" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1971 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 8, 'TRANS': 242} Chain breaks: 4 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 38 Unusual residues: {' MG': 1, ' ZN': 1, 'D3T': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10704 SG CYS A1069 66.915 77.611 65.309 1.00 55.37 S ATOM 10741 SG CYS A1074 60.429 76.776 65.411 1.00 57.04 S ATOM 10607 SG CYS A1056 64.716 73.893 61.030 1.00 54.43 S ATOM 10633 SG CYS A1059 62.362 80.162 61.171 1.00 55.72 S ATOM 10237 SG CYS A1009 61.638 35.989 62.186 1.00 88.63 S ATOM 10254 SG CYS A1012 59.853 34.377 65.075 1.00 86.87 S ATOM 10340 SG CYS A1024 61.065 32.444 62.025 1.00 85.29 S ATOM 10360 SG CYS A1027 58.240 34.636 61.146 1.00 83.64 S Time building chain proxies: 4.00, per 1000 atoms: 0.20 Number of scatterers: 19553 At special positions: 0 Unit cell: (109.032, 144.55, 161.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 4 26.01 S 95 16.00 P 49 15.00 Mg 2 11.99 O 3834 8.00 N 3232 7.00 C 12336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 83 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 639.5 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1101 " pdb="FE1 SF4 A1101 " - pdb=" SG CYS A1069 " pdb="FE2 SF4 A1101 " - pdb=" SG CYS A1074 " pdb="FE3 SF4 A1101 " - pdb=" SG CYS A1056 " pdb="FE4 SF4 A1101 " - pdb=" SG CYS A1059 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1104 " pdb="ZN ZN A1104 " - pdb=" SG CYS A1012 " pdb="ZN ZN A1104 " - pdb=" SG CYS A1027 " pdb="ZN ZN A1104 " - pdb=" SG CYS A1024 " pdb="ZN ZN A1104 " - pdb=" SG CYS A1009 " Number of angles added : 6 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4430 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 22 sheets defined 30.7% alpha, 21.4% beta 19 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'F' and resid 8 through 18 removed outlier: 4.100A pdb=" N PHE F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 153 Processing helix chain 'F' and resid 209 through 216 removed outlier: 4.272A pdb=" N ASP F 214 " --> pdb=" O LYS F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 220 removed outlier: 4.423A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 217 through 220' Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.852A pdb=" N ASN A 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 188 Processing helix chain 'A' and resid 221 through 234 removed outlier: 4.266A pdb=" N ASN A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS A 226 " --> pdb=" O HIS A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 306 through 310 removed outlier: 4.112A pdb=" N TRP A 309 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 310 " --> pdb=" O GLY A 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 306 through 310' Processing helix chain 'A' and resid 378 through 394 Processing helix chain 'A' and resid 406 through 418 Processing helix chain 'A' and resid 464 through 472 Processing helix chain 'A' and resid 478 through 486 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 506 through 531 removed outlier: 3.709A pdb=" N ARG A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) Proline residue: A 524 - end of helix Processing helix chain 'A' and resid 532 through 544 Processing helix chain 'A' and resid 549 through 554 removed outlier: 3.639A pdb=" N ALA A 553 " --> pdb=" O SER A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 570 removed outlier: 3.834A pdb=" N VAL A 560 " --> pdb=" O GLN A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 620 Processing helix chain 'A' and resid 629 through 637 Processing helix chain 'A' and resid 662 through 683 removed outlier: 3.643A pdb=" N ARG A 676 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 713 removed outlier: 3.508A pdb=" N LEU A 700 " --> pdb=" O ARG A 696 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 746 removed outlier: 3.697A pdb=" N SER A 724 " --> pdb=" O CYS A 720 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR A 746 " --> pdb=" O VAL A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 792 removed outlier: 3.605A pdb=" N ALA A 778 " --> pdb=" O ASP A 774 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 792 " --> pdb=" O TYR A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 859 removed outlier: 3.677A pdb=" N SER A 847 " --> pdb=" O CYS A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 879 Processing helix chain 'A' and resid 883 through 888 removed outlier: 4.042A pdb=" N ILE A 888 " --> pdb=" O SER A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 914 Processing helix chain 'A' and resid 934 through 938 Processing helix chain 'A' and resid 941 through 949 Processing helix chain 'A' and resid 953 through 960 Processing helix chain 'A' and resid 962 through 975 Proline residue: A 972 - end of helix Processing helix chain 'A' and resid 975 through 982 removed outlier: 4.182A pdb=" N MET A 982 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1031 Processing helix chain 'A' and resid 1033 through 1061 Processing helix chain 'A' and resid 1079 through 1095 Processing helix chain 'B' and resid 8 through 14 removed outlier: 3.987A pdb=" N ARG B 12 " --> pdb=" O PHE B 8 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER B 13 " --> pdb=" O ASN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 76 removed outlier: 3.991A pdb=" N TYR B 57 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LYS B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 228 through 241 Processing helix chain 'B' and resid 274 through 291 Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 321 through 328 Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 393 through 405 Processing helix chain 'C' and resid 5 through 16 removed outlier: 3.516A pdb=" N GLU C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 30 Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'E' and resid 9 through 23 removed outlier: 3.842A pdb=" N LYS E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG E 14 " --> pdb=" O SER E 10 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY E 18 " --> pdb=" O ARG E 14 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP E 21 " --> pdb=" O ASP E 17 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS E 22 " --> pdb=" O GLY E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 80 Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 209 through 217 removed outlier: 3.502A pdb=" N LYS E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 221 Processing helix chain 'G' and resid 8 through 18 removed outlier: 4.062A pdb=" N PHE G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 153 removed outlier: 4.101A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 219 No H-bonds generated for 'chain 'G' and resid 217 through 219' Processing sheet with id=AA1, first strand: chain 'F' and resid 59 through 60 removed outlier: 4.120A pdb=" N GLU F 104 " --> pdb=" O THR F 87 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA F 112 " --> pdb=" O PHE F 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 66 through 71 removed outlier: 7.126A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY F 34 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE F 239 " --> pdb=" O LEU F 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 126 through 128 Processing sheet with id=AA4, first strand: chain 'F' and resid 203 through 208 removed outlier: 6.470A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR F 163 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU E 104 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU E 88 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 92 " --> pdb=" O LEU E 2 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU E 59 " --> pdb=" O LYS E 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 279 removed outlier: 7.730A pdb=" N VAL A 293 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU A 150 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE A 295 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ASN A 152 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A 151 " --> pdb=" O PHE A 139 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 136 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN A 122 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG A 138 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 120 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE A 140 " --> pdb=" O ILE A 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 163 removed outlier: 4.391A pdb=" N SER A 193 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N VAL A 574 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN A 200 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 375 removed outlier: 3.682A pdb=" N PHE A 320 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 462 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY A 400 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 436 through 441 Processing sheet with id=AA9, first strand: chain 'A' and resid 598 through 600 removed outlier: 3.501A pdb=" N GLY A 598 " --> pdb=" O LEU A 810 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N PHE A 801 " --> pdb=" O ASP A 608 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASP A 608 " --> pdb=" O PHE A 801 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 803 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 598 through 600 removed outlier: 3.501A pdb=" N GLY A 598 " --> pdb=" O LEU A 810 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR A 808 " --> pdb=" O LEU A 819 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU A 819 " --> pdb=" O TYR A 808 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU A 810 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA A 817 " --> pdb=" O LEU A 810 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 815 " --> pdb=" O ASN A 812 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 627 through 628 removed outlier: 3.983A pdb=" N TYR A 652 " --> pdb=" O CYS A 628 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 757 through 761 removed outlier: 6.577A pdb=" N MET A 767 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 889 through 892 Processing sheet with id=AB5, first strand: chain 'B' and resid 145 through 149 removed outlier: 4.039A pdb=" N GLY B 106 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 173 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY B 174 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE B 190 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B 176 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 295 through 299 removed outlier: 6.433A pdb=" N LEU B 257 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N MET B 299 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 259 " --> pdb=" O MET B 299 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LYS B 213 " --> pdb=" O ARG B 256 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N LEU B 258 " --> pdb=" O LYS B 213 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA B 215 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N CYS B 260 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL B 217 " --> pdb=" O CYS B 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 343 through 347 removed outlier: 6.813A pdb=" N ASP B 351 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ILE B 437 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU B 353 " --> pdb=" O ILE B 437 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ALA B 439 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL B 355 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N GLN B 441 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TYR B 436 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL B 461 " --> pdb=" O TYR B 436 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL B 438 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 454 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 451 " --> pdb=" O LYS B 454 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 445 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 66 through 68 removed outlier: 3.833A pdb=" N LYS C 66 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS C 58 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 56 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN C 53 " --> pdb=" O PHE C 88 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N PHE C 88 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL C 55 " --> pdb=" O TYR C 86 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP C 82 " --> pdb=" O CYS C 59 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 66 through 71 removed outlier: 3.649A pdb=" N VAL E 26 " --> pdb=" O MET E 70 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU E 25 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL E 40 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASN E 27 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN E 38 " --> pdb=" O ASN E 27 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 157 through 160 removed outlier: 4.183A pdb=" N LEU E 205 " --> pdb=" O ILE E 160 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 167 through 172 removed outlier: 4.388A pdb=" N LEU G 88 " --> pdb=" O PHE G 6 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU G 3 " --> pdb=" O TYR G 60 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR G 60 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS G 5 " --> pdb=" O GLN G 58 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 66 through 68 removed outlier: 3.670A pdb=" N GLY G 244 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU G 250 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N SER G 230 " --> pdb=" O PRO G 234 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 157 through 160 removed outlier: 4.019A pdb=" N LEU G 205 " --> pdb=" O ILE G 160 " (cutoff:3.500A) 762 hydrogen bonds defined for protein. 2139 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 4.01 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 8313 1.43 - 1.64: 11553 1.64 - 1.85: 136 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 20014 Sorted by residual: bond pdb=" O3B D3T A1102 " pdb=" PG D3T A1102 " ideal model delta sigma weight residual 1.743 1.637 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" N1 D3T A1102 " pdb=" C6 D3T A1102 " ideal model delta sigma weight residual 1.366 1.440 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" N VAL G 186 " pdb=" CA VAL G 186 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" O3A D3T A1102 " pdb=" PA D3T A1102 " ideal model delta sigma weight residual 1.625 1.689 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C3' DT T 9 " pdb=" C2' DT T 9 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.62e+00 ... (remaining 20009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.44: 27234 5.44 - 10.89: 26 10.89 - 16.33: 1 16.33 - 21.78: 5 21.78 - 27.22: 1 Bond angle restraints: 27267 Sorted by residual: angle pdb=" O3A D3T A1102 " pdb=" PB D3T A1102 " pdb=" O3B D3T A1102 " ideal model delta sigma weight residual 98.07 125.29 -27.22 3.00e+00 1.11e-01 8.23e+01 angle pdb=" O1G D3T A1102 " pdb=" PG D3T A1102 " pdb=" O3B D3T A1102 " ideal model delta sigma weight residual 103.73 124.35 -20.62 3.00e+00 1.11e-01 4.72e+01 angle pdb=" O1B D3T A1102 " pdb=" PB D3T A1102 " pdb=" O2B D3T A1102 " ideal model delta sigma weight residual 119.18 99.04 20.14 3.00e+00 1.11e-01 4.51e+01 angle pdb=" O1A D3T A1102 " pdb=" PA D3T A1102 " pdb=" O2A D3T A1102 " ideal model delta sigma weight residual 120.91 100.89 20.02 3.00e+00 1.11e-01 4.45e+01 angle pdb=" O5' D3T A1102 " pdb=" PA D3T A1102 " pdb=" O3A D3T A1102 " ideal model delta sigma weight residual 101.23 119.92 -18.69 3.00e+00 1.11e-01 3.88e+01 ... (remaining 27262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10588 17.96 - 35.92: 1106 35.92 - 53.88: 318 53.88 - 71.84: 53 71.84 - 89.80: 17 Dihedral angle restraints: 12082 sinusoidal: 5246 harmonic: 6836 Sorted by residual: dihedral pdb=" CA CYS C 58 " pdb=" CB CYS C 58 " pdb=" SG CYS C 58 " pdb=" SG CYS C 83 " ideal model delta sinusoidal sigma weight residual -73.00 -4.87 -68.13 1 2.00e+01 2.50e-03 1.51e+01 dihedral pdb=" CA TYR C 113 " pdb=" C TYR C 113 " pdb=" N GLU C 114 " pdb=" CA GLU C 114 " ideal model delta harmonic sigma weight residual -180.00 -160.89 -19.11 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA PRO C 96 " pdb=" C PRO C 96 " pdb=" N TYR C 97 " pdb=" CA TYR C 97 " ideal model delta harmonic sigma weight residual 180.00 -163.08 -16.92 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 12079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2737 0.074 - 0.147: 347 0.147 - 0.221: 24 0.221 - 0.294: 4 0.294 - 0.368: 1 Chirality restraints: 3113 Sorted by residual: chirality pdb=" C4' D3T A1102 " pdb=" C5' D3T A1102 " pdb=" O4' D3T A1102 " pdb=" C3' D3T A1102 " both_signs ideal model delta sigma weight residual False -2.34 -2.71 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA ILE A 596 " pdb=" N ILE A 596 " pdb=" C ILE A 596 " pdb=" CB ILE A 596 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ARG A1058 " pdb=" N ARG A1058 " pdb=" C ARG A1058 " pdb=" CB ARG A1058 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 3110 not shown) Planarity restraints: 3317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO E 184 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C PRO E 184 " 0.045 2.00e-02 2.50e+03 pdb=" O PRO E 184 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE E 185 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 182 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C ILE E 182 " 0.040 2.00e-02 2.50e+03 pdb=" O ILE E 182 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS E 183 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 179 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C SER G 179 " 0.033 2.00e-02 2.50e+03 pdb=" O SER G 179 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL G 180 " -0.011 2.00e-02 2.50e+03 ... (remaining 3314 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2114 2.75 - 3.29: 19758 3.29 - 3.82: 32629 3.82 - 4.36: 39678 4.36 - 4.90: 66979 Nonbonded interactions: 161158 Sorted by model distance: nonbonded pdb=" O PHE E 185 " pdb=" OD2 ASP G 109 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR A 159 " pdb=" OD2 ASP A 261 " model vdw 2.228 3.040 nonbonded pdb=" O ASP A 337 " pdb=" OH TYR A 410 " model vdw 2.231 3.040 nonbonded pdb=" OP1 DA P 21 " pdb=" OH TYR A 897 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR B 44 " pdb=" OD1 ASP B 307 " model vdw 2.250 3.040 ... (remaining 161153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'E' and (resid 1 through 69 or resid 71 through 254)) selection = (chain 'F' and (resid 1 through 69 or resid 71 through 118 or resid 120 through \ 160 or resid 162 through 198 or resid 200 through 254)) selection = (chain 'G' and resid 1 through 254) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.250 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.209 20023 Z= 0.281 Angle : 0.865 37.635 27287 Z= 0.440 Chirality : 0.048 0.368 3113 Planarity : 0.003 0.038 3317 Dihedral : 16.044 89.797 7649 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.90 % Allowed : 13.03 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -3.23 (0.16), residues: 2300 helix: -0.87 (0.18), residues: 654 sheet: -2.17 (0.21), residues: 514 loop : -2.94 (0.16), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 597 TYR 0.028 0.001 TYR A 760 PHE 0.012 0.001 PHE A 140 TRP 0.013 0.001 TRP A1053 HIS 0.004 0.001 HIS C 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.27 (20014) covalent geometry : angle 0.72752 / 0.44 (27267) SS BOND : bond 0.00002 / 0.00 ( 1) SS BOND : angle 1.31557 / 2.23 ( 2) hydrogen bonds : bond 0.16442 / 18.06 ( 805) hydrogen bonds : angle 7.53736 / 7.92 ( 2231) metal coordination : bond 0.11375 / 13.24 ( 8) metal coordination : angle 18.22155 / 36.40 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 246 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8280 (mt) REVERT: F 124 ASP cc_start: 0.7479 (t0) cc_final: 0.6840 (t0) REVERT: F 199 MET cc_start: 0.4941 (tpp) cc_final: 0.3799 (tpt) REVERT: A 841 ASP cc_start: 0.7554 (p0) cc_final: 0.6938 (t0) REVERT: A 908 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7291 (tm-30) REVERT: A 1012 CYS cc_start: 0.7769 (OUTLIER) cc_final: 0.6918 (p) REVERT: B 86 LEU cc_start: 0.6932 (mm) cc_final: 0.6657 (mm) REVERT: B 234 GLU cc_start: 0.8175 (tp30) cc_final: 0.7680 (tm-30) REVERT: B 358 LYS cc_start: 0.9017 (tptt) cc_final: 0.8784 (tptp) REVERT: C 8 PHE cc_start: 0.8311 (t80) cc_final: 0.7995 (t80) REVERT: C 12 LYS cc_start: 0.8987 (mtmt) cc_final: 0.8485 (mtmt) REVERT: C 21 LEU cc_start: 0.8475 (mm) cc_final: 0.8087 (mp) REVERT: C 24 ASP cc_start: 0.8391 (m-30) cc_final: 0.7835 (m-30) REVERT: E 58 GLN cc_start: 0.7499 (tp40) cc_final: 0.6829 (tm-30) REVERT: E 66 VAL cc_start: 0.7193 (OUTLIER) cc_final: 0.6729 (t) REVERT: G 24 GLN cc_start: 0.7690 (mt0) cc_final: 0.7426 (tp40) REVERT: G 29 GLN cc_start: 0.6067 (OUTLIER) cc_final: 0.5734 (mm-40) REVERT: G 181 ILE cc_start: 0.8179 (tp) cc_final: 0.7840 (tt) REVERT: G 182 ILE cc_start: 0.6593 (OUTLIER) cc_final: 0.6019 (mp) REVERT: G 245 PHE cc_start: 0.7176 (p90) cc_final: 0.5374 (p90) outliers start: 61 outliers final: 29 residues processed: 301 average time/residue: 0.1615 time to fit residues: 72.3049 Evaluate side-chains 199 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1012 CYS Chi-restraints excluded: chain A residue 1056 CYS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain G residue 29 GLN Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 225 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 200] chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 238 GLN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 ASN A 754 HIS A 851 ASN A 919 ASN B 52 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN C 27 HIS E 255 ASN G 27 ASN G 153 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.101708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.077992 restraints weight = 57685.557| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.65 r_work: 0.3280 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20023 Z= 0.172 Angle : 0.643 18.254 27287 Z= 0.324 Chirality : 0.045 0.193 3113 Planarity : 0.004 0.057 3317 Dihedral : 14.139 88.370 3103 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.23 % Allowed : 15.93 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.16), residues: 2300 helix: 0.07 (0.20), residues: 653 sheet: -1.76 (0.21), residues: 515 loop : -2.54 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 110 TYR 0.020 0.001 TYR C 97 PHE 0.023 0.001 PHE G 245 TRP 0.012 0.001 TRP B 103 HIS 0.009 0.001 HIS G 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (20014) covalent geometry : angle 0.60704 / 0.32 (27267) SS BOND : bond 0.00056 / 0.03 ( 1) SS BOND : angle 1.82094 / 3.07 ( 2) hydrogen bonds : bond 0.04524 / 5.05 ( 805) hydrogen bonds : angle 5.85626 / 6.17 ( 2231) metal coordination : bond 0.00890 / 1.09 ( 8) metal coordination : angle 8.30029 / 15.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 181 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8277 (mt) REVERT: F 199 MET cc_start: 0.5469 (tpp) cc_final: 0.4221 (tpt) REVERT: A 131 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7388 (mt-10) REVERT: A 841 ASP cc_start: 0.7985 (p0) cc_final: 0.7386 (t0) REVERT: A 908 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7945 (tm-30) REVERT: A 991 ASN cc_start: 0.8468 (t0) cc_final: 0.8241 (t0) REVERT: B 249 ASP cc_start: 0.5909 (t0) cc_final: 0.5401 (t0) REVERT: B 358 LYS cc_start: 0.9119 (tptt) cc_final: 0.8909 (tptp) REVERT: C 8 PHE cc_start: 0.8377 (t80) cc_final: 0.7684 (t80) REVERT: C 12 LYS cc_start: 0.8945 (mtmt) cc_final: 0.8544 (mtmt) REVERT: C 21 LEU cc_start: 0.8559 (mm) cc_final: 0.8037 (mp) REVERT: C 24 ASP cc_start: 0.8598 (m-30) cc_final: 0.8149 (m-30) REVERT: C 76 GLN cc_start: 0.8064 (mp10) cc_final: 0.7800 (mp10) REVERT: E 58 GLN cc_start: 0.7896 (tp40) cc_final: 0.7182 (tm-30) REVERT: E 211 TYR cc_start: 0.8015 (m-80) cc_final: 0.7804 (m-80) REVERT: G 24 GLN cc_start: 0.7809 (mt0) cc_final: 0.7443 (tp40) REVERT: G 29 GLN cc_start: 0.5855 (OUTLIER) cc_final: 0.5235 (mm-40) outliers start: 68 outliers final: 35 residues processed: 235 average time/residue: 0.1385 time to fit residues: 51.4009 Evaluate side-chains 195 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain G residue 29 GLN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 225 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: [70, 148, 162, 103, 82, 51, 119, 39, 23, 188, 138] chunk 70 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 188 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 153 GLN A 754 HIS A 832 GLN C 27 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.101340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.077674 restraints weight = 57701.330| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.64 r_work: 0.3275 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20023 Z= 0.165 Angle : 0.606 14.901 27287 Z= 0.311 Chirality : 0.044 0.181 3113 Planarity : 0.004 0.071 3317 Dihedral : 14.025 87.356 3081 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.57 % Allowed : 16.17 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.17), residues: 2300 helix: 0.45 (0.20), residues: 654 sheet: -1.50 (0.21), residues: 517 loop : -2.30 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 80 TYR 0.014 0.001 TYR A1040 PHE 0.019 0.001 PHE C 84 TRP 0.011 0.001 TRP A1053 HIS 0.005 0.001 HIS C 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (20014) covalent geometry : angle 0.58621 / 0.31 (27267) SS BOND : bond 0.00066 / 0.03 ( 1) SS BOND : angle 1.64477 / 2.74 ( 2) hydrogen bonds : bond 0.03981 / 4.46 ( 805) hydrogen bonds : angle 5.50450 / 5.83 ( 2231) metal coordination : bond 0.00684 / 0.65 ( 8) metal coordination : angle 5.92905 / 9.79 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 170 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8334 (mt) REVERT: F 161 MET cc_start: 0.8607 (mtt) cc_final: 0.7921 (mtm) REVERT: F 199 MET cc_start: 0.5446 (tpp) cc_final: 0.4135 (tpt) REVERT: A 132 ASN cc_start: 0.8158 (t0) cc_final: 0.7771 (t0) REVERT: A 540 MET cc_start: 0.8136 (ttm) cc_final: 0.7520 (tpp) REVERT: A 841 ASP cc_start: 0.7884 (p0) cc_final: 0.7373 (t0) REVERT: A 908 GLU cc_start: 0.8445 (tm-30) cc_final: 0.7951 (tm-30) REVERT: A 991 ASN cc_start: 0.8470 (t0) cc_final: 0.8252 (t0) REVERT: B 82 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8224 (tt) REVERT: B 249 ASP cc_start: 0.5920 (t0) cc_final: 0.5650 (t0) REVERT: C 8 PHE cc_start: 0.8303 (t80) cc_final: 0.7816 (t80) REVERT: C 12 LYS cc_start: 0.8938 (mtmt) cc_final: 0.8617 (mtmt) REVERT: C 21 LEU cc_start: 0.8571 (mm) cc_final: 0.8006 (mp) REVERT: C 24 ASP cc_start: 0.8656 (m-30) cc_final: 0.8123 (m-30) REVERT: C 76 GLN cc_start: 0.8065 (mp10) cc_final: 0.7755 (mp10) REVERT: E 58 GLN cc_start: 0.7901 (tp40) cc_final: 0.7223 (tm-30) REVERT: E 188 MET cc_start: 0.5865 (ptt) cc_final: 0.5425 (ptt) REVERT: E 211 TYR cc_start: 0.7972 (m-80) cc_final: 0.7761 (m-80) REVERT: G 24 GLN cc_start: 0.7788 (mt0) cc_final: 0.7423 (tp40) REVERT: G 188 MET cc_start: 0.6851 (ttm) cc_final: 0.5316 (tpt) outliers start: 75 outliers final: 47 residues processed: 231 average time/residue: 0.1340 time to fit residues: 49.2525 Evaluate side-chains 203 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 154 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 225 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: [209, 202, 87, 204, 111, 7, 169, 150, 34, 219, 98] chunk 209 optimal weight: 0.9990 chunk 202 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 204 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 219 optimal weight: 20.0000 chunk 98 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 84 ASN A 754 HIS B 407 ASN E 238 GLN G 190 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.101869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.078194 restraints weight = 57680.449| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.66 r_work: 0.3290 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20023 Z= 0.134 Angle : 0.575 14.017 27287 Z= 0.295 Chirality : 0.043 0.177 3113 Planarity : 0.004 0.060 3317 Dihedral : 13.918 86.860 3073 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.23 % Allowed : 17.17 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.66 (0.17), residues: 2300 helix: 0.66 (0.21), residues: 654 sheet: -1.25 (0.22), residues: 513 loop : -2.13 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 257 TYR 0.013 0.001 TYR A1040 PHE 0.019 0.001 PHE C 41 TRP 0.011 0.001 TRP B 103 HIS 0.009 0.001 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (20014) covalent geometry : angle 0.55947 / 0.29 (27267) SS BOND : bond 0.00088 / 0.04 ( 1) SS BOND : angle 1.47181 / 2.46 ( 2) hydrogen bonds : bond 0.03593 / 4.03 ( 805) hydrogen bonds : angle 5.26045 / 5.60 ( 2231) metal coordination : bond 0.00605 / 0.56 ( 8) metal coordination : angle 5.18934 / 7.93 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 161 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8276 (mt) REVERT: F 161 MET cc_start: 0.8663 (mtt) cc_final: 0.7971 (mtm) REVERT: F 199 MET cc_start: 0.5459 (tpp) cc_final: 0.4137 (tpt) REVERT: A 132 ASN cc_start: 0.8178 (t0) cc_final: 0.7682 (t0) REVERT: A 540 MET cc_start: 0.8081 (ttm) cc_final: 0.7443 (tpp) REVERT: A 811 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8747 (mp) REVERT: A 841 ASP cc_start: 0.7900 (p0) cc_final: 0.7375 (t0) REVERT: A 908 GLU cc_start: 0.8467 (tm-30) cc_final: 0.7943 (tm-30) REVERT: A 991 ASN cc_start: 0.8462 (t0) cc_final: 0.8240 (t0) REVERT: A 1089 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7504 (mm-30) REVERT: B 82 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8164 (tt) REVERT: B 249 ASP cc_start: 0.5942 (t0) cc_final: 0.5669 (t0) REVERT: C 8 PHE cc_start: 0.8247 (t80) cc_final: 0.7896 (t80) REVERT: C 12 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8606 (mtmt) REVERT: C 21 LEU cc_start: 0.8556 (mm) cc_final: 0.7930 (mp) REVERT: C 24 ASP cc_start: 0.8639 (m-30) cc_final: 0.8136 (m-30) REVERT: C 76 GLN cc_start: 0.8081 (mp10) cc_final: 0.7743 (mp10) REVERT: E 58 GLN cc_start: 0.7910 (tp40) cc_final: 0.7245 (tm-30) REVERT: E 188 MET cc_start: 0.5809 (ptt) cc_final: 0.5228 (ptt) REVERT: E 211 TYR cc_start: 0.7936 (m-80) cc_final: 0.7730 (m-80) REVERT: G 24 GLN cc_start: 0.7865 (mt0) cc_final: 0.7422 (tp40) REVERT: G 188 MET cc_start: 0.6790 (ttm) cc_final: 0.6111 (tpt) REVERT: G 247 GLN cc_start: 0.8744 (mt0) cc_final: 0.8255 (mt0) outliers start: 68 outliers final: 48 residues processed: 215 average time/residue: 0.1331 time to fit residues: 45.4172 Evaluate side-chains 200 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 225 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: [208, 21, 198, 134, 44, 119, 42, 170, 61, 36, 160] chunk 208 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 198 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 170 optimal weight: 0.0030 chunk 61 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 84 ASN A 177 ASN B 52 GLN B 124 ASN E 153 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.100124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.076325 restraints weight = 57788.005| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.64 r_work: 0.3251 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20023 Z= 0.220 Angle : 0.630 11.534 27287 Z= 0.325 Chirality : 0.045 0.184 3113 Planarity : 0.005 0.072 3317 Dihedral : 14.061 87.885 3071 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.04 % Allowed : 17.55 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.65 (0.17), residues: 2300 helix: 0.54 (0.21), residues: 655 sheet: -1.18 (0.22), residues: 517 loop : -2.07 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1017 TYR 0.021 0.002 TYR C 98 PHE 0.020 0.002 PHE A 355 TRP 0.012 0.002 TRP B 103 HIS 0.003 0.001 HIS A 903 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 (20014) covalent geometry : angle 0.61789 / 0.32 (27267) SS BOND : bond 0.00075 / 0.04 ( 1) SS BOND : angle 1.82722 / 3.05 ( 2) hydrogen bonds : bond 0.04040 / 4.54 ( 805) hydrogen bonds : angle 5.30756 / 5.68 ( 2231) metal coordination : bond 0.01049 / 1.00 ( 8) metal coordination : angle 4.87096 / 7.87 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 150 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 199 MET cc_start: 0.5363 (tpp) cc_final: 0.3971 (tpt) REVERT: A 110 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8587 (tp) REVERT: A 132 ASN cc_start: 0.8198 (t0) cc_final: 0.7658 (t0) REVERT: A 540 MET cc_start: 0.8114 (ttm) cc_final: 0.7458 (tpp) REVERT: A 811 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8786 (mp) REVERT: A 841 ASP cc_start: 0.7975 (p0) cc_final: 0.7409 (t0) REVERT: A 908 GLU cc_start: 0.8502 (tm-30) cc_final: 0.7971 (tm-30) REVERT: A 991 ASN cc_start: 0.8559 (t0) cc_final: 0.8329 (t0) REVERT: B 112 MET cc_start: 0.8837 (mpp) cc_final: 0.8337 (mtm) REVERT: B 249 ASP cc_start: 0.6068 (t0) cc_final: 0.5613 (t0) REVERT: C 21 LEU cc_start: 0.8524 (mm) cc_final: 0.7725 (mp) REVERT: C 24 ASP cc_start: 0.8675 (m-30) cc_final: 0.8134 (m-30) REVERT: C 76 GLN cc_start: 0.8103 (mp10) cc_final: 0.7757 (mp10) REVERT: E 58 GLN cc_start: 0.7866 (tp40) cc_final: 0.7207 (tm-30) REVERT: E 88 LEU cc_start: 0.4227 (OUTLIER) cc_final: 0.3650 (tt) REVERT: E 188 MET cc_start: 0.5749 (OUTLIER) cc_final: 0.5073 (ptt) REVERT: G 24 GLN cc_start: 0.7896 (mt0) cc_final: 0.7452 (tp40) REVERT: G 186 VAL cc_start: 0.5782 (OUTLIER) cc_final: 0.5576 (m) REVERT: G 245 PHE cc_start: 0.8107 (p90) cc_final: 0.7711 (p90) outliers start: 85 outliers final: 55 residues processed: 221 average time/residue: 0.1284 time to fit residues: 45.3367 Evaluate side-chains 202 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 142 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 225 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: [151, 11, 59, 56, 136, 82, 110, 157, 199, 42, 183] chunk 151 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 136 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 84 ASN B 407 ASN E 238 GLN G 247 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.100883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.077267 restraints weight = 57397.038| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.63 r_work: 0.3270 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20023 Z= 0.157 Angle : 0.586 12.265 27287 Z= 0.301 Chirality : 0.044 0.188 3113 Planarity : 0.004 0.060 3317 Dihedral : 14.017 87.550 3069 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.90 % Allowed : 18.45 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.45 (0.17), residues: 2300 helix: 0.71 (0.21), residues: 651 sheet: -1.05 (0.22), residues: 517 loop : -1.96 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 80 TYR 0.015 0.001 TYR C 98 PHE 0.019 0.001 PHE C 41 TRP 0.013 0.001 TRP B 103 HIS 0.004 0.001 HIS G 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (20014) covalent geometry : angle 0.57320 / 0.30 (27267) SS BOND : bond 0.00076 / 0.04 ( 1) SS BOND : angle 1.66622 / 2.78 ( 2) hydrogen bonds : bond 0.03614 / 4.07 ( 805) hydrogen bonds : angle 5.16568 / 5.52 ( 2231) metal coordination : bond 0.00818 / 0.77 ( 8) metal coordination : angle 4.72755 / 7.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 155 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 199 MET cc_start: 0.5494 (tpp) cc_final: 0.4103 (tpt) REVERT: A 540 MET cc_start: 0.8107 (ttm) cc_final: 0.7458 (tpp) REVERT: A 811 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8767 (mp) REVERT: A 841 ASP cc_start: 0.7961 (p0) cc_final: 0.7420 (t0) REVERT: A 908 GLU cc_start: 0.8504 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 991 ASN cc_start: 0.8541 (t0) cc_final: 0.8304 (t0) REVERT: A 1089 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7608 (mm-30) REVERT: B 112 MET cc_start: 0.8816 (mpp) cc_final: 0.8340 (mtm) REVERT: B 249 ASP cc_start: 0.6087 (t0) cc_final: 0.5853 (t0) REVERT: C 12 LYS cc_start: 0.8906 (mtmt) cc_final: 0.8585 (mtmt) REVERT: C 21 LEU cc_start: 0.8484 (mm) cc_final: 0.7774 (mp) REVERT: C 24 ASP cc_start: 0.8685 (m-30) cc_final: 0.8096 (m-30) REVERT: C 76 GLN cc_start: 0.8090 (mp10) cc_final: 0.7406 (mp10) REVERT: E 14 ARG cc_start: 0.8590 (mpp80) cc_final: 0.8274 (mpp80) REVERT: E 58 GLN cc_start: 0.7871 (tp40) cc_final: 0.7202 (tm-30) REVERT: E 188 MET cc_start: 0.5792 (OUTLIER) cc_final: 0.5084 (ptt) REVERT: G 24 GLN cc_start: 0.7911 (mt0) cc_final: 0.7471 (tp40) REVERT: G 186 VAL cc_start: 0.5828 (OUTLIER) cc_final: 0.5621 (m) REVERT: G 245 PHE cc_start: 0.8163 (p90) cc_final: 0.7637 (p90) outliers start: 82 outliers final: 55 residues processed: 225 average time/residue: 0.1259 time to fit residues: 44.9635 Evaluate side-chains 204 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 146 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 225 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: [117, 37, 169, 42, 119, 162, 147, 144, 4, 183, 98] chunk 117 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 169 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 119 optimal weight: 8.9990 chunk 162 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 84 ASN B 52 GLN ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.101682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.078042 restraints weight = 57679.895| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.66 r_work: 0.3286 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20023 Z= 0.124 Angle : 0.577 11.859 27287 Z= 0.294 Chirality : 0.043 0.174 3113 Planarity : 0.004 0.072 3317 Dihedral : 13.939 87.037 3069 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.61 % Allowed : 19.31 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.28 (0.17), residues: 2300 helix: 0.87 (0.21), residues: 651 sheet: -0.91 (0.22), residues: 511 loop : -1.89 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1017 TYR 0.019 0.001 TYR E 211 PHE 0.021 0.001 PHE C 41 TRP 0.013 0.001 TRP B 103 HIS 0.004 0.001 HIS G 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (20014) covalent geometry : angle 0.56411 / 0.29 (27267) SS BOND : bond 0.00119 / 0.06 ( 1) SS BOND : angle 1.29001 / 2.15 ( 2) hydrogen bonds : bond 0.03397 / 3.83 ( 805) hydrogen bonds : angle 5.03857 / 5.38 ( 2231) metal coordination : bond 0.00581 / 0.54 ( 8) metal coordination : angle 4.66000 / 6.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 158 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 199 MET cc_start: 0.5382 (tpp) cc_final: 0.4050 (tpt) REVERT: A 132 ASN cc_start: 0.8168 (t0) cc_final: 0.7833 (t0) REVERT: A 811 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8728 (mp) REVERT: A 841 ASP cc_start: 0.7966 (p0) cc_final: 0.7443 (t0) REVERT: A 908 GLU cc_start: 0.8487 (tm-30) cc_final: 0.7962 (tm-30) REVERT: A 991 ASN cc_start: 0.8525 (t0) cc_final: 0.8285 (t0) REVERT: A 1089 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7613 (mm-30) REVERT: B 112 MET cc_start: 0.8738 (mpp) cc_final: 0.8282 (mtm) REVERT: B 249 ASP cc_start: 0.5995 (t0) cc_final: 0.5760 (t0) REVERT: C 9 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7237 (tt) REVERT: C 12 LYS cc_start: 0.8908 (mtmt) cc_final: 0.8588 (mtmt) REVERT: C 21 LEU cc_start: 0.8492 (mm) cc_final: 0.7656 (mp) REVERT: C 24 ASP cc_start: 0.8657 (m-30) cc_final: 0.8051 (m-30) REVERT: C 41 PHE cc_start: 0.6980 (t80) cc_final: 0.6775 (t80) REVERT: C 76 GLN cc_start: 0.8110 (mp10) cc_final: 0.7472 (mp10) REVERT: E 14 ARG cc_start: 0.8553 (mpp80) cc_final: 0.8312 (mpp80) REVERT: E 58 GLN cc_start: 0.7822 (tp40) cc_final: 0.7152 (tm-30) REVERT: E 188 MET cc_start: 0.5713 (OUTLIER) cc_final: 0.4990 (ptt) REVERT: G 24 GLN cc_start: 0.7911 (mt0) cc_final: 0.7502 (tp40) REVERT: G 186 VAL cc_start: 0.5782 (OUTLIER) cc_final: 0.5569 (m) REVERT: G 188 MET cc_start: 0.6929 (ttm) cc_final: 0.5728 (tpt) REVERT: G 190 HIS cc_start: 0.7792 (t-90) cc_final: 0.7123 (t70) REVERT: G 245 PHE cc_start: 0.8138 (p90) cc_final: 0.7649 (p90) outliers start: 76 outliers final: 57 residues processed: 221 average time/residue: 0.1261 time to fit residues: 45.1339 Evaluate side-chains 208 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 147 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 243 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: [68, 85, 100, 6, 119, 78, 138, 28, 137, 162, 175] chunk 68 optimal weight: 0.9980 chunk 85 optimal weight: 0.2980 chunk 100 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 84 ASN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.101741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.078087 restraints weight = 57717.134| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.67 r_work: 0.3289 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20023 Z= 0.129 Angle : 0.578 11.322 27287 Z= 0.295 Chirality : 0.043 0.314 3113 Planarity : 0.004 0.068 3317 Dihedral : 13.889 86.650 3067 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.52 % Allowed : 19.40 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.19 (0.17), residues: 2300 helix: 0.90 (0.21), residues: 653 sheet: -0.85 (0.22), residues: 525 loop : -1.81 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 14 TYR 0.015 0.001 TYR E 211 PHE 0.016 0.001 PHE C 41 TRP 0.012 0.001 TRP B 103 HIS 0.003 0.001 HIS E 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (20014) covalent geometry : angle 0.56589 / 0.30 (27267) SS BOND : bond 0.00110 / 0.06 ( 1) SS BOND : angle 1.31184 / 2.19 ( 2) hydrogen bonds : bond 0.03388 / 3.82 ( 805) hydrogen bonds : angle 5.00301 / 5.32 ( 2231) metal coordination : bond 0.00603 / 0.56 ( 8) metal coordination : angle 4.58706 / 6.72 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 154 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 83 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7573 (p0) REVERT: F 199 MET cc_start: 0.5534 (tpp) cc_final: 0.4101 (tpt) REVERT: A 811 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8752 (mp) REVERT: A 841 ASP cc_start: 0.7970 (p0) cc_final: 0.7454 (t0) REVERT: A 908 GLU cc_start: 0.8485 (tm-30) cc_final: 0.7958 (tm-30) REVERT: A 991 ASN cc_start: 0.8533 (t0) cc_final: 0.8285 (t0) REVERT: A 1089 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7621 (mm-30) REVERT: B 112 MET cc_start: 0.8696 (mpp) cc_final: 0.8287 (mtm) REVERT: B 249 ASP cc_start: 0.5963 (t0) cc_final: 0.5727 (t0) REVERT: C 9 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7335 (tt) REVERT: C 12 LYS cc_start: 0.8919 (mtmt) cc_final: 0.8587 (mtmt) REVERT: C 21 LEU cc_start: 0.8507 (mm) cc_final: 0.7810 (mp) REVERT: C 24 ASP cc_start: 0.8618 (m-30) cc_final: 0.8214 (m-30) REVERT: C 41 PHE cc_start: 0.6918 (t80) cc_final: 0.6702 (t80) REVERT: C 76 GLN cc_start: 0.8113 (mp10) cc_final: 0.7464 (mp10) REVERT: E 14 ARG cc_start: 0.8368 (mpp80) cc_final: 0.8079 (mpp80) REVERT: E 58 GLN cc_start: 0.7814 (tp40) cc_final: 0.7141 (tm-30) REVERT: E 188 MET cc_start: 0.5807 (OUTLIER) cc_final: 0.5114 (ptt) REVERT: G 24 GLN cc_start: 0.7943 (mt0) cc_final: 0.7535 (tp40) REVERT: G 186 VAL cc_start: 0.5781 (OUTLIER) cc_final: 0.5575 (m) REVERT: G 188 MET cc_start: 0.6946 (ttm) cc_final: 0.5798 (tpt) REVERT: G 190 HIS cc_start: 0.7648 (t-90) cc_final: 0.6986 (t70) REVERT: G 245 PHE cc_start: 0.8114 (p90) cc_final: 0.7620 (p90) outliers start: 74 outliers final: 59 residues processed: 216 average time/residue: 0.1317 time to fit residues: 45.7827 Evaluate side-chains 214 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 150 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 243 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: [9, 177, 159, 37, 59, 229, 25, 29, 96, 202, 191] chunk 9 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 229 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.101630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.077992 restraints weight = 57406.869| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.66 r_work: 0.3286 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20023 Z= 0.134 Angle : 0.571 10.580 27287 Z= 0.292 Chirality : 0.043 0.248 3113 Planarity : 0.004 0.060 3317 Dihedral : 13.857 86.346 3067 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.19 % Allowed : 19.73 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.10 (0.17), residues: 2300 helix: 0.98 (0.21), residues: 654 sheet: -0.82 (0.22), residues: 531 loop : -1.76 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1017 TYR 0.015 0.001 TYR C 98 PHE 0.013 0.001 PHE C 41 TRP 0.012 0.001 TRP B 103 HIS 0.003 0.001 HIS E 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (20014) covalent geometry : angle 0.55901 / 0.29 (27267) SS BOND : bond 0.00068 / 0.03 ( 1) SS BOND : angle 1.39315 / 2.33 ( 2) hydrogen bonds : bond 0.03365 / 3.80 ( 805) hydrogen bonds : angle 4.94401 / 5.29 ( 2231) metal coordination : bond 0.00628 / 0.61 ( 8) metal coordination : angle 4.51945 / 6.77 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 154 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 199 MET cc_start: 0.5519 (tpp) cc_final: 0.4050 (tpt) REVERT: F 201 GLN cc_start: 0.7954 (pt0) cc_final: 0.7674 (pm20) REVERT: A 811 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8755 (mp) REVERT: A 841 ASP cc_start: 0.7923 (p0) cc_final: 0.7441 (t0) REVERT: A 908 GLU cc_start: 0.8483 (tm-30) cc_final: 0.7950 (tm-30) REVERT: A 991 ASN cc_start: 0.8528 (t0) cc_final: 0.8278 (t0) REVERT: B 112 MET cc_start: 0.8665 (mpp) cc_final: 0.8271 (mtm) REVERT: B 249 ASP cc_start: 0.5940 (t0) cc_final: 0.5708 (t0) REVERT: C 9 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7299 (tt) REVERT: C 12 LYS cc_start: 0.8916 (mtmt) cc_final: 0.8580 (mtmt) REVERT: C 21 LEU cc_start: 0.8480 (mm) cc_final: 0.8024 (mp) REVERT: C 41 PHE cc_start: 0.6916 (t80) cc_final: 0.6677 (t80) REVERT: C 76 GLN cc_start: 0.8111 (mp10) cc_final: 0.7466 (mp10) REVERT: E 14 ARG cc_start: 0.8219 (mpp80) cc_final: 0.7745 (mpp80) REVERT: E 58 GLN cc_start: 0.7858 (tp40) cc_final: 0.7198 (tm-30) REVERT: E 188 MET cc_start: 0.5678 (OUTLIER) cc_final: 0.4920 (ptt) REVERT: G 24 GLN cc_start: 0.7956 (mt0) cc_final: 0.7550 (tp40) REVERT: G 188 MET cc_start: 0.6883 (ttm) cc_final: 0.5731 (tpt) REVERT: G 190 HIS cc_start: 0.7607 (t-90) cc_final: 0.6939 (t70) REVERT: G 245 PHE cc_start: 0.8177 (p90) cc_final: 0.7731 (p90) outliers start: 67 outliers final: 57 residues processed: 210 average time/residue: 0.1388 time to fit residues: 46.3470 Evaluate side-chains 207 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 147 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 243 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: [26, 206, 231, 58, 51, 170, 73, 223, 150, 21, 167] chunk 26 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 231 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 170 optimal weight: 0.0870 chunk 73 optimal weight: 0.9980 chunk 223 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 167 optimal weight: 0.7980 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.101213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.077653 restraints weight = 57658.331| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.65 r_work: 0.3279 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20023 Z= 0.150 Angle : 0.579 10.356 27287 Z= 0.296 Chirality : 0.043 0.227 3113 Planarity : 0.004 0.055 3317 Dihedral : 13.859 86.499 3067 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.04 % Allowed : 19.83 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.09 (0.17), residues: 2300 helix: 0.98 (0.21), residues: 654 sheet: -0.80 (0.22), residues: 531 loop : -1.75 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1017 TYR 0.028 0.001 TYR C 98 PHE 0.012 0.001 PHE C 41 TRP 0.012 0.001 TRP B 103 HIS 0.003 0.001 HIS E 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (20014) covalent geometry : angle 0.56721 / 0.30 (27267) SS BOND : bond 0.00058 / 0.03 ( 1) SS BOND : angle 1.89002 / 3.16 ( 2) hydrogen bonds : bond 0.03435 / 3.87 ( 805) hydrogen bonds : angle 4.95529 / 5.31 ( 2231) metal coordination : bond 0.00758 / 0.72 ( 8) metal coordination : angle 4.51456 / 6.87 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 150 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 199 MET cc_start: 0.5519 (tpp) cc_final: 0.3990 (tpt) REVERT: F 201 GLN cc_start: 0.7949 (pt0) cc_final: 0.7713 (pm20) REVERT: A 132 ASN cc_start: 0.8151 (t0) cc_final: 0.7842 (t0) REVERT: A 811 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8769 (mp) REVERT: A 841 ASP cc_start: 0.7942 (p0) cc_final: 0.7452 (t0) REVERT: A 908 GLU cc_start: 0.8498 (tm-30) cc_final: 0.7956 (tm-30) REVERT: A 991 ASN cc_start: 0.8557 (t0) cc_final: 0.8288 (t0) REVERT: B 112 MET cc_start: 0.8677 (mpp) cc_final: 0.8306 (mtm) REVERT: B 249 ASP cc_start: 0.5948 (t0) cc_final: 0.5717 (t0) REVERT: C 9 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7363 (tt) REVERT: C 12 LYS cc_start: 0.8916 (mtmt) cc_final: 0.8587 (mtmt) REVERT: C 21 LEU cc_start: 0.8512 (mm) cc_final: 0.8039 (mp) REVERT: C 76 GLN cc_start: 0.8112 (mp10) cc_final: 0.7467 (mp10) REVERT: E 14 ARG cc_start: 0.8215 (mpp80) cc_final: 0.7750 (mpp80) REVERT: E 58 GLN cc_start: 0.7874 (tp40) cc_final: 0.7191 (tm-30) REVERT: E 188 MET cc_start: 0.5657 (OUTLIER) cc_final: 0.4912 (ptt) REVERT: G 24 GLN cc_start: 0.7940 (mt0) cc_final: 0.7580 (tp40) REVERT: G 188 MET cc_start: 0.6817 (ttm) cc_final: 0.6270 (tpt) REVERT: G 190 HIS cc_start: 0.7579 (t-90) cc_final: 0.7053 (t70) REVERT: G 245 PHE cc_start: 0.8136 (p90) cc_final: 0.7699 (p90) outliers start: 64 outliers final: 59 residues processed: 204 average time/residue: 0.1317 time to fit residues: 42.9936 Evaluate side-chains 211 residues out of total 2104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 149 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 243 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: [156, 69, 42, 78, 219, 63, 183, 33, 178, 135, 222] chunk 156 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 222 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.100909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.077204 restraints weight = 57885.572| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.67 r_work: 0.3268 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20023 Z= 0.163 Angle : 0.591 13.401 27287 Z= 0.301 Chirality : 0.044 0.201 3113 Planarity : 0.004 0.053 3317 Dihedral : 13.879 86.882 3067 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.33 % Allowed : 19.73 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.08 (0.17), residues: 2300 helix: 0.99 (0.21), residues: 653 sheet: -0.79 (0.22), residues: 531 loop : -1.74 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1017 TYR 0.022 0.001 TYR C 98 PHE 0.025 0.001 PHE C 41 TRP 0.012 0.001 TRP B 103 HIS 0.003 0.001 HIS E 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (20014) covalent geometry : angle 0.57957 / 0.30 (27267) SS BOND : bond 0.00062 / 0.03 ( 1) SS BOND : angle 1.66597 / 2.78 ( 2) hydrogen bonds : bond 0.03523 / 3.96 ( 805) hydrogen bonds : angle 4.97510 / 5.36 ( 2231) metal coordination : bond 0.00843 / 0.80 ( 8) metal coordination : angle 4.55486 / 7.07 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4239.89 seconds wall clock time: 73 minutes 54.23 seconds (4434.23 seconds total)