Starting phenix.real_space_refine on Mon Oct 26 05:36:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tny_10539/10_2026/6tny_10539_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tny_10539/10_2026/6tny_10539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tny_10539/10_2026/6tny_10539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tny_10539/10_2026/6tny_10539.map" model { file = "/net/cci-nas-00/data/ceres_data/6tny_10539/10_2026/6tny_10539_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tny_10539/10_2026/6tny_10539_neut.cif" } resolution = 3.08 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 1 6.06 5 P 53 5.49 5 S 125 5.16 5 C 12326 2.51 5 N 3377 2.21 5 O 3840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.02s 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: 19726 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7926 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1010, 7922 Classifications: {'peptide': 1010} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 62, 'TRANS': 942} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 1010, 7922 Classifications: {'peptide': 1010} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 62, 'TRANS': 942} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 8085 Chain: "B" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3304 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 399} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1130 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "D" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 554 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 7, 'TRANS': 58} Chain: "E" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1924 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1913 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 241} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1913 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 7, 'TRANS': 241} Chain breaks: 1 Chain: "P" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Unusual residues: {'DOC': 1} Classifications: {'DNA': 22, 'undetermined': 1} Link IDs: {'rna3p': 21, None: 1} Not linked: pdbres=" DG P 24 " pdbres="DOC P 25 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "T" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 555 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {' ZN': 1, 'SF4': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7157 SG CYS A1012 93.068 71.259 44.294 1.00 40.62 S ATOM 7175 SG CYS A1015 95.509 70.329 47.207 1.00 40.62 S ATOM 7248 SG CYS A1026 96.869 69.692 43.613 1.00 40.62 S ATOM 7264 SG CYS A1029 93.666 68.034 44.806 1.00 40.62 S ATOM 7616 SG CYS A1071 58.117 95.238 52.833 1.00 40.62 S ATOM 7654 SG CYS A1076 59.246 90.776 56.637 1.00 30.94 S ATOM 7515 SG CYS A1058 59.456 89.840 49.733 1.00 40.62 S ATOM 7541 SG CYS A1061 54.296 90.957 53.405 1.00 24.79 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY A1100 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A1100 " occ=0.50 Time building chain proxies: 5.05, per 1000 atoms: 0.26 Number of scatterers: 19726 At special positions: 0 Unit cell: (145.29, 161.82, 137.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 4 26.01 S 125 16.00 P 53 15.00 O 3840 8.00 N 3377 7.00 C 12326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1202 " pdb="FE2 SF4 A1202 " - pdb=" SG CYS A1076 " pdb="FE1 SF4 A1202 " - pdb=" SG CYS A1071 " pdb="FE3 SF4 A1202 " - pdb=" SG CYS A1058 " pdb="FE4 SF4 A1202 " - pdb=" SG CYS A1061 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1029 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1015 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1012 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1026 " Number of angles added : 6 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4502 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 20 sheets defined 31.1% alpha, 22.3% beta 22 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.640A pdb=" N SER A 176 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 177' Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.924A pdb=" N GLU A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 259 Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.591A pdb=" N GLN A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 389 removed outlier: 3.573A pdb=" N LEU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 413 Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 473 through 482 Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 501 through 526 Proline residue: A 519 - end of helix Processing helix chain 'A' and resid 527 through 540 removed outlier: 3.590A pdb=" N ASN A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 removed outlier: 3.641A pdb=" N LEU A 547 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 548 " --> pdb=" O TYR A 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 544 through 548' Processing helix chain 'A' and resid 551 through 564 removed outlier: 4.127A pdb=" N VAL A 555 " --> pdb=" O GLN A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 614 Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 655 through 675 Processing helix chain 'A' and resid 679 through 705 removed outlier: 3.886A pdb=" N TYR A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY A 705 " --> pdb=" O TYR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 739 removed outlier: 3.935A pdb=" N SER A 717 " --> pdb=" O CYS A 713 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR A 739 " --> pdb=" O VAL A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 783 Processing helix chain 'A' and resid 837 through 853 Processing helix chain 'A' and resid 856 through 873 Processing helix chain 'A' and resid 898 through 906 removed outlier: 3.630A pdb=" N GLU A 902 " --> pdb=" O GLN A 898 " (cutoff:3.500A) 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 971 removed outlier: 3.563A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 990 Processing helix chain 'A' and resid 1001 through 1005 removed outlier: 3.794A pdb=" N ALA A1004 " --> pdb=" O GLY A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1056 removed outlier: 4.884A pdb=" N GLU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A1041 " --> pdb=" O TYR A1037 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER A1042 " --> pdb=" O GLN A1038 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N HIS A1043 " --> pdb=" O LYS A1039 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A1052 " --> pdb=" O GLU A1048 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A1053 " --> pdb=" O GLU A1049 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A1054 " --> pdb=" O ARG A1050 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1063 removed outlier: 3.573A pdb=" N ARG A1060 " --> pdb=" O THR A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1096 removed outlier: 3.691A pdb=" N MET A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LYS A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS A1084 " --> pdb=" O TYR A1080 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL A1085 " --> pdb=" O MET A1081 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ARG A1086 " --> pdb=" O ARG A1082 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS A1087 " --> pdb=" O LYS A1083 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A1094 " --> pdb=" O GLU A1090 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A1096 " --> pdb=" O GLN A1092 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 8 removed outlier: 3.600A pdb=" N ALA B 7 " --> pdb=" O GLU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 Processing helix chain 'B' and resid 50 through 74 removed outlier: 4.280A pdb=" N TYR B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 56 " --> pdb=" O HIS B 52 " (cutoff:3.500A) Proline residue: B 63 - end of helix removed outlier: 3.900A pdb=" N GLN B 71 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 272 through 288 removed outlier: 3.966A pdb=" N VAL B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 removed outlier: 3.627A pdb=" N MET B 315 " --> pdb=" O HIS B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.802A pdb=" N TYR B 322 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 355 removed outlier: 3.557A pdb=" N TYR B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 371 Processing helix chain 'C' and resid 3 through 15 removed outlier: 3.672A pdb=" N THR C 15 " --> pdb=" O ASP C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 30 removed outlier: 3.896A pdb=" N LEU C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 52 removed outlier: 3.888A pdb=" N ASN C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 92 removed outlier: 3.507A pdb=" N VAL C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 124 removed outlier: 3.822A pdb=" N ASN C 116 " --> pdb=" O GLY C 112 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 124 " --> pdb=" O ASP C 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 53 removed outlier: 3.598A pdb=" N LEU D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 49 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.854A pdb=" N ARG D 69 " --> pdb=" O THR D 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 18 removed outlier: 4.177A pdb=" N LYS E 13 " --> pdb=" O GLY E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 72 through 80 Processing helix chain 'E' and resid 141 through 153 removed outlier: 3.811A pdb=" N HIS E 153 " --> pdb=" O ARG E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 216 Processing helix chain 'E' and resid 217 through 222 Proline residue: E 220 - end of helix No H-bonds generated for 'chain 'E' and resid 217 through 222' Processing helix chain 'F' and resid 8 through 20 removed outlier: 4.057A pdb=" N LEU F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 79 Processing helix chain 'F' and resid 141 through 152 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 222 Proline residue: F 220 - end of helix No H-bonds generated for 'chain 'F' and resid 217 through 222' Processing helix chain 'G' and resid 8 through 20 removed outlier: 4.016A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 79 Processing helix chain 'G' and resid 141 through 155 removed outlier: 3.591A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY G 155 " --> pdb=" O LEU G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 222 Proline residue: G 220 - end of helix No H-bonds generated for 'chain 'G' and resid 217 through 222' Processing sheet with id=AA1, first strand: chain 'A' and resid 286 through 291 removed outlier: 6.564A pdb=" N SER A 136 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA A 288 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N CYS A 138 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL A 290 " --> pdb=" O CYS A 138 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS A 140 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 100 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A 130 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLN A 98 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP A 265 " --> pdb=" O HIS A 298 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 151 Processing sheet with id=AA3, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.531A pdb=" N GLN A 369 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 336 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG A 311 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N THR A 394 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A 313 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 393 " --> pdb=" O MET A 457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 431 through 438 Processing sheet with id=AA5, first strand: chain 'A' and resid 592 through 594 removed outlier: 5.417A pdb=" N PHE A 794 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASP A 602 " --> pdb=" O PHE A 794 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS A 796 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR A 753 " --> pdb=" O MET A 760 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG A 762 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL A 751 " --> pdb=" O ARG A 762 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 592 through 594 removed outlier: 6.208A pdb=" N TYR A 798 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE A 814 " --> pdb=" O TYR A 798 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 812 " --> pdb=" O PRO A 800 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ARG A 808 " --> pdb=" O ILE A 804 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 621 through 622 removed outlier: 4.674A pdb=" N GLU A 645 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 883 through 886 Processing sheet with id=AA9, first strand: chain 'A' and resid 992 through 993 removed outlier: 3.787A pdb=" N THR A 993 " --> pdb=" O ASP F 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 141 through 143 removed outlier: 3.652A pdb=" N GLU B 132 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA B 160 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR B 176 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHE B 162 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 325 through 327 removed outlier: 7.701A pdb=" N PHE B 195 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 241 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU B 197 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU B 243 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL B 199 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N SER C 73 " --> pdb=" O CYS B 447 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS C 75 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL C 79 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N HIS C 58 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE C 103 " --> pdb=" O HIS C 58 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR C 60 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS C 99 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 97 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE C 103 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL C 21 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 332 through 336 removed outlier: 6.615A pdb=" N ARG B 340 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N PHE B 403 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B 342 " --> pdb=" O PHE B 403 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 426 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY B 411 " --> pdb=" O THR B 427 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 60 through 61 Processing sheet with id=AB5, first strand: chain 'E' and resid 66 through 71 removed outlier: 7.298A pdb=" N GLU E 25 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N MET E 40 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N CYS E 27 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS E 240 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR E 224 " --> pdb=" O LYS E 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 178 through 183 Processing sheet with id=AB7, first strand: chain 'F' and resid 59 through 62 removed outlier: 4.358A pdb=" N VAL F 111 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS G 181 " --> pdb=" O VAL F 111 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP F 113 " --> pdb=" O ASN G 179 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN G 179 " --> pdb=" O ASP F 113 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN G 177 " --> pdb=" O GLU F 115 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 68 through 71 removed outlier: 7.287A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN F 36 " --> pdb=" O ASP F 29 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 178 through 183 Processing sheet with id=AC1, first strand: chain 'G' and resid 59 through 62 removed outlier: 3.646A pdb=" N THR G 59 " --> pdb=" O ARG G 5 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 66 through 71 removed outlier: 7.094A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) 789 hydrogen bonds defined for protein. 2211 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue (no planarity definition) Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 4.25 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 8016 1.40 - 1.63: 11994 1.63 - 1.85: 188 1.85 - 2.08: 0 2.08 - 2.31: 12 Bond restraints: 20210 Sorted by residual: bond pdb=" C2' TTP A1203 " pdb=" C3' TTP A1203 " ideal model delta sigma weight residual 1.522 1.216 0.306 2.00e-02 2.50e+03 2.33e+02 bond pdb=" C3' DOC P 25 " pdb=" C2' DOC P 25 " ideal model delta sigma weight residual 1.521 1.305 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C4' TTP A1203 " pdb=" O4' TTP A1203 " ideal model delta sigma weight residual 1.426 1.270 0.156 2.00e-02 2.50e+03 6.12e+01 bond pdb=" C4' DOC P 25 " pdb=" O4' DOC P 25 " ideal model delta sigma weight residual 1.431 1.278 0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" O4' DOC P 25 " pdb=" C1' DOC P 25 " ideal model delta sigma weight residual 1.405 1.552 -0.147 2.00e-02 2.50e+03 5.38e+01 ... (remaining 20205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 26846 2.86 - 5.72: 637 5.72 - 8.58: 106 8.58 - 11.44: 15 11.44 - 14.30: 5 Bond angle restraints: 27609 Sorted by residual: angle pdb=" N ARG A 985 " pdb=" CA ARG A 985 " pdb=" C ARG A 985 " ideal model delta sigma weight residual 111.07 102.80 8.27 1.07e+00 8.73e-01 5.98e+01 angle pdb=" N ALA B 179 " pdb=" CA ALA B 179 " pdb=" C ALA B 179 " ideal model delta sigma weight residual 111.28 119.44 -8.16 1.09e+00 8.42e-01 5.60e+01 angle pdb=" N ARG A1098 " pdb=" CA ARG A1098 " pdb=" C ARG A1098 " ideal model delta sigma weight residual 111.36 103.72 7.64 1.09e+00 8.42e-01 4.92e+01 angle pdb=" N GLY A 592 " pdb=" CA GLY A 592 " pdb=" C GLY A 592 " ideal model delta sigma weight residual 110.20 118.98 -8.78 1.32e+00 5.74e-01 4.42e+01 angle pdb=" N ALA A1024 " pdb=" CA ALA A1024 " pdb=" C ALA A1024 " ideal model delta sigma weight residual 111.28 118.45 -7.17 1.09e+00 8.42e-01 4.32e+01 ... (remaining 27604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.44: 10750 20.44 - 40.88: 1116 40.88 - 61.32: 301 61.32 - 81.76: 27 81.76 - 102.20: 15 Dihedral angle restraints: 12209 sinusoidal: 5246 harmonic: 6963 Sorted by residual: dihedral pdb=" N HIS A1021 " pdb=" C HIS A1021 " pdb=" CA HIS A1021 " pdb=" CB HIS A1021 " ideal model delta harmonic sigma weight residual 122.80 137.51 -14.71 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" CA PRO A 818 " pdb=" C PRO A 818 " pdb=" N ASP A 819 " pdb=" CA ASP A 819 " ideal model delta harmonic sigma weight residual 180.00 151.65 28.35 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA LEU A 962 " pdb=" C LEU A 962 " pdb=" N ALA A 963 " pdb=" CA ALA A 963 " ideal model delta harmonic sigma weight residual -180.00 -153.19 -26.81 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 12206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2808 0.099 - 0.197: 320 0.197 - 0.296: 20 0.296 - 0.394: 0 0.394 - 0.493: 4 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CA ASP B 180 " pdb=" N ASP B 180 " pdb=" C ASP B 180 " pdb=" CB ASP B 180 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.07e+00 chirality pdb=" CA HIS A1021 " pdb=" N HIS A1021 " pdb=" C HIS A1021 " pdb=" CB HIS A1021 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" C3' TTP A1203 " pdb=" C2' TTP A1203 " pdb=" C4' TTP A1203 " pdb=" O3' TTP A1203 " both_signs ideal model delta sigma weight residual False -2.70 -2.30 -0.40 2.00e-01 2.50e+01 4.03e+00 ... (remaining 3149 not shown) Planarity restraints: 3387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1099 " -0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C PHE A1099 " 0.079 2.00e-02 2.50e+03 pdb=" O PHE A1099 " -0.029 2.00e-02 2.50e+03 pdb=" N AGLY A1100 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1099 " -0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C PHE A1099 " 0.079 2.00e-02 2.50e+03 pdb=" O PHE A1099 " -0.029 2.00e-02 2.50e+03 pdb=" N BGLY A1100 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 128 " -0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO B 129 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " -0.041 5.00e-02 4.00e+02 ... (remaining 3384 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 58 2.44 - 3.06: 10622 3.06 - 3.67: 28267 3.67 - 4.29: 41327 4.29 - 4.90: 68833 Nonbonded interactions: 149107 Sorted by model distance: nonbonded pdb=" OE1 GLN B 308 " pdb=" ND2 ASN B 330 " model vdw 1.826 3.120 nonbonded pdb=" CG1 VAL A 861 " pdb=" NE ARG A 985 " model vdw 1.943 3.540 nonbonded pdb=" O GLN B 308 " pdb=" CG2 THR B 329 " model vdw 2.129 3.460 nonbonded pdb=" O CYS A1011 " pdb=" NH2 ARG A1098 " model vdw 2.224 3.120 nonbonded pdb=" CG1 VAL A 861 " pdb=" CD ARG A 985 " model vdw 2.251 3.860 ... (remaining 149102 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 107 or resid 109 through 185 or resid 191 or res \ id 194 through 255)) selection = (chain 'F' and (resid 1 through 191 or resid 194 through 255)) selection = (chain 'G' and (resid 1 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 109 through 185 or resid 193 through 255)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 26.470 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 : 0.009 0.306 20219 Z= 0.470 Angle : 1.191 39.352 27627 Z= 0.668 Chirality : 0.064 0.493 3152 Planarity : 0.009 0.075 3387 Dihedral : 17.693 102.199 7707 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.42 % Favored : 93.24 % Rotamer: Outliers : 0.83 % Allowed : 8.84 % Favored : 90.33 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -3.49 (0.15), residues: 2370 helix: -2.41 (0.16), residues: 669 sheet: -0.89 (0.20), residues: 604 loop : -3.10 (0.15), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 276 TYR 0.025 0.003 TYR A 618 PHE 0.032 0.003 PHE A 637 TRP 0.036 0.003 TRP A 344 HIS 0.011 0.002 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00885 / 0.46 (20210) covalent geometry : angle 1.13589 / 0.67 (27609) hydrogen bonds : bond 0.14082 / 9.48 ( 837) hydrogen bonds : angle 6.98537 / 4.89 ( 2315) metal coordination : bond 0.12633 / 6.20 ( 8) metal coordination : angle 14.02892 / 8.49 ( 18) Misc. bond : bond 0.00610 / 0.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 282 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 79 GLU cc_start: 0.4441 (OUTLIER) cc_final: 0.3914 (tp30) REVERT: E 118 LEU cc_start: 0.4217 (mm) cc_final: 0.4001 (tp) REVERT: E 130 GLU cc_start: 0.5212 (mm-30) cc_final: 0.4975 (tp30) REVERT: G 116 MET cc_start: 0.5901 (ttp) cc_final: 0.5585 (tpt) outliers start: 17 outliers final: 6 residues processed: 297 average time/residue: 0.1853 time to fit residues: 78.6271 Evaluate side-chains 179 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 172 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS A 369 GLN A 430 ASN A 558 GLN A 726 GLN A 842 ASN A 865 GLN A 948 HIS A1038 GLN A1066 HIS A1092 GLN B 21 ASN B 70 GLN B 86 GLN B 140 GLN B 184 GLN C 58 HIS C 127 GLN E 125 GLN F 65 ASN F 204 GLN G 49 GLN G 108 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.110793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.085646 restraints weight = 55564.975| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.55 r_work: 0.3412 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20219 Z= 0.153 Angle : 0.741 19.564 27627 Z= 0.381 Chirality : 0.047 0.251 3152 Planarity : 0.006 0.070 3387 Dihedral : 15.476 97.420 3207 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 1.41 % Allowed : 13.22 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -2.36 (0.16), residues: 2370 helix: -0.80 (0.19), residues: 677 sheet: -0.46 (0.20), residues: 615 loop : -2.78 (0.16), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 985 TYR 0.018 0.001 TYR G 211 PHE 0.018 0.002 PHE A 254 TRP 0.017 0.002 TRP A 344 HIS 0.018 0.001 HIS A1021 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (20210) covalent geometry : angle 0.71361 / 0.38 (27609) hydrogen bonds : bond 0.05351 / 3.61 ( 837) hydrogen bonds : angle 5.57866 / 3.87 ( 2315) metal coordination : bond 0.01153 / 0.47 ( 8) metal coordination : angle 7.78871 / 4.78 ( 18) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 108 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6403 (pp) REVERT: E 28 TRP cc_start: 0.7992 (m-10) cc_final: 0.7338 (m-10) REVERT: E 53 ARG cc_start: 0.7564 (mmt-90) cc_final: 0.7235 (mmt-90) REVERT: E 118 LEU cc_start: 0.5025 (mm) cc_final: 0.4196 (tp) REVERT: E 119 MET cc_start: 0.4565 (pmm) cc_final: 0.2856 (ptt) REVERT: E 130 GLU cc_start: 0.5577 (mm-30) cc_final: 0.5005 (tp30) REVERT: E 249 TYR cc_start: 0.8663 (m-10) cc_final: 0.8368 (m-10) REVERT: G 116 MET cc_start: 0.6927 (ttp) cc_final: 0.6137 (tpt) REVERT: G 144 PHE cc_start: 0.8087 (t80) cc_final: 0.7513 (t80) REVERT: G 199 MET cc_start: 0.7537 (ppp) cc_final: 0.6672 (ppp) REVERT: G 229 MET cc_start: 0.7348 (ppp) cc_final: 0.7101 (ppp) outliers start: 29 outliers final: 14 residues processed: 223 average time/residue: 0.1511 time to fit residues: 51.0745 Evaluate side-chains 181 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 160 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [170, 97, 1, 118, 149, 81, 186, 32, 24, 182, 6] chunk 170 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 118 optimal weight: 0.4980 chunk 149 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 186 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN A1038 GLN C 17 GLN C 127 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.109034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.083199 restraints weight = 55748.590| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.48 r_work: 0.3370 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20219 Z= 0.177 Angle : 0.705 14.565 27627 Z= 0.365 Chirality : 0.047 0.173 3152 Planarity : 0.006 0.055 3387 Dihedral : 15.153 92.541 3196 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.75 % Favored : 94.21 % Rotamer: Outliers : 2.38 % Allowed : 14.38 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -1.87 (0.16), residues: 2370 helix: -0.21 (0.20), residues: 680 sheet: -0.21 (0.21), residues: 619 loop : -2.62 (0.16), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 985 TYR 0.023 0.002 TYR E 211 PHE 0.025 0.002 PHE E 144 TRP 0.016 0.002 TRP F 28 HIS 0.018 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (20210) covalent geometry : angle 0.68852 / 0.36 (27609) hydrogen bonds : bond 0.05310 / 3.60 ( 837) hydrogen bonds : angle 5.29118 / 3.65 ( 2315) metal coordination : bond 0.01223 / 0.58 ( 8) metal coordination : angle 5.88921 / 3.84 ( 18) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.5301 (mmp) cc_final: 0.3986 (tpp) REVERT: A 1087 LYS cc_start: 0.8134 (mmtm) cc_final: 0.7853 (mmtt) REVERT: B 299 PHE cc_start: 0.6443 (OUTLIER) cc_final: 0.5765 (m-80) REVERT: E 28 TRP cc_start: 0.8027 (m-10) cc_final: 0.7402 (m-10) REVERT: E 118 LEU cc_start: 0.4906 (mm) cc_final: 0.4150 (tp) REVERT: E 119 MET cc_start: 0.4494 (pmm) cc_final: 0.3017 (ptt) REVERT: E 130 GLU cc_start: 0.5330 (mm-30) cc_final: 0.4894 (tp30) REVERT: E 249 TYR cc_start: 0.8621 (m-10) cc_final: 0.8346 (m-10) REVERT: G 53 ARG cc_start: 0.6159 (mtm180) cc_final: 0.5885 (mpp80) REVERT: G 116 MET cc_start: 0.7050 (ttp) cc_final: 0.6382 (tpt) REVERT: G 199 MET cc_start: 0.7611 (ppp) cc_final: 0.6725 (ppp) REVERT: G 229 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7282 (ppp) outliers start: 49 outliers final: 27 residues processed: 215 average time/residue: 0.1511 time to fit residues: 49.2973 Evaluate side-chains 187 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 239 TYR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 229 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [17, 202, 142, 183, 34, 153, 201, 140, 184, 56, 161] chunk 17 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 153 optimal weight: 0.0270 chunk 201 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 948 HIS C 127 GLN D 91 HIS D 103 HIS ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 ASN G 131 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.108046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.079660 restraints weight = 56120.866| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.19 r_work: 0.3372 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20219 Z= 0.187 Angle : 0.694 12.765 27627 Z= 0.357 Chirality : 0.046 0.191 3152 Planarity : 0.006 0.052 3387 Dihedral : 15.087 95.951 3195 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.87 % Rotamer: Outliers : 3.01 % Allowed : 15.55 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -1.67 (0.17), residues: 2370 helix: 0.05 (0.20), residues: 685 sheet: -0.20 (0.21), residues: 624 loop : -2.51 (0.17), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 53 TYR 0.022 0.002 TYR A1080 PHE 0.016 0.002 PHE A 350 TRP 0.014 0.002 TRP F 28 HIS 0.013 0.002 HIS A1021 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (20210) covalent geometry : angle 0.68158 / 0.36 (27609) hydrogen bonds : bond 0.05147 / 3.47 ( 837) hydrogen bonds : angle 5.15288 / 3.55 ( 2315) metal coordination : bond 0.01239 / 0.57 ( 8) metal coordination : angle 5.17381 / 3.41 ( 18) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 171 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.5245 (mmp) cc_final: 0.3957 (tpt) REVERT: A 1087 LYS cc_start: 0.8141 (mmtm) cc_final: 0.7828 (mmtt) REVERT: B 299 PHE cc_start: 0.6393 (OUTLIER) cc_final: 0.5757 (m-80) REVERT: C 7 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8726 (tt) REVERT: C 43 ASP cc_start: 0.7998 (t70) cc_final: 0.7659 (t0) REVERT: D 79 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.5662 (tp30) REVERT: E 28 TRP cc_start: 0.8014 (m-10) cc_final: 0.7382 (m-10) REVERT: E 118 LEU cc_start: 0.4838 (OUTLIER) cc_final: 0.3599 (mm) REVERT: E 119 MET cc_start: 0.4545 (pmm) cc_final: 0.3602 (ptt) REVERT: E 130 GLU cc_start: 0.5046 (mm-30) cc_final: 0.4543 (tp30) REVERT: E 215 PHE cc_start: 0.6632 (m-10) cc_final: 0.6266 (m-10) REVERT: E 249 TYR cc_start: 0.8584 (m-10) cc_final: 0.8042 (m-10) REVERT: F 146 ARG cc_start: 0.8041 (mmp80) cc_final: 0.7810 (mmp80) REVERT: G 53 ARG cc_start: 0.6191 (mtm180) cc_final: 0.5923 (mpp80) REVERT: G 91 ARG cc_start: 0.5383 (OUTLIER) cc_final: 0.4881 (mtm-85) REVERT: G 116 MET cc_start: 0.6971 (ttp) cc_final: 0.6199 (tpt) REVERT: G 131 GLN cc_start: 0.5386 (OUTLIER) cc_final: 0.5093 (pt0) REVERT: G 139 MET cc_start: 0.8397 (mpp) cc_final: 0.7684 (ttt) REVERT: G 199 MET cc_start: 0.7630 (ppp) cc_final: 0.6772 (ppp) REVERT: G 229 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6997 (ppp) outliers start: 62 outliers final: 40 residues processed: 218 average time/residue: 0.1473 time to fit residues: 49.4921 Evaluate side-chains 208 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1021 HIS Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 239 TYR Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 91 ARG Chi-restraints excluded: chain G residue 131 GLN Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [161, 75, 100, 195, 188, 132, 81, 45, 136, 165, 14] chunk 161 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 195 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 14 optimal weight: 0.0470 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 127 GLN ** G 246 HIS ** 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 = 0.4106 r_free = 0.4106 target = 0.109255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.083553 restraints weight = 55579.762| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 3.03 r_work: 0.3409 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20219 Z= 0.124 Angle : 0.643 15.656 27627 Z= 0.326 Chirality : 0.044 0.174 3152 Planarity : 0.005 0.050 3387 Dihedral : 14.898 97.877 3195 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.99 % Favored : 94.97 % Rotamer: Outliers : 2.33 % Allowed : 16.28 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -1.29 (0.17), residues: 2370 helix: 0.49 (0.20), residues: 680 sheet: 0.05 (0.21), residues: 608 loop : -2.35 (0.17), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 146 TYR 0.016 0.001 TYR G 211 PHE 0.014 0.001 PHE A 254 TRP 0.013 0.001 TRP F 28 HIS 0.011 0.001 HIS A1021 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (20210) covalent geometry : angle 0.63046 / 0.33 (27609) hydrogen bonds : bond 0.04324 / 2.93 ( 837) hydrogen bonds : angle 4.95080 / 3.41 ( 2315) metal coordination : bond 0.00716 / 0.33 ( 8) metal coordination : angle 4.93592 / 3.17 ( 18) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.5159 (mmp) cc_final: 0.4160 (tpt) REVERT: B 299 PHE cc_start: 0.6338 (OUTLIER) cc_final: 0.5719 (m-80) REVERT: C 7 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8635 (mp) REVERT: E 28 TRP cc_start: 0.8041 (m-10) cc_final: 0.7436 (m-10) REVERT: E 118 LEU cc_start: 0.4785 (OUTLIER) cc_final: 0.3585 (mm) REVERT: E 119 MET cc_start: 0.4414 (pmm) cc_final: 0.3421 (ptt) REVERT: E 130 GLU cc_start: 0.5162 (mm-30) cc_final: 0.4673 (tp30) REVERT: E 215 PHE cc_start: 0.6607 (m-10) cc_final: 0.6320 (m-10) REVERT: E 249 TYR cc_start: 0.8531 (m-10) cc_final: 0.7925 (m-10) REVERT: G 53 ARG cc_start: 0.6141 (mtm180) cc_final: 0.5869 (mpp80) REVERT: G 116 MET cc_start: 0.6941 (ttp) cc_final: 0.6193 (tpt) REVERT: G 199 MET cc_start: 0.7511 (ppp) cc_final: 0.6639 (ppp) REVERT: G 229 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7144 (ppp) outliers start: 48 outliers final: 35 residues processed: 203 average time/residue: 0.1525 time to fit residues: 47.2532 Evaluate side-chains 200 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 239 TYR Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 229 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [203, 104, 221, 205, 160, 236, 179, 1, 84, 98, 156] chunk 203 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 ASN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN E 65 ASN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.106211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.080591 restraints weight = 55653.745| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.65 r_work: 0.3316 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 20219 Z= 0.254 Angle : 0.767 12.729 27627 Z= 0.391 Chirality : 0.049 0.220 3152 Planarity : 0.006 0.056 3387 Dihedral : 15.035 104.057 3195 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.59 % Favored : 93.32 % Rotamer: Outliers : 3.30 % Allowed : 16.62 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -1.57 (0.17), residues: 2370 helix: 0.14 (0.20), residues: 684 sheet: -0.24 (0.20), residues: 641 loop : -2.40 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 210 TYR 0.031 0.002 TYR A1080 PHE 0.022 0.002 PHE A 418 TRP 0.012 0.002 TRP F 28 HIS 0.010 0.002 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.25 (20210) covalent geometry : angle 0.75703 / 0.39 (27609) hydrogen bonds : bond 0.05911 / 3.97 ( 837) hydrogen bonds : angle 5.19086 / 3.57 ( 2315) metal coordination : bond 0.01618 / 0.78 ( 8) metal coordination : angle 4.86080 / 3.32 ( 18) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 169 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.5494 (mmp) cc_final: 0.4307 (tpt) REVERT: B 299 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.5842 (m-80) REVERT: C 7 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8637 (tt) REVERT: C 43 ASP cc_start: 0.8025 (t70) cc_final: 0.7636 (t0) REVERT: E 28 TRP cc_start: 0.7983 (m-10) cc_final: 0.7420 (m-10) REVERT: E 118 LEU cc_start: 0.5025 (OUTLIER) cc_final: 0.3775 (mm) REVERT: E 119 MET cc_start: 0.4537 (pmm) cc_final: 0.3708 (ptt) REVERT: E 130 GLU cc_start: 0.4976 (mm-30) cc_final: 0.4688 (tp30) REVERT: E 175 LEU cc_start: 0.4705 (OUTLIER) cc_final: 0.4285 (pp) REVERT: E 179 ASN cc_start: 0.7523 (p0) cc_final: 0.7287 (p0) REVERT: E 211 TYR cc_start: 0.8529 (m-80) cc_final: 0.8223 (m-10) REVERT: E 215 PHE cc_start: 0.6994 (m-10) cc_final: 0.6718 (m-10) REVERT: E 249 TYR cc_start: 0.8575 (m-10) cc_final: 0.8078 (m-10) REVERT: F 66 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7884 (tt) REVERT: G 53 ARG cc_start: 0.6338 (mtm180) cc_final: 0.6050 (mpp80) REVERT: G 91 ARG cc_start: 0.5504 (OUTLIER) cc_final: 0.5050 (mtm-85) REVERT: G 116 MET cc_start: 0.7037 (ttp) cc_final: 0.6129 (tpt) REVERT: G 199 MET cc_start: 0.7668 (ppp) cc_final: 0.6811 (ppp) REVERT: G 229 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6886 (ppp) outliers start: 68 outliers final: 48 residues processed: 220 average time/residue: 0.1406 time to fit residues: 47.6029 Evaluate side-chains 214 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 239 TYR Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 91 ARG Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [100, 92, 75, 207, 187, 96, 113, 193, 159, 205, 66] chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 187 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 159 optimal weight: 0.0970 chunk 205 optimal weight: 0.6980 chunk 66 optimal weight: 0.0570 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN ** G 246 HIS ** 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 = 0.4094 r_free = 0.4094 target = 0.108587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.083492 restraints weight = 55803.952| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.68 r_work: 0.3377 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20219 Z= 0.125 Angle : 0.649 13.218 27627 Z= 0.330 Chirality : 0.044 0.258 3152 Planarity : 0.005 0.050 3387 Dihedral : 14.792 105.823 3195 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.60 % Favored : 95.35 % Rotamer: Outliers : 2.24 % Allowed : 17.78 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -1.12 (0.17), residues: 2370 helix: 0.62 (0.20), residues: 682 sheet: 0.13 (0.21), residues: 611 loop : -2.24 (0.17), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 985 TYR 0.017 0.001 TYR E 211 PHE 0.015 0.001 PHE A 254 TRP 0.014 0.001 TRP A 381 HIS 0.008 0.001 HIS A1021 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (20210) covalent geometry : angle 0.63708 / 0.33 (27609) hydrogen bonds : bond 0.04273 / 2.89 ( 837) hydrogen bonds : angle 4.90430 / 3.37 ( 2315) metal coordination : bond 0.00796 / 0.33 ( 8) metal coordination : angle 4.82754 / 3.09 ( 18) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.5197 (mmp) cc_final: 0.4317 (tpt) REVERT: A 978 ARG cc_start: 0.7913 (mmm160) cc_final: 0.7327 (mmm-85) REVERT: B 299 PHE cc_start: 0.6236 (OUTLIER) cc_final: 0.5763 (m-80) REVERT: C 7 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8633 (mp) REVERT: C 36 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7466 (tm-30) REVERT: E 28 TRP cc_start: 0.8024 (m-10) cc_final: 0.7447 (m-10) REVERT: E 118 LEU cc_start: 0.4845 (OUTLIER) cc_final: 0.3642 (mm) REVERT: E 119 MET cc_start: 0.4440 (pmm) cc_final: 0.3660 (ptt) REVERT: E 179 ASN cc_start: 0.7540 (p0) cc_final: 0.7273 (p0) REVERT: E 211 TYR cc_start: 0.8531 (m-80) cc_final: 0.8195 (m-10) REVERT: E 249 TYR cc_start: 0.8535 (m-10) cc_final: 0.8036 (m-10) REVERT: F 146 ARG cc_start: 0.8089 (mmp80) cc_final: 0.7826 (mmp80) REVERT: G 53 ARG cc_start: 0.6250 (mtm180) cc_final: 0.5954 (mpp80) REVERT: G 97 ASP cc_start: 0.4358 (p0) cc_final: 0.4057 (m-30) REVERT: G 116 MET cc_start: 0.6980 (ttp) cc_final: 0.6124 (tpt) REVERT: G 199 MET cc_start: 0.7640 (ppp) cc_final: 0.6805 (ppp) REVERT: G 229 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7134 (ppp) outliers start: 46 outliers final: 36 residues processed: 207 average time/residue: 0.1463 time to fit residues: 46.4635 Evaluate side-chains 206 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [88, 11, 145, 168, 138, 232, 156, 105, 60, 119, 92] chunk 88 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 232 optimal weight: 6.9990 chunk 156 optimal weight: 0.0050 chunk 105 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 874 ASN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.106694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.080553 restraints weight = 55784.721| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.12 r_work: 0.3343 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20219 Z= 0.212 Angle : 0.707 11.850 27627 Z= 0.360 Chirality : 0.047 0.290 3152 Planarity : 0.005 0.049 3387 Dihedral : 14.837 110.753 3195 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.04 % Favored : 93.92 % Rotamer: Outliers : 2.43 % Allowed : 17.93 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -1.23 (0.17), residues: 2370 helix: 0.49 (0.20), residues: 683 sheet: -0.02 (0.21), residues: 631 loop : -2.26 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 146 TYR 0.022 0.002 TYR A1080 PHE 0.018 0.002 PHE A1099 TRP 0.012 0.002 TRP F 28 HIS 0.015 0.002 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (20210) covalent geometry : angle 0.69760 / 0.36 (27609) hydrogen bonds : bond 0.05168 / 3.48 ( 837) hydrogen bonds : angle 5.01621 / 3.45 ( 2315) metal coordination : bond 0.01351 / 0.66 ( 8) metal coordination : angle 4.61506 / 3.10 ( 18) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.5355 (mmp) cc_final: 0.4302 (tpt) REVERT: A 978 ARG cc_start: 0.8096 (mmm160) cc_final: 0.7239 (mmm-85) REVERT: B 93 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8481 (p) REVERT: B 299 PHE cc_start: 0.6318 (OUTLIER) cc_final: 0.5845 (m-80) REVERT: C 7 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8705 (tt) REVERT: C 43 ASP cc_start: 0.8137 (t0) cc_final: 0.7801 (t0) REVERT: E 28 TRP cc_start: 0.8029 (m-10) cc_final: 0.7437 (m-10) REVERT: E 118 LEU cc_start: 0.4889 (OUTLIER) cc_final: 0.3679 (mm) REVERT: E 119 MET cc_start: 0.4428 (pmm) cc_final: 0.3518 (ptt) REVERT: E 130 GLU cc_start: 0.4995 (mm-30) cc_final: 0.4549 (tp30) REVERT: E 179 ASN cc_start: 0.7557 (p0) cc_final: 0.7289 (p0) REVERT: E 249 TYR cc_start: 0.8252 (m-10) cc_final: 0.8041 (m-10) REVERT: F 146 ARG cc_start: 0.8139 (mmp80) cc_final: 0.7933 (mmp80) REVERT: F 149 ARG cc_start: 0.7876 (ptm160) cc_final: 0.7180 (mtm110) REVERT: G 53 ARG cc_start: 0.6229 (mtm180) cc_final: 0.5930 (mpp80) REVERT: G 116 MET cc_start: 0.6933 (ttp) cc_final: 0.6038 (tpt) REVERT: G 199 MET cc_start: 0.7665 (ppp) cc_final: 0.6846 (ppp) REVERT: G 229 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6995 (ppp) outliers start: 50 outliers final: 41 residues processed: 201 average time/residue: 0.1493 time to fit residues: 45.8195 Evaluate side-chains 207 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [154, 175, 224, 234, 167, 196, 212, 80, 122, 28, 118] chunk 154 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 chunk 224 optimal weight: 0.8980 chunk 234 optimal weight: 0.4980 chunk 167 optimal weight: 0.0060 chunk 196 optimal weight: 1.9990 chunk 212 optimal weight: 0.0020 chunk 80 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** 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 = 0.4065 r_free = 0.4065 target = 0.106887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.080322 restraints weight = 55620.584| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.22 r_work: 0.3340 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 20219 Z= 0.194 Angle : 0.840 59.200 27627 Z= 0.460 Chirality : 0.046 0.263 3152 Planarity : 0.005 0.056 3387 Dihedral : 14.835 110.654 3195 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.00 % Rotamer: Outliers : 2.28 % Allowed : 17.98 % Favored : 79.74 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -1.23 (0.17), residues: 2370 helix: 0.51 (0.20), residues: 683 sheet: -0.04 (0.21), residues: 633 loop : -2.26 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 146 TYR 0.022 0.002 TYR A1080 PHE 0.016 0.002 PHE A1099 TRP 0.012 0.001 TRP F 28 HIS 0.012 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (20210) covalent geometry : angle 0.83218 / 0.46 (27609) hydrogen bonds : bond 0.05023 / 3.38 ( 837) hydrogen bonds : angle 5.01099 / 3.45 ( 2315) metal coordination : bond 0.01163 / 0.55 ( 8) metal coordination : angle 4.62643 / 3.10 ( 18) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.5326 (mmp) cc_final: 0.4300 (tpt) REVERT: A 978 ARG cc_start: 0.8105 (mmm160) cc_final: 0.7238 (mmm-85) REVERT: B 93 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8476 (p) REVERT: B 299 PHE cc_start: 0.6317 (OUTLIER) cc_final: 0.5842 (m-80) REVERT: C 7 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8697 (tt) REVERT: C 43 ASP cc_start: 0.8130 (t0) cc_final: 0.7796 (t0) REVERT: E 28 TRP cc_start: 0.8013 (m-10) cc_final: 0.7425 (m-10) REVERT: E 118 LEU cc_start: 0.4895 (OUTLIER) cc_final: 0.3679 (mm) REVERT: E 119 MET cc_start: 0.4441 (pmm) cc_final: 0.3578 (ptt) REVERT: E 125 GLN cc_start: 0.0233 (OUTLIER) cc_final: -0.0499 (mt0) REVERT: E 130 GLU cc_start: 0.5007 (mm-30) cc_final: 0.4554 (tp30) REVERT: E 179 ASN cc_start: 0.7554 (p0) cc_final: 0.7274 (p0) REVERT: E 244 MET cc_start: 0.5628 (tpp) cc_final: 0.5375 (tpp) REVERT: F 146 ARG cc_start: 0.8139 (mmp80) cc_final: 0.7936 (mmp80) REVERT: F 149 ARG cc_start: 0.7863 (ptm160) cc_final: 0.7163 (mtm110) REVERT: G 53 ARG cc_start: 0.6231 (mtm180) cc_final: 0.5931 (mpp80) REVERT: G 91 ARG cc_start: 0.5457 (OUTLIER) cc_final: 0.5076 (mpp80) REVERT: G 116 MET cc_start: 0.6913 (ttp) cc_final: 0.6036 (tpt) REVERT: G 199 MET cc_start: 0.7667 (ppp) cc_final: 0.6847 (ppp) REVERT: G 229 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.6987 (ppp) outliers start: 47 outliers final: 40 residues processed: 196 average time/residue: 0.1525 time to fit residues: 45.5428 Evaluate side-chains 206 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 91 ARG Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [88, 190, 233, 182, 114, 26, 240, 223, 189, 35, 185] chunk 88 optimal weight: 2.9990 chunk 190 optimal weight: 0.2980 chunk 233 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 chunk 185 optimal weight: 0.0770 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** 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 = 0.4065 r_free = 0.4065 target = 0.106900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.080822 restraints weight = 55747.160| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.07 r_work: 0.3349 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 20219 Z= 0.194 Angle : 0.840 59.200 27627 Z= 0.460 Chirality : 0.046 0.263 3152 Planarity : 0.005 0.056 3387 Dihedral : 14.835 110.654 3195 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.00 % Rotamer: Outliers : 2.28 % Allowed : 17.98 % Favored : 79.74 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -1.23 (0.17), residues: 2370 helix: 0.51 (0.20), residues: 683 sheet: -0.04 (0.21), residues: 633 loop : -2.26 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 146 TYR 0.022 0.002 TYR A1080 PHE 0.016 0.002 PHE A1099 TRP 0.012 0.001 TRP F 28 HIS 0.012 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (20210) covalent geometry : angle 0.83218 / 0.46 (27609) hydrogen bonds : bond 0.05023 / 3.38 ( 837) hydrogen bonds : angle 5.01099 / 3.45 ( 2315) metal coordination : bond 0.01163 / 0.55 ( 8) metal coordination : angle 4.62643 / 3.10 ( 18) Misc. bond : bond 0.00019 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.5325 (mmp) cc_final: 0.4295 (tpt) REVERT: A 978 ARG cc_start: 0.8104 (mmm160) cc_final: 0.7249 (mmm-85) REVERT: B 93 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8477 (p) REVERT: B 299 PHE cc_start: 0.6305 (OUTLIER) cc_final: 0.5841 (m-80) REVERT: C 7 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8704 (tt) REVERT: C 43 ASP cc_start: 0.8104 (t0) cc_final: 0.7772 (t0) REVERT: E 28 TRP cc_start: 0.8022 (m-10) cc_final: 0.7431 (m-10) REVERT: E 118 LEU cc_start: 0.4903 (OUTLIER) cc_final: 0.3686 (mm) REVERT: E 119 MET cc_start: 0.4434 (pmm) cc_final: 0.3557 (ptt) REVERT: E 125 GLN cc_start: 0.0219 (OUTLIER) cc_final: -0.0509 (mt0) REVERT: E 130 GLU cc_start: 0.4993 (mm-30) cc_final: 0.4546 (tp30) REVERT: E 179 ASN cc_start: 0.7561 (p0) cc_final: 0.7282 (p0) REVERT: E 244 MET cc_start: 0.5634 (tpp) cc_final: 0.5382 (tpp) REVERT: F 146 ARG cc_start: 0.8130 (mmp80) cc_final: 0.7927 (mmp80) REVERT: F 149 ARG cc_start: 0.7866 (ptm160) cc_final: 0.7169 (mtm110) REVERT: G 53 ARG cc_start: 0.6237 (mtm180) cc_final: 0.5935 (mpp80) REVERT: G 91 ARG cc_start: 0.5455 (OUTLIER) cc_final: 0.5075 (mpp80) REVERT: G 116 MET cc_start: 0.6912 (ttp) cc_final: 0.6037 (tpt) REVERT: G 199 MET cc_start: 0.7667 (ppp) cc_final: 0.6844 (ppp) REVERT: G 229 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6994 (ppp) outliers start: 47 outliers final: 40 residues processed: 192 average time/residue: 0.1488 time to fit residues: 43.5043 Evaluate side-chains 206 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 91 ARG Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: [202, 33, 2, 56, 168, 29, 189, 212, 68, 13, 232] chunk 202 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 189 optimal weight: 8.9990 chunk 212 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 13 optimal weight: 0.0570 chunk 232 optimal weight: 7.9990 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** 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 = 0.4065 r_free = 0.4065 target = 0.106900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.080821 restraints weight = 55752.721| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.07 r_work: 0.3349 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 20219 Z= 0.194 Angle : 0.840 59.200 27627 Z= 0.460 Chirality : 0.046 0.263 3152 Planarity : 0.005 0.056 3387 Dihedral : 14.835 110.654 3195 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.00 % Rotamer: Outliers : 2.28 % Allowed : 17.98 % Favored : 79.74 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -1.23 (0.17), residues: 2370 helix: 0.51 (0.20), residues: 683 sheet: -0.04 (0.21), residues: 633 loop : -2.26 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 146 TYR 0.022 0.002 TYR A1080 PHE 0.016 0.002 PHE A1099 TRP 0.012 0.001 TRP F 28 HIS 0.012 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (20210) covalent geometry : angle 0.83218 / 0.46 (27609) hydrogen bonds : bond 0.05023 / 3.38 ( 837) hydrogen bonds : angle 5.01099 / 3.45 ( 2315) metal coordination : bond 0.01163 / 0.55 ( 8) metal coordination : angle 4.62643 / 3.10 ( 18) Misc. bond : bond 0.00019 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6094.79 seconds wall clock time: 104 minutes 36.14 seconds (6276.14 seconds total)