Starting phenix.real_space_refine on Mon Oct 26 05:19:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s1m_10080/10_2026/6s1m_10080_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s1m_10080/10_2026/6s1m_10080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6s1m_10080/10_2026/6s1m_10080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s1m_10080/10_2026/6s1m_10080.map" model { file = "/net/cci-nas-00/data/ceres_data/6s1m_10080/10_2026/6s1m_10080_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s1m_10080/10_2026/6s1m_10080_neut.cif" } resolution = 4.27 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= 0.002 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 48 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: 11 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: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' ZN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'TTP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7157 SG CYS A1012 97.416 99.127 74.603 1.00 40.62 S ATOM 7175 SG CYS A1015 100.426 97.328 76.337 1.00 40.62 S ATOM 7248 SG CYS A1026 101.047 101.039 75.328 1.00 40.62 S ATOM 7264 SG CYS A1029 100.061 98.862 72.781 1.00 40.62 S ATOM 7616 SG CYS A1071 58.262 80.827 75.866 1.00 40.62 S ATOM 7654 SG CYS A1076 62.825 77.203 74.560 1.00 30.94 S ATOM 7515 SG CYS A1058 62.089 83.415 71.486 1.00 40.62 S ATOM 7541 SG CYS A1061 58.417 78.187 70.743 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: 5.39, per 1000 atoms: 0.27 Number of scatterers: 19726 At special positions: 0 Unit cell: (143.64, 128.52, 166.32, 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: 1.28 Conformation dependent library (CDL) restraints added in 791.2 milliseconds 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: 67 helices and 21 sheets defined 31.1% alpha, 22.6% beta 22 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.639A 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: 3.925A 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: 3.572A pdb=" N LEU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.581A 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: 3.640A 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: 4.128A 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: 3.936A 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: 3.628A 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 988 Processing helix chain 'A' and resid 1001 through 1005 removed outlier: 3.795A pdb=" N ALA A1004 " --> pdb=" O GLY A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1056 removed outlier: 4.886A 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: 3.995A pdb=" N SER A1042 " --> pdb=" O GLN A1038 " (cutoff:3.500A) removed outlier: 6.704A 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: 3.560A 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: 3.574A pdb=" N ARG A1060 " --> pdb=" O THR A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1096 removed outlier: 3.920A 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: 4.508A pdb=" N ARG A1086 " --> pdb=" O ARG A1082 " (cutoff:3.500A) removed outlier: 4.026A 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: 3.729A 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: 4.282A pdb=" N TYR B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.542A 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: 3.671A 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: 3.889A 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: 3.628A 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: 4.145A pdb=" N ASP C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER C 124 " --> pdb=" O ASP C 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 53 removed outlier: 3.599A pdb=" N LEU D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 49 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 3.880A 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 20 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 152 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 9 through 20 Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 80 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 9 through 20 Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 152 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: 6.786A 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: 6.428A 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: 6.606A 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: 6.472A 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: 5.416A 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: 3.993A 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: 5.504A 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: 7.434A pdb=" N PHE A 814 " --> pdb=" O TYR A 798 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 812 " --> pdb=" O PRO A 800 " (cutoff:3.500A) removed outlier: 6.983A 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 Processing sheet with id=AB1, first strand: chain 'B' and resid 141 through 143 removed outlier: 3.651A 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: 4.616A pdb=" N TYR B 176 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.972A 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: 7.703A pdb=" N PHE B 195 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 241 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU B 197 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU B 243 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 6.915A 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: 3.545A pdb=" N HIS C 75 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 3.805A 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: 6.662A pdb=" N THR C 60 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 3.686A 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: 3.651A 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: 8.065A 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: 3.693A pdb=" N GLY B 411 " --> pdb=" O THR B 427 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 2 through 6 removed outlier: 4.927A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 25 through 30 Processing sheet with id=AB6, first strand: chain 'E' and resid 34 through 40 removed outlier: 4.713A pdb=" N LYS E 240 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR E 224 " --> pdb=" O LYS E 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 203 through 208 removed outlier: 6.020A pdb=" N ALA E 157 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER E 172 " --> pdb=" O ALA E 157 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.912A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 25 through 29 removed outlier: 3.747A pdb=" N TRP F 28 " --> pdb=" O MET F 68 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET F 68 " --> pdb=" O TRP F 28 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 34 through 40 removed outlier: 4.717A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 25 through 30 Processing sheet with id=AC3, first strand: chain 'G' and resid 34 through 40 removed outlier: 4.728A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) 800 hydrogen bonds defined for protein. 2259 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: 4.15 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.40: 7993 1.40 - 1.63: 12017 1.63 - 1.85: 186 1.85 - 2.08: 2 2.08 - 2.31: 12 Bond restraints: 20210 Sorted by residual: bond pdb=" C2' TTP T 101 " pdb=" C3' TTP T 101 " ideal model delta sigma weight residual 1.522 1.217 0.305 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 1.304 0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C4' TTP T 101 " pdb=" O4' TTP T 101 " 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 1.277 0.154 2.00e-02 2.50e+03 5.90e+01 bond pdb=" O4' DOC P 25 " pdb=" C1' DOC P 25 " ideal model delta sigma weight residual 1.405 1.551 -0.146 2.00e-02 2.50e+03 5.31e+01 ... (remaining 20205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 26560 2.85 - 5.71: 875 5.71 - 8.56: 152 8.56 - 11.41: 17 11.41 - 14.26: 5 Bond angle restraints: 27609 Sorted by residual: angle pdb=" N ALA B 179 " pdb=" CA ALA B 179 " pdb=" C ALA B 179 " ideal model delta sigma weight residual 111.28 119.43 -8.15 1.09e+00 8.42e-01 5.58e+01 angle pdb=" N ASN G 107 " pdb=" CA ASN G 107 " pdb=" C ASN G 107 " ideal model delta sigma weight residual 109.96 98.94 11.02 1.50e+00 4.44e-01 5.40e+01 angle pdb=" N ARG A1098 " pdb=" CA ARG A1098 " pdb=" C ARG A1098 " ideal model delta sigma weight residual 111.36 103.75 7.61 1.09e+00 8.42e-01 4.88e+01 angle pdb=" N ASN G 200 " pdb=" CA ASN G 200 " pdb=" C ASN G 200 " ideal model delta sigma weight residual 113.41 105.15 8.26 1.22e+00 6.72e-01 4.58e+01 angle pdb=" N ASN E 200 " pdb=" CA ASN E 200 " pdb=" C ASN E 200 " ideal model delta sigma weight residual 113.41 105.21 8.20 1.22e+00 6.72e-01 4.51e+01 ... (remaining 27604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.44: 10818 20.44 - 40.89: 991 40.89 - 61.33: 334 61.33 - 81.77: 55 81.77 - 102.22: 11 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 122.80 137.59 -14.79 0 2.50e+00 1.60e-01 3.50e+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 180.00 151.66 28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" N ASP B 180 " pdb=" C ASP B 180 " pdb=" CA ASP B 180 " pdb=" CB ASP B 180 " ideal model delta harmonic sigma weight residual 122.80 136.25 -13.45 0 2.50e+00 1.60e-01 2.89e+01 ... (remaining 12206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2605 0.099 - 0.198: 477 0.198 - 0.297: 64 0.297 - 0.397: 2 0.397 - 0.496: 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 2.01 0.50 2.00e-01 2.50e+01 6.15e+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 6.03e+00 chirality pdb=" C3' TTP T 101 " pdb=" C2' TTP T 101 " pdb=" C4' TTP T 101 " pdb=" O3' TTP T 101 " both_signs ideal model delta sigma weight residual False -2.70 -2.30 -0.40 2.00e-01 2.50e+01 4.08e+00 ... (remaining 3149 not shown) Planarity restraints: 3387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 249 " -0.086 2.00e-02 2.50e+03 4.57e-02 4.18e+01 pdb=" CG TYR G 249 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR G 249 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR G 249 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR G 249 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR G 249 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR G 249 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR G 249 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 249 " -0.077 2.00e-02 2.50e+03 3.98e-02 3.17e+01 pdb=" CG TYR F 249 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR F 249 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR F 249 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR F 249 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR F 249 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR F 249 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 249 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 249 " -0.074 2.00e-02 2.50e+03 3.85e-02 2.96e+01 pdb=" CG TYR E 249 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR E 249 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR E 249 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR E 249 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR E 249 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR E 249 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 249 " -0.054 2.00e-02 2.50e+03 ... (remaining 3384 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 5 1.93 - 2.68: 532 2.68 - 3.42: 24762 3.42 - 4.16: 45732 4.16 - 4.90: 81406 Nonbonded interactions: 152437 Sorted by model distance: nonbonded pdb=" ND2 ASN G 84 " pdb=" OP1 DG P 7 " model vdw 1.193 3.120 nonbonded pdb=" CD2 LEU A 995 " pdb=" O ASP F 122 " model vdw 1.806 3.460 nonbonded pdb=" CD1 LEU A 995 " pdb=" CG GLU F 124 " model vdw 1.906 3.860 nonbonded pdb=" O PHE A1005 " pdb=" O GLY F 127 " model vdw 1.927 3.040 nonbonded pdb=" CG1 VAL A 861 " pdb=" CD ARG A 985 " model vdw 1.932 3.860 ... (remaining 152432 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 group one per residue 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: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 25.890 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5891 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 : 0.010 0.317 20219 Z= 0.518 Angle : 1.311 39.356 27627 Z= 0.772 Chirality : 0.078 0.496 3152 Planarity : 0.008 0.075 3387 Dihedral : 17.839 102.216 7707 Min Nonbonded Distance : 1.193 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.22 % Favored : 91.93 % Rotamer: Outliers : 1.46 % Allowed : 7.09 % Favored : 91.45 % 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: -3.67 (0.14), residues: 2370 helix: -2.50 (0.16), residues: 671 sheet: -1.14 (0.19), residues: 615 loop : -3.18 (0.15), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 276 TYR 0.086 0.007 TYR G 249 PHE 0.042 0.005 PHE E 207 TRP 0.036 0.003 TRP A 344 HIS 0.010 0.002 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00932 / 0.51 (20210) covalent geometry : angle 1.25461 / 0.77 (27609) hydrogen bonds : bond 0.16874 / 11.05 ( 848) hydrogen bonds : angle 7.48762 / 5.32 ( 2363) metal coordination : bond 0.14974 / 7.39 ( 8) metal coordination : angle 14.95476 / 8.97 ( 18) Misc. bond : bond 0.00468 / 0.25 ( 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 750 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 720 time to evaluate : 0.666 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.4099 (m-80) cc_final: 0.3559 (m-80) REVERT: A 433 ASP cc_start: 0.6570 (m-30) cc_final: 0.6262 (t0) REVERT: A 479 PHE cc_start: 0.8341 (t80) cc_final: 0.8125 (t80) REVERT: A 719 SER cc_start: 0.7565 (m) cc_final: 0.6635 (t) REVERT: A 865 GLN cc_start: 0.7551 (mt0) cc_final: 0.7032 (tm-30) REVERT: A 903 LEU cc_start: 0.8021 (tp) cc_final: 0.7710 (tp) REVERT: A 944 PHE cc_start: 0.8407 (t80) cc_final: 0.8014 (t80) REVERT: D 79 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6846 (tp30) REVERT: E 116 MET cc_start: 0.4464 (ttp) cc_final: 0.2798 (tmm) REVERT: F 50 LEU cc_start: 0.8423 (tp) cc_final: 0.8123 (tp) REVERT: F 75 MET cc_start: 0.6677 (ttt) cc_final: 0.6134 (ttm) REVERT: F 213 ASN cc_start: 0.6758 (m-40) cc_final: 0.6512 (m-40) outliers start: 30 outliers final: 4 residues processed: 744 average time/residue: 0.1587 time to fit residues: 173.3384 Evaluate side-chains 371 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 366 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.0270 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS A 165 GLN A 285 GLN A 336 GLN A 430 ASN A 558 GLN A 726 GLN A 842 ASN A 865 GLN A1066 HIS A1092 GLN B 70 GLN B 104 GLN B 140 GLN B 246 ASN C 17 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN F 65 ASN G 65 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.126369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.103555 restraints weight = 72490.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.106532 restraints weight = 41889.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.108529 restraints weight = 27322.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.109879 restraints weight = 19504.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.110852 restraints weight = 14964.941| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 20219 Z= 0.192 Angle : 0.894 25.328 27627 Z= 0.434 Chirality : 0.051 0.239 3152 Planarity : 0.007 0.092 3387 Dihedral : 15.127 87.494 3194 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.85 % Rotamer: Outliers : 0.15 % Allowed : 3.60 % Favored : 96.26 % 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: -2.30 (0.16), residues: 2370 helix: -0.90 (0.19), residues: 673 sheet: -0.39 (0.21), residues: 604 loop : -2.64 (0.16), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 141 TYR 0.029 0.002 TYR A 607 PHE 0.033 0.002 PHE E 215 TRP 0.023 0.002 TRP F 28 HIS 0.011 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (20210) covalent geometry : angle 0.83148 / 0.43 (27609) hydrogen bonds : bond 0.05346 / 3.55 ( 848) hydrogen bonds : angle 5.93565 / 4.15 ( 2363) metal coordination : bond 0.04821 / 3.48 ( 8) metal coordination : angle 12.88764 / 9.83 ( 18) Misc. bond : bond 0.00018 / 0.01 ( 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 458 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 455 time to evaluate : 0.611 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 PHE cc_start: 0.7685 (t80) cc_final: 0.7415 (t80) REVERT: A 255 MET cc_start: 0.8455 (mtt) cc_final: 0.8065 (mtm) REVERT: A 433 ASP cc_start: 0.8219 (m-30) cc_final: 0.7194 (t0) REVERT: A 527 MET cc_start: 0.8549 (ttm) cc_final: 0.8130 (ttm) REVERT: A 760 MET cc_start: 0.6840 (mpp) cc_final: 0.6569 (mpp) REVERT: A 830 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7969 (tm-30) REVERT: A 844 VAL cc_start: 0.9613 (t) cc_final: 0.9386 (t) REVERT: A 865 GLN cc_start: 0.8639 (mt0) cc_final: 0.7738 (mp10) REVERT: A 940 GLU cc_start: 0.7899 (tp30) cc_final: 0.7183 (tp30) REVERT: A 944 PHE cc_start: 0.8605 (t80) cc_final: 0.7994 (t80) REVERT: A 955 GLN cc_start: 0.8699 (pp30) cc_final: 0.8363 (pp30) REVERT: A 1069 VAL cc_start: 0.7717 (t) cc_final: 0.7513 (p) REVERT: B 101 MET cc_start: 0.7539 (mtp) cc_final: 0.6976 (tpp) REVERT: B 366 GLU cc_start: 0.8806 (pt0) cc_final: 0.8011 (pp20) REVERT: B 385 TYR cc_start: 0.8564 (t80) cc_final: 0.8332 (t80) REVERT: B 406 ASN cc_start: 0.8427 (p0) cc_final: 0.8200 (p0) REVERT: B 430 ASP cc_start: 0.6342 (t0) cc_final: 0.5825 (t70) REVERT: C 8 GLU cc_start: 0.8648 (tp30) cc_final: 0.8347 (tp30) REVERT: C 68 ILE cc_start: 0.7895 (mt) cc_final: 0.7579 (tt) REVERT: C 85 LEU cc_start: 0.8613 (tp) cc_final: 0.8335 (tp) REVERT: E 68 MET cc_start: 0.4534 (mpp) cc_final: 0.3346 (mpp) REVERT: E 71 ASN cc_start: 0.5820 (t0) cc_final: 0.5424 (t0) REVERT: E 75 MET cc_start: 0.9178 (ttp) cc_final: 0.8633 (ptm) REVERT: E 84 ASN cc_start: 0.7903 (t0) cc_final: 0.7252 (t0) REVERT: E 116 MET cc_start: 0.1361 (ttp) cc_final: 0.0678 (tmm) REVERT: E 139 MET cc_start: 0.7212 (pmm) cc_final: 0.6263 (pmm) REVERT: E 169 PHE cc_start: 0.8658 (m-10) cc_final: 0.8190 (m-10) REVERT: F 1 MET cc_start: 0.7062 (mmt) cc_final: 0.6847 (mmt) REVERT: F 24 ASN cc_start: 0.7956 (t0) cc_final: 0.7744 (t0) REVERT: F 41 ASP cc_start: 0.5805 (p0) cc_final: 0.5552 (p0) REVERT: F 71 ASN cc_start: 0.8932 (p0) cc_final: 0.8526 (p0) REVERT: F 182 LEU cc_start: 0.9024 (mt) cc_final: 0.8740 (mt) REVERT: F 229 MET cc_start: 0.6512 (ptt) cc_final: 0.6248 (ptt) REVERT: F 249 TYR cc_start: 0.8156 (m-80) cc_final: 0.7859 (m-80) REVERT: G 16 LEU cc_start: 0.7856 (mp) cc_final: 0.7555 (pp) REVERT: G 114 TYR cc_start: 0.8171 (m-80) cc_final: 0.7494 (m-80) REVERT: G 195 VAL cc_start: 0.7585 (t) cc_final: 0.7059 (t) outliers start: 3 outliers final: 0 residues processed: 458 average time/residue: 0.1361 time to fit residues: 95.6504 Evaluate side-chains 345 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 97 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 149 optimal weight: 0.1980 chunk 81 optimal weight: 5.9990 chunk 186 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 0.0770 chunk 182 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 overall best weight: 1.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 HIS A1030 GLN ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN F 213 ASN G 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.121614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.098874 restraints weight = 75149.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.101578 restraints weight = 44353.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.103417 restraints weight = 29555.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.104669 restraints weight = 21420.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.105581 restraints weight = 16598.412| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3895 r_free = 0.3895 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3895 r_free = 0.3895 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20219 Z= 0.172 Angle : 0.807 32.392 27627 Z= 0.391 Chirality : 0.048 0.220 3152 Planarity : 0.006 0.072 3387 Dihedral : 14.949 90.936 3194 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.19 % Allowed : 3.79 % Favored : 96.02 % 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: -1.64 (0.17), residues: 2370 helix: -0.29 (0.20), residues: 670 sheet: -0.09 (0.21), residues: 634 loop : -2.26 (0.17), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 126 TYR 0.042 0.002 TYR A 801 PHE 0.019 0.002 PHE A 479 TRP 0.046 0.002 TRP E 28 HIS 0.012 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (20210) covalent geometry : angle 0.75378 / 0.39 (27609) hydrogen bonds : bond 0.04580 / 3.10 ( 848) hydrogen bonds : angle 5.47942 / 3.81 ( 2363) metal coordination : bond 0.02135 / 1.46 ( 8) metal coordination : angle 11.31246 / 6.96 ( 18) Misc. bond : bond 0.00129 / 0.07 ( 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 428 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 424 time to evaluate : 0.687 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: symmetry clash 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: 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 250 PHE cc_start: 0.7820 (t80) cc_final: 0.7509 (t80) REVERT: A 255 MET cc_start: 0.8244 (mtt) cc_final: 0.7949 (mtm) REVERT: A 353 LEU cc_start: 0.9279 (tp) cc_final: 0.8973 (tt) REVERT: A 433 ASP cc_start: 0.8538 (m-30) cc_final: 0.7370 (t0) REVERT: A 451 MET cc_start: 0.6049 (mmm) cc_final: 0.4711 (mmm) REVERT: A 527 MET cc_start: 0.8590 (ttm) cc_final: 0.8195 (ttt) REVERT: A 535 MET cc_start: 0.9336 (mmt) cc_final: 0.9066 (mmm) REVERT: A 660 LEU cc_start: 0.8946 (mm) cc_final: 0.8561 (pp) REVERT: A 726 GLN cc_start: 0.8361 (tt0) cc_final: 0.7977 (tm-30) REVERT: A 727 MET cc_start: 0.8201 (ttp) cc_final: 0.7467 (ttm) REVERT: A 760 MET cc_start: 0.7355 (mpp) cc_final: 0.6919 (mpp) REVERT: A 840 VAL cc_start: 0.9251 (t) cc_final: 0.8614 (t) REVERT: A 865 GLN cc_start: 0.8677 (mt0) cc_final: 0.7773 (mm110) REVERT: A 940 GLU cc_start: 0.8165 (tp30) cc_final: 0.7396 (tp30) REVERT: A 944 PHE cc_start: 0.8725 (t80) cc_final: 0.8247 (t80) REVERT: A 946 LEU cc_start: 0.8821 (tt) cc_final: 0.8591 (tt) REVERT: A 955 GLN cc_start: 0.8818 (pp30) cc_final: 0.8309 (pp30) REVERT: A 1065 LEU cc_start: 0.9250 (mt) cc_final: 0.9044 (mm) REVERT: A 1081 MET cc_start: 0.9300 (ttt) cc_final: 0.8908 (ttm) REVERT: B 52 HIS cc_start: 0.7857 (m-70) cc_final: 0.7435 (m-70) REVERT: B 101 MET cc_start: 0.7883 (mtp) cc_final: 0.7488 (tpp) REVERT: B 131 ASP cc_start: 0.6535 (p0) cc_final: 0.6002 (p0) REVERT: B 366 GLU cc_start: 0.8966 (pt0) cc_final: 0.7985 (tm-30) REVERT: B 388 TYR cc_start: 0.8295 (p90) cc_final: 0.7804 (p90) REVERT: C 8 GLU cc_start: 0.8702 (tp30) cc_final: 0.8435 (tp30) REVERT: C 68 ILE cc_start: 0.8166 (mt) cc_final: 0.7801 (tt) REVERT: C 120 ASP cc_start: 0.8166 (m-30) cc_final: 0.7955 (m-30) REVERT: E 40 MET cc_start: 0.3596 (tpp) cc_final: 0.3323 (tpp) REVERT: E 64 ARG cc_start: 0.6933 (tpp80) cc_final: 0.6600 (ttp80) REVERT: E 68 MET cc_start: 0.4697 (mpp) cc_final: 0.3291 (mpp) REVERT: E 75 MET cc_start: 0.9106 (ttp) cc_final: 0.8363 (ptm) REVERT: E 169 PHE cc_start: 0.8687 (m-10) cc_final: 0.8252 (m-10) REVERT: E 215 PHE cc_start: 0.7129 (m-10) cc_final: 0.6783 (m-80) REVERT: F 1 MET cc_start: 0.7009 (mmt) cc_final: 0.6779 (mmt) REVERT: F 71 ASN cc_start: 0.9149 (p0) cc_final: 0.8792 (p0) REVERT: F 81 CYS cc_start: 0.7528 (m) cc_final: 0.7080 (m) REVERT: F 207 PHE cc_start: 0.7927 (m-10) cc_final: 0.7659 (m-10) REVERT: G 114 TYR cc_start: 0.8419 (m-80) cc_final: 0.7650 (m-80) REVERT: G 154 ILE cc_start: 0.8335 (mm) cc_final: 0.7921 (tp) REVERT: G 229 MET cc_start: 0.5933 (tpp) cc_final: 0.5437 (tpp) outliers start: 4 outliers final: 0 residues processed: 427 average time/residue: 0.1375 time to fit residues: 90.5638 Evaluate side-chains 332 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 202 optimal weight: 2.9990 chunk 142 optimal weight: 0.4980 chunk 183 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 chunk 184 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 161 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 HIS A1059 GLN B 435 GLN C 17 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS D 68 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.120253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.097747 restraints weight = 74733.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.100433 restraints weight = 43799.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.102258 restraints weight = 29028.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.103500 restraints weight = 20934.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.104386 restraints weight = 16185.079| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20219 Z= 0.153 Angle : 0.780 30.475 27627 Z= 0.373 Chirality : 0.047 0.264 3152 Planarity : 0.006 0.083 3387 Dihedral : 14.730 90.890 3194 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.38 % 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: -1.43 (0.17), residues: 2370 helix: -0.16 (0.20), residues: 679 sheet: 0.11 (0.21), residues: 632 loop : -2.18 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 549 TYR 0.028 0.002 TYR G 133 PHE 0.027 0.002 PHE B 195 TRP 0.019 0.002 TRP D 102 HIS 0.009 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (20210) covalent geometry : angle 0.72640 / 0.37 (27609) hydrogen bonds : bond 0.04151 / 2.76 ( 848) hydrogen bonds : angle 5.29809 / 3.69 ( 2363) metal coordination : bond 0.01649 / 1.18 ( 8) metal coordination : angle 11.17514 / 6.93 ( 18) Misc. bond : bond 0.00047 / 0.02 ( 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 420 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 419 time to evaluate : 0.563 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 250 PHE cc_start: 0.7798 (t80) cc_final: 0.7519 (t80) REVERT: A 255 MET cc_start: 0.8285 (mtt) cc_final: 0.7952 (mtm) REVERT: A 353 LEU cc_start: 0.9273 (tp) cc_final: 0.9042 (tt) REVERT: A 433 ASP cc_start: 0.8534 (m-30) cc_final: 0.7398 (t0) REVERT: A 451 MET cc_start: 0.5878 (mmm) cc_final: 0.5606 (mmm) REVERT: A 527 MET cc_start: 0.8596 (ttm) cc_final: 0.8283 (ttt) REVERT: A 534 GLU cc_start: 0.8335 (pp20) cc_final: 0.7822 (pp20) REVERT: A 535 MET cc_start: 0.9315 (mmt) cc_final: 0.8937 (tpp) REVERT: A 564 MET cc_start: 0.8485 (tmm) cc_final: 0.8122 (tmm) REVERT: A 660 LEU cc_start: 0.8933 (mm) cc_final: 0.8533 (pp) REVERT: A 726 GLN cc_start: 0.8377 (tt0) cc_final: 0.7939 (tm-30) REVERT: A 727 MET cc_start: 0.8190 (ttm) cc_final: 0.7623 (ttm) REVERT: A 729 GLU cc_start: 0.8051 (mp0) cc_final: 0.7713 (mp0) REVERT: A 760 MET cc_start: 0.7456 (mpp) cc_final: 0.6953 (mpp) REVERT: A 865 GLN cc_start: 0.8667 (mt0) cc_final: 0.7921 (mm-40) REVERT: A 940 GLU cc_start: 0.8218 (tp30) cc_final: 0.7244 (tp30) REVERT: A 944 PHE cc_start: 0.8640 (t80) cc_final: 0.8092 (t80) REVERT: A 955 GLN cc_start: 0.8848 (pp30) cc_final: 0.8170 (pp30) REVERT: B 1 MET cc_start: 0.7151 (tmm) cc_final: 0.6353 (tmm) REVERT: B 52 HIS cc_start: 0.7931 (m-70) cc_final: 0.7612 (m-70) REVERT: B 131 ASP cc_start: 0.6349 (p0) cc_final: 0.6024 (p0) REVERT: B 304 TYR cc_start: 0.8497 (t80) cc_final: 0.8249 (t80) REVERT: B 366 GLU cc_start: 0.8995 (pt0) cc_final: 0.7974 (tm-30) REVERT: B 388 TYR cc_start: 0.8355 (p90) cc_final: 0.8120 (p90) REVERT: B 406 ASN cc_start: 0.8385 (p0) cc_final: 0.8083 (p0) REVERT: C 7 LEU cc_start: 0.8864 (mt) cc_final: 0.8272 (mt) REVERT: C 8 GLU cc_start: 0.8708 (tp30) cc_final: 0.8319 (tp30) REVERT: C 11 ASP cc_start: 0.8296 (m-30) cc_final: 0.6883 (m-30) REVERT: C 68 ILE cc_start: 0.8176 (mt) cc_final: 0.7790 (tt) REVERT: C 120 ASP cc_start: 0.8142 (m-30) cc_final: 0.7927 (m-30) REVERT: D 48 LEU cc_start: 0.8735 (tt) cc_final: 0.7379 (tp) REVERT: D 58 TYR cc_start: 0.8336 (m-80) cc_final: 0.7973 (m-80) REVERT: D 69 ARG cc_start: 0.8131 (ttt90) cc_final: 0.7854 (ttt180) REVERT: E 64 ARG cc_start: 0.7072 (tpp80) cc_final: 0.6663 (ttp80) REVERT: E 75 MET cc_start: 0.8836 (ttp) cc_final: 0.8499 (ptp) REVERT: E 84 ASN cc_start: 0.7817 (t0) cc_final: 0.7437 (t0) REVERT: E 118 LEU cc_start: 0.5569 (mt) cc_final: 0.5284 (mt) REVERT: E 139 MET cc_start: 0.7382 (ppp) cc_final: 0.7156 (ppp) REVERT: E 169 PHE cc_start: 0.8689 (m-10) cc_final: 0.8246 (m-10) REVERT: E 215 PHE cc_start: 0.7062 (m-10) cc_final: 0.6690 (m-80) REVERT: F 41 ASP cc_start: 0.5370 (p0) cc_final: 0.5087 (p0) REVERT: F 249 TYR cc_start: 0.8808 (m-80) cc_final: 0.7941 (m-80) REVERT: G 16 LEU cc_start: 0.7755 (mp) cc_final: 0.7390 (pp) REVERT: G 76 SER cc_start: 0.9064 (t) cc_final: 0.8842 (p) REVERT: G 79 LEU cc_start: 0.8839 (tp) cc_final: 0.8376 (tp) REVERT: G 114 TYR cc_start: 0.8406 (m-80) cc_final: 0.7801 (m-80) REVERT: G 154 ILE cc_start: 0.8341 (mm) cc_final: 0.7964 (tp) outliers start: 1 outliers final: 0 residues processed: 420 average time/residue: 0.1284 time to fit residues: 84.3170 Evaluate side-chains 334 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 75 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 195 optimal weight: 0.6980 chunk 188 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN A 558 GLN ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN B 285 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN E 153 HIS F 153 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.116995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.094184 restraints weight = 75021.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.096757 restraints weight = 44489.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.098488 restraints weight = 29793.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.099656 restraints weight = 21735.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.100516 restraints weight = 16982.318| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3807 r_free = 0.3807 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3807 r_free = 0.3807 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.5577 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= 0.166 Angle : 0.783 30.534 27627 Z= 0.374 Chirality : 0.047 0.195 3152 Planarity : 0.006 0.075 3387 Dihedral : 14.642 91.334 3194 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.10 % Allowed : 2.09 % Favored : 97.81 % 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: -1.20 (0.17), residues: 2370 helix: 0.07 (0.20), residues: 675 sheet: 0.15 (0.21), residues: 628 loop : -1.98 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 549 TYR 0.039 0.002 TYR A 801 PHE 0.023 0.002 PHE G 144 TRP 0.018 0.001 TRP A1055 HIS 0.011 0.001 HIS A 948 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (20210) covalent geometry : angle 0.72539 / 0.37 (27609) hydrogen bonds : bond 0.04078 / 2.68 ( 848) hydrogen bonds : angle 5.21057 / 3.63 ( 2363) metal coordination : bond 0.01641 / 1.17 ( 8) metal coordination : angle 11.60969 / 7.03 ( 18) Misc. bond : bond 0.00013 / 0.01 ( 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 415 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 413 time to evaluate : 0.656 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.6176 (mmm) cc_final: 0.4842 (mmm) REVERT: A 527 MET cc_start: 0.8628 (ttm) cc_final: 0.8328 (ttt) REVERT: A 534 GLU cc_start: 0.8341 (pp20) cc_final: 0.8118 (tm-30) REVERT: A 564 MET cc_start: 0.8527 (tmm) cc_final: 0.8147 (tmm) REVERT: A 660 LEU cc_start: 0.9150 (mm) cc_final: 0.8648 (pp) REVERT: A 726 GLN cc_start: 0.8401 (tt0) cc_final: 0.7976 (tm-30) REVERT: A 727 MET cc_start: 0.8268 (ttm) cc_final: 0.7719 (ttm) REVERT: A 760 MET cc_start: 0.7599 (mpp) cc_final: 0.7100 (mpp) REVERT: A 865 GLN cc_start: 0.8758 (mt0) cc_final: 0.7974 (mm-40) REVERT: A 940 GLU cc_start: 0.8110 (tp30) cc_final: 0.7553 (tp30) REVERT: A 1048 GLU cc_start: 0.8773 (tp30) cc_final: 0.8170 (tm-30) REVERT: A 1049 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8130 (tm-30) REVERT: B 1 MET cc_start: 0.7174 (tmm) cc_final: 0.6862 (tmm) REVERT: B 52 HIS cc_start: 0.8066 (m-70) cc_final: 0.7848 (m-70) REVERT: B 131 ASP cc_start: 0.6445 (p0) cc_final: 0.6232 (p0) REVERT: B 304 TYR cc_start: 0.8584 (t80) cc_final: 0.7966 (t80) REVERT: B 366 GLU cc_start: 0.9059 (pt0) cc_final: 0.8095 (tm-30) REVERT: B 385 TYR cc_start: 0.8741 (t80) cc_final: 0.8142 (t80) REVERT: B 388 TYR cc_start: 0.8385 (p90) cc_final: 0.8107 (p90) REVERT: B 406 ASN cc_start: 0.8404 (p0) cc_final: 0.8083 (p0) REVERT: B 430 ASP cc_start: 0.7338 (t0) cc_final: 0.6741 (t70) REVERT: C 7 LEU cc_start: 0.8901 (mt) cc_final: 0.8279 (mt) REVERT: C 8 GLU cc_start: 0.8712 (tp30) cc_final: 0.8288 (mm-30) REVERT: C 11 ASP cc_start: 0.8318 (m-30) cc_final: 0.6858 (m-30) REVERT: C 68 ILE cc_start: 0.8250 (mt) cc_final: 0.7871 (tt) REVERT: C 120 ASP cc_start: 0.8343 (m-30) cc_final: 0.8075 (m-30) REVERT: E 40 MET cc_start: 0.3929 (tpp) cc_final: 0.3616 (tpp) REVERT: E 64 ARG cc_start: 0.7136 (tpp80) cc_final: 0.6749 (ttp80) REVERT: E 84 ASN cc_start: 0.7866 (t0) cc_final: 0.7520 (t0) REVERT: E 169 PHE cc_start: 0.8668 (m-10) cc_final: 0.8197 (m-10) REVERT: E 215 PHE cc_start: 0.7005 (m-10) cc_final: 0.6675 (m-80) REVERT: E 227 LEU cc_start: 0.8267 (pp) cc_final: 0.7970 (tt) REVERT: F 1 MET cc_start: 0.7754 (mmt) cc_final: 0.7384 (mmt) REVERT: F 35 VAL cc_start: 0.7434 (t) cc_final: 0.6988 (p) REVERT: F 41 ASP cc_start: 0.5502 (p0) cc_final: 0.4984 (p0) REVERT: F 45 VAL cc_start: 0.8099 (t) cc_final: 0.7876 (m) REVERT: F 116 MET cc_start: 0.6996 (ppp) cc_final: 0.6546 (ppp) REVERT: F 249 TYR cc_start: 0.8686 (m-80) cc_final: 0.7831 (m-80) REVERT: G 16 LEU cc_start: 0.7848 (mp) cc_final: 0.7430 (pp) REVERT: G 76 SER cc_start: 0.9044 (t) cc_final: 0.8824 (p) REVERT: G 114 TYR cc_start: 0.8543 (m-80) cc_final: 0.7838 (m-80) REVERT: G 154 ILE cc_start: 0.8405 (mm) cc_final: 0.8064 (tp) outliers start: 2 outliers final: 0 residues processed: 415 average time/residue: 0.1280 time to fit residues: 82.5884 Evaluate side-chains 332 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 221 optimal weight: 0.0870 chunk 205 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 236 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 0.0980 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 GLN ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 GLN A1059 GLN B 128 HIS C 9 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.115397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.091575 restraints weight = 73414.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.094211 restraints weight = 42887.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.096005 restraints weight = 28559.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.097227 restraints weight = 20770.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.098121 restraints weight = 16181.489| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20219 Z= 0.154 Angle : 0.756 28.999 27627 Z= 0.359 Chirality : 0.046 0.277 3152 Planarity : 0.005 0.075 3387 Dihedral : 14.553 91.515 3194 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.05 % Allowed : 1.12 % Favored : 98.83 % 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: -1.03 (0.17), residues: 2370 helix: 0.16 (0.20), residues: 676 sheet: 0.29 (0.21), residues: 624 loop : -1.87 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 149 TYR 0.019 0.002 TYR A 936 PHE 0.035 0.002 PHE F 214 TRP 0.037 0.002 TRP E 28 HIS 0.011 0.001 HIS A 948 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (20210) covalent geometry : angle 0.69793 / 0.36 (27609) hydrogen bonds : bond 0.03836 / 2.51 ( 848) hydrogen bonds : angle 5.19788 / 3.62 ( 2363) metal coordination : bond 0.01514 / 1.10 ( 8) metal coordination : angle 11.40857 / 6.94 ( 18) Misc. bond : bond 0.00015 / 0.01 ( 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 413 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 412 time to evaluate : 0.641 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.6513 (mmm) cc_final: 0.5167 (mmm) REVERT: A 527 MET cc_start: 0.8683 (ttm) cc_final: 0.8304 (ttt) REVERT: A 564 MET cc_start: 0.8597 (tmm) cc_final: 0.8240 (tmm) REVERT: A 660 LEU cc_start: 0.9126 (mm) cc_final: 0.8575 (pp) REVERT: A 726 GLN cc_start: 0.8418 (tt0) cc_final: 0.7910 (tm-30) REVERT: A 727 MET cc_start: 0.8458 (ttm) cc_final: 0.7823 (ttm) REVERT: A 760 MET cc_start: 0.7592 (mpp) cc_final: 0.6947 (mpp) REVERT: A 865 GLN cc_start: 0.8785 (mt0) cc_final: 0.8285 (mm-40) REVERT: A 940 GLU cc_start: 0.8231 (tp30) cc_final: 0.7781 (tp30) REVERT: B 1 MET cc_start: 0.7435 (tmm) cc_final: 0.6974 (tmm) REVERT: B 52 HIS cc_start: 0.8145 (m-70) cc_final: 0.7881 (m-70) REVERT: B 304 TYR cc_start: 0.8570 (t80) cc_final: 0.8215 (t80) REVERT: B 366 GLU cc_start: 0.9140 (pt0) cc_final: 0.8131 (tm-30) REVERT: B 388 TYR cc_start: 0.8389 (p90) cc_final: 0.8167 (p90) REVERT: B 406 ASN cc_start: 0.8554 (p0) cc_final: 0.8259 (p0) REVERT: B 430 ASP cc_start: 0.7703 (t0) cc_final: 0.7029 (t70) REVERT: C 7 LEU cc_start: 0.8912 (mt) cc_final: 0.8334 (mt) REVERT: C 8 GLU cc_start: 0.8822 (tp30) cc_final: 0.8399 (mm-30) REVERT: C 11 ASP cc_start: 0.8395 (m-30) cc_final: 0.6904 (m-30) REVERT: C 68 ILE cc_start: 0.8350 (mt) cc_final: 0.8008 (tt) REVERT: C 120 ASP cc_start: 0.8436 (m-30) cc_final: 0.8162 (m-30) REVERT: E 64 ARG cc_start: 0.7153 (tpp80) cc_final: 0.6913 (ttp80) REVERT: E 84 ASN cc_start: 0.7897 (t0) cc_final: 0.7555 (t0) REVERT: E 169 PHE cc_start: 0.8673 (m-10) cc_final: 0.8220 (m-10) REVERT: E 215 PHE cc_start: 0.6969 (m-10) cc_final: 0.6731 (m-80) REVERT: E 227 LEU cc_start: 0.8238 (pp) cc_final: 0.7942 (tt) REVERT: F 1 MET cc_start: 0.7720 (mmt) cc_final: 0.7263 (mmt) REVERT: F 35 VAL cc_start: 0.7486 (t) cc_final: 0.7084 (p) REVERT: F 41 ASP cc_start: 0.5716 (p0) cc_final: 0.5392 (p0) REVERT: F 116 MET cc_start: 0.7183 (ppp) cc_final: 0.6665 (ppp) REVERT: F 211 TYR cc_start: 0.8855 (m-80) cc_final: 0.8619 (m-80) REVERT: F 249 TYR cc_start: 0.8605 (m-80) cc_final: 0.7941 (m-80) REVERT: G 16 LEU cc_start: 0.7818 (mp) cc_final: 0.7454 (pp) REVERT: G 79 LEU cc_start: 0.8867 (tp) cc_final: 0.8178 (tp) REVERT: G 154 ILE cc_start: 0.8434 (mm) cc_final: 0.8127 (tp) outliers start: 1 outliers final: 0 residues processed: 413 average time/residue: 0.1298 time to fit residues: 84.1357 Evaluate side-chains 336 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 92 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 193 optimal weight: 0.0980 chunk 159 optimal weight: 0.3980 chunk 205 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN A 558 GLN ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN E 153 HIS F 36 ASN F 213 ASN F 246 HIS ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.115992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.092106 restraints weight = 72783.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.094758 restraints weight = 42452.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.096548 restraints weight = 28171.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.097796 restraints weight = 20445.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.098668 restraints weight = 15881.236| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20219 Z= 0.132 Angle : 0.745 26.302 27627 Z= 0.350 Chirality : 0.045 0.187 3152 Planarity : 0.005 0.087 3387 Dihedral : 14.528 91.135 3194 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.15 % Allowed : 1.21 % Favored : 98.64 % 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: -0.92 (0.17), residues: 2370 helix: 0.28 (0.20), residues: 679 sheet: 0.36 (0.21), residues: 631 loop : -1.83 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 141 TYR 0.039 0.002 TYR A 801 PHE 0.024 0.002 PHE E 2 TRP 0.020 0.001 TRP F 28 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (20210) covalent geometry : angle 0.68876 / 0.35 (27609) hydrogen bonds : bond 0.03673 / 2.42 ( 848) hydrogen bonds : angle 5.12200 / 3.56 ( 2363) metal coordination : bond 0.01442 / 1.05 ( 8) metal coordination : angle 11.18096 / 6.73 ( 18) Misc. bond : bond 0.00006 / 0.00 ( 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 407 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 404 time to evaluate : 0.712 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: symmetry clash 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 451 MET cc_start: 0.6562 (mmm) cc_final: 0.5235 (mmm) REVERT: A 527 MET cc_start: 0.8728 (ttm) cc_final: 0.8339 (ttt) REVERT: A 726 GLN cc_start: 0.8342 (tt0) cc_final: 0.7905 (tm-30) REVERT: A 727 MET cc_start: 0.8383 (ttm) cc_final: 0.8053 (ttp) REVERT: A 760 MET cc_start: 0.7333 (mpp) cc_final: 0.6806 (mpp) REVERT: A 865 GLN cc_start: 0.8711 (mt0) cc_final: 0.8229 (mm-40) REVERT: A 940 GLU cc_start: 0.8199 (tp30) cc_final: 0.7359 (tp30) REVERT: A 944 PHE cc_start: 0.8920 (t80) cc_final: 0.8228 (t80) REVERT: A 958 LEU cc_start: 0.9429 (tp) cc_final: 0.9172 (tp) REVERT: A 959 GLU cc_start: 0.8396 (pm20) cc_final: 0.8101 (pm20) REVERT: B 1 MET cc_start: 0.7515 (tmm) cc_final: 0.7058 (tmm) REVERT: B 52 HIS cc_start: 0.8145 (m-70) cc_final: 0.7867 (m-70) REVERT: B 300 ASP cc_start: 0.7769 (m-30) cc_final: 0.7485 (m-30) REVERT: B 304 TYR cc_start: 0.8562 (t80) cc_final: 0.7962 (t80) REVERT: B 366 GLU cc_start: 0.9155 (pt0) cc_final: 0.8150 (tm-30) REVERT: B 388 TYR cc_start: 0.8347 (p90) cc_final: 0.8070 (p90) REVERT: B 406 ASN cc_start: 0.8574 (p0) cc_final: 0.8300 (p0) REVERT: B 422 THR cc_start: 0.8736 (t) cc_final: 0.8478 (p) REVERT: B 430 ASP cc_start: 0.7632 (t0) cc_final: 0.6962 (t70) REVERT: C 7 LEU cc_start: 0.8940 (mt) cc_final: 0.8347 (mt) REVERT: C 8 GLU cc_start: 0.8810 (tp30) cc_final: 0.8404 (mm-30) REVERT: C 11 ASP cc_start: 0.8389 (m-30) cc_final: 0.6908 (m-30) REVERT: C 40 MET cc_start: 0.8290 (mtt) cc_final: 0.7910 (mtp) REVERT: C 68 ILE cc_start: 0.8425 (mt) cc_final: 0.8067 (tt) REVERT: C 120 ASP cc_start: 0.8353 (m-30) cc_final: 0.7980 (m-30) REVERT: E 64 ARG cc_start: 0.7211 (tpp80) cc_final: 0.6988 (ttp80) REVERT: E 84 ASN cc_start: 0.7879 (t0) cc_final: 0.7550 (t0) REVERT: E 169 PHE cc_start: 0.8659 (m-10) cc_final: 0.8411 (m-10) REVERT: E 199 MET cc_start: 0.4138 (ptp) cc_final: 0.2527 (ttt) REVERT: E 215 PHE cc_start: 0.7072 (m-10) cc_final: 0.6740 (m-80) REVERT: F 1 MET cc_start: 0.7625 (mmt) cc_final: 0.7279 (mmt) REVERT: F 35 VAL cc_start: 0.7385 (t) cc_final: 0.6997 (p) REVERT: F 41 ASP cc_start: 0.5808 (p0) cc_final: 0.5553 (p0) REVERT: F 116 MET cc_start: 0.7284 (ppp) cc_final: 0.6742 (ppp) REVERT: F 211 TYR cc_start: 0.8882 (m-80) cc_final: 0.8638 (m-10) REVERT: G 16 LEU cc_start: 0.7868 (mp) cc_final: 0.7445 (pp) REVERT: G 79 LEU cc_start: 0.8892 (tp) cc_final: 0.8543 (tp) REVERT: G 114 TYR cc_start: 0.8541 (m-80) cc_final: 0.7850 (m-80) REVERT: G 149 ARG cc_start: 0.9192 (ptp-170) cc_final: 0.8855 (ptm160) REVERT: G 249 TYR cc_start: 0.3156 (m-80) cc_final: 0.2669 (m-80) outliers start: 3 outliers final: 1 residues processed: 406 average time/residue: 0.1256 time to fit residues: 80.9482 Evaluate side-chains 326 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 325 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 11 optimal weight: 0.0570 chunk 145 optimal weight: 0.3980 chunk 168 optimal weight: 7.9990 chunk 138 optimal weight: 0.7980 chunk 232 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 92 optimal weight: 0.0470 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 HIS B 8 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 HIS G 153 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.115842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.092165 restraints weight = 72368.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.094779 restraints weight = 42324.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.096549 restraints weight = 28132.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.097801 restraints weight = 20480.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.098678 restraints weight = 15870.986| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20219 Z= 0.126 Angle : 0.740 25.088 27627 Z= 0.347 Chirality : 0.045 0.285 3152 Planarity : 0.005 0.080 3387 Dihedral : 14.459 90.205 3194 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.05 % Allowed : 0.73 % Favored : 99.22 % 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: -0.77 (0.17), residues: 2370 helix: 0.34 (0.20), residues: 679 sheet: 0.47 (0.21), residues: 630 loop : -1.71 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 141 TYR 0.032 0.001 TYR A 801 PHE 0.032 0.002 PHE A 135 TRP 0.012 0.001 TRP F 28 HIS 0.010 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (20210) covalent geometry : angle 0.68536 / 0.35 (27609) hydrogen bonds : bond 0.03572 / 2.32 ( 848) hydrogen bonds : angle 5.03319 / 3.50 ( 2363) metal coordination : bond 0.01415 / 1.05 ( 8) metal coordination : angle 10.93747 / 6.56 ( 18) Misc. bond : bond 0.00001 / 0.00 ( 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 413 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 412 time to evaluate : 0.755 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: symmetry clash 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: symmetry clash REVERT: A 433 ASP cc_start: 0.8854 (m-30) cc_final: 0.7775 (t0) REVERT: A 451 MET cc_start: 0.6637 (mmm) cc_final: 0.5465 (mmm) REVERT: A 527 MET cc_start: 0.8624 (ttm) cc_final: 0.8251 (ttt) REVERT: A 611 MET cc_start: 0.9122 (mtm) cc_final: 0.8759 (mtm) REVERT: A 660 LEU cc_start: 0.8777 (mt) cc_final: 0.8350 (pp) REVERT: A 726 GLN cc_start: 0.8270 (tt0) cc_final: 0.7852 (tm-30) REVERT: A 727 MET cc_start: 0.8373 (ttm) cc_final: 0.8138 (ttp) REVERT: A 760 MET cc_start: 0.7293 (mpp) cc_final: 0.6868 (mpp) REVERT: A 840 VAL cc_start: 0.8970 (t) cc_final: 0.8765 (t) REVERT: A 865 GLN cc_start: 0.8719 (mt0) cc_final: 0.8182 (mm-40) REVERT: A 940 GLU cc_start: 0.8096 (tp30) cc_final: 0.7352 (tp30) REVERT: A 944 PHE cc_start: 0.8597 (t80) cc_final: 0.8113 (t80) REVERT: A 958 LEU cc_start: 0.9364 (tp) cc_final: 0.9041 (tp) REVERT: A 959 GLU cc_start: 0.8340 (pm20) cc_final: 0.8043 (pm20) REVERT: B 52 HIS cc_start: 0.8086 (m-70) cc_final: 0.7854 (m-70) REVERT: B 304 TYR cc_start: 0.8457 (t80) cc_final: 0.7940 (t80) REVERT: B 366 GLU cc_start: 0.9181 (pt0) cc_final: 0.8803 (pt0) REVERT: B 388 TYR cc_start: 0.8310 (p90) cc_final: 0.8038 (p90) REVERT: B 406 ASN cc_start: 0.8474 (p0) cc_final: 0.8241 (p0) REVERT: B 422 THR cc_start: 0.8686 (t) cc_final: 0.8430 (p) REVERT: B 430 ASP cc_start: 0.7565 (t0) cc_final: 0.6891 (t70) REVERT: C 7 LEU cc_start: 0.8898 (mt) cc_final: 0.8285 (mt) REVERT: C 8 GLU cc_start: 0.8757 (tp30) cc_final: 0.8355 (mm-30) REVERT: C 11 ASP cc_start: 0.8343 (m-30) cc_final: 0.6834 (m-30) REVERT: C 68 ILE cc_start: 0.8474 (mt) cc_final: 0.8104 (tt) REVERT: C 121 ILE cc_start: 0.8281 (tt) cc_final: 0.8062 (tt) REVERT: E 36 ASN cc_start: 0.8748 (p0) cc_final: 0.7744 (t0) REVERT: E 64 ARG cc_start: 0.7385 (tpp80) cc_final: 0.7132 (ttp80) REVERT: E 84 ASN cc_start: 0.7865 (t0) cc_final: 0.7120 (p0) REVERT: E 179 ASN cc_start: 0.7710 (p0) cc_final: 0.7026 (t0) REVERT: E 199 MET cc_start: 0.4097 (ptp) cc_final: 0.2575 (ttt) REVERT: E 215 PHE cc_start: 0.6958 (m-10) cc_final: 0.6679 (m-80) REVERT: F 1 MET cc_start: 0.7548 (mmt) cc_final: 0.7294 (mmt) REVERT: F 45 VAL cc_start: 0.7750 (t) cc_final: 0.7518 (t) REVERT: F 116 MET cc_start: 0.7275 (ppp) cc_final: 0.6729 (ppp) REVERT: F 182 LEU cc_start: 0.9254 (mt) cc_final: 0.8943 (mt) REVERT: F 210 ARG cc_start: 0.8919 (ttp80) cc_final: 0.8714 (ttp80) REVERT: F 211 TYR cc_start: 0.8785 (m-80) cc_final: 0.8514 (m-10) REVERT: G 16 LEU cc_start: 0.7899 (mp) cc_final: 0.7439 (pp) REVERT: G 79 LEU cc_start: 0.8781 (tp) cc_final: 0.8096 (tp) REVERT: G 114 TYR cc_start: 0.8549 (m-80) cc_final: 0.7877 (m-80) REVERT: G 149 ARG cc_start: 0.9167 (ptp-170) cc_final: 0.8820 (ptm160) REVERT: G 229 MET cc_start: 0.6379 (mmt) cc_final: 0.6161 (mmt) REVERT: G 249 TYR cc_start: 0.3036 (m-80) cc_final: 0.2721 (m-80) outliers start: 1 outliers final: 0 residues processed: 413 average time/residue: 0.1247 time to fit residues: 81.5136 Evaluate side-chains 331 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 224 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 118 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 ASN ** A 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 HIS ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 ASN F 246 HIS ** G 153 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 = 0.3981 r_free = 0.3981 target = 0.110331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.086730 restraints weight = 73663.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.089122 restraints weight = 43681.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.090741 restraints weight = 29465.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.091877 restraints weight = 21704.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.092687 restraints weight = 17051.134| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.6914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20219 Z= 0.204 Angle : 0.821 29.017 27627 Z= 0.391 Chirality : 0.046 0.173 3152 Planarity : 0.006 0.100 3387 Dihedral : 14.564 89.022 3194 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.66 % Favored : 94.30 % Rotamer: Outliers : 0.05 % Allowed : 0.49 % Favored : 99.47 % 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: -0.95 (0.17), residues: 2370 helix: 0.16 (0.20), residues: 680 sheet: 0.43 (0.21), residues: 610 loop : -1.81 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 549 TYR 0.041 0.002 TYR A 801 PHE 0.027 0.002 PHE G 144 TRP 0.021 0.002 TRP A 79 HIS 0.017 0.002 HIS A 948 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (20210) covalent geometry : angle 0.76096 / 0.39 (27609) hydrogen bonds : bond 0.04358 / 2.86 ( 848) hydrogen bonds : angle 5.27704 / 3.66 ( 2363) metal coordination : bond 0.01529 / 1.07 ( 8) metal coordination : angle 12.08313 / 7.29 ( 18) Misc. bond : bond 0.00000 / 0.00 ( 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 389 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 388 time to evaluate : 0.659 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 MET cc_start: 0.8562 (ttm) cc_final: 0.8260 (ttt) REVERT: A 564 MET cc_start: 0.8633 (tmm) cc_final: 0.8319 (tmm) REVERT: A 726 GLN cc_start: 0.8284 (tt0) cc_final: 0.7847 (tm-30) REVERT: A 727 MET cc_start: 0.8360 (ttm) cc_final: 0.8039 (ttp) REVERT: A 760 MET cc_start: 0.7693 (mpp) cc_final: 0.6792 (mpp) REVERT: A 840 VAL cc_start: 0.9036 (t) cc_final: 0.8828 (t) REVERT: A 865 GLN cc_start: 0.8871 (mt0) cc_final: 0.8367 (mm-40) REVERT: A 940 GLU cc_start: 0.8218 (tp30) cc_final: 0.7679 (tp30) REVERT: A 944 PHE cc_start: 0.8975 (t80) cc_final: 0.8582 (t80) REVERT: A 958 LEU cc_start: 0.9341 (tp) cc_final: 0.8985 (tp) REVERT: A 959 GLU cc_start: 0.8279 (pm20) cc_final: 0.8022 (pm20) REVERT: B 1 MET cc_start: 0.7578 (tmm) cc_final: 0.6938 (tmm) REVERT: B 304 TYR cc_start: 0.8538 (t80) cc_final: 0.8059 (t80) REVERT: B 366 GLU cc_start: 0.9229 (pt0) cc_final: 0.8876 (pt0) REVERT: B 388 TYR cc_start: 0.8458 (p90) cc_final: 0.8086 (p90) REVERT: B 406 ASN cc_start: 0.8598 (p0) cc_final: 0.8395 (p0) REVERT: B 430 ASP cc_start: 0.8009 (t0) cc_final: 0.7280 (t0) REVERT: C 7 LEU cc_start: 0.9023 (mt) cc_final: 0.8369 (mt) REVERT: C 8 GLU cc_start: 0.8706 (tp30) cc_final: 0.8356 (mm-30) REVERT: C 11 ASP cc_start: 0.8524 (m-30) cc_final: 0.6927 (m-30) REVERT: C 40 MET cc_start: 0.8611 (mtt) cc_final: 0.8234 (mtp) REVERT: C 57 LEU cc_start: 0.6545 (tp) cc_final: 0.6246 (tp) REVERT: C 68 ILE cc_start: 0.8664 (mt) cc_final: 0.8305 (tt) REVERT: C 120 ASP cc_start: 0.8561 (m-30) cc_final: 0.8320 (m-30) REVERT: D 69 ARG cc_start: 0.8353 (ttt90) cc_final: 0.8142 (ttt180) REVERT: E 64 ARG cc_start: 0.7460 (tpp80) cc_final: 0.7253 (ttp80) REVERT: E 68 MET cc_start: 0.4436 (mpp) cc_final: 0.3139 (mpp) REVERT: E 84 ASN cc_start: 0.7902 (t0) cc_final: 0.7595 (t0) REVERT: E 179 ASN cc_start: 0.8097 (p0) cc_final: 0.7501 (t0) REVERT: E 199 MET cc_start: 0.4031 (ptp) cc_final: 0.2542 (ttt) REVERT: F 1 MET cc_start: 0.7806 (mmt) cc_final: 0.7528 (mmt) REVERT: F 44 HIS cc_start: 0.7934 (m90) cc_final: 0.7679 (m-70) REVERT: F 116 MET cc_start: 0.7439 (ppp) cc_final: 0.6910 (ppp) REVERT: F 182 LEU cc_start: 0.9395 (mt) cc_final: 0.9193 (mt) REVERT: F 193 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8475 (mp0) REVERT: F 211 TYR cc_start: 0.8949 (m-80) cc_final: 0.8648 (m-10) REVERT: G 16 LEU cc_start: 0.7955 (mp) cc_final: 0.7524 (pp) REVERT: G 79 LEU cc_start: 0.8947 (tp) cc_final: 0.8379 (tp) REVERT: G 112 SER cc_start: 0.8097 (m) cc_final: 0.7758 (m) REVERT: G 114 TYR cc_start: 0.8483 (m-80) cc_final: 0.7781 (m-80) REVERT: G 149 ARG cc_start: 0.9187 (ptp-170) cc_final: 0.8847 (ptm160) REVERT: G 249 TYR cc_start: 0.3633 (m-80) cc_final: 0.3201 (m-80) outliers start: 1 outliers final: 0 residues processed: 389 average time/residue: 0.1284 time to fit residues: 78.6319 Evaluate side-chains 310 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 190 optimal weight: 2.9990 chunk 233 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 240 optimal weight: 10.0000 chunk 223 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 GLN ** A 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** G 153 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 = 0.3978 r_free = 0.3978 target = 0.110025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.086390 restraints weight = 73055.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.088753 restraints weight = 42886.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.090375 restraints weight = 28743.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.091507 restraints weight = 21084.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.092232 restraints weight = 16568.763| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.7248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20219 Z= 0.166 Angle : 0.791 29.619 27627 Z= 0.371 Chirality : 0.046 0.207 3152 Planarity : 0.005 0.092 3387 Dihedral : 14.543 88.451 3194 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.44 % Favored : 95.52 % Rotamer: Outliers : 0.05 % Allowed : 0.29 % Favored : 99.66 % 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: -0.79 (0.17), residues: 2370 helix: 0.30 (0.20), residues: 681 sheet: 0.33 (0.21), residues: 629 loop : -1.62 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 141 TYR 0.034 0.002 TYR A 801 PHE 0.048 0.002 PHE F 215 TRP 0.023 0.002 TRP A 79 HIS 0.008 0.001 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (20210) covalent geometry : angle 0.72611 / 0.37 (27609) hydrogen bonds : bond 0.03881 / 2.51 ( 848) hydrogen bonds : angle 5.24679 / 3.61 ( 2363) metal coordination : bond 0.01489 / 1.07 ( 8) metal coordination : angle 12.33071 / 7.55 ( 18) Misc. bond : bond 0.00003 / 0.00 ( 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 396 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 395 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: 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 96 PHE cc_start: 0.8885 (p90) cc_final: 0.8650 (p90) REVERT: A 449 VAL cc_start: 0.8664 (t) cc_final: 0.8437 (t) REVERT: A 451 MET cc_start: 0.7025 (mmm) cc_final: 0.5878 (mmm) REVERT: A 527 MET cc_start: 0.8522 (ttm) cc_final: 0.8161 (ttt) REVERT: A 564 MET cc_start: 0.8638 (tmm) cc_final: 0.8352 (tmm) REVERT: A 726 GLN cc_start: 0.8320 (tt0) cc_final: 0.7872 (tm-30) REVERT: A 760 MET cc_start: 0.7611 (mpp) cc_final: 0.6905 (mpp) REVERT: A 795 GLU cc_start: 0.9025 (tp30) cc_final: 0.8505 (tp30) REVERT: A 870 ASP cc_start: 0.9059 (p0) cc_final: 0.8793 (p0) REVERT: A 907 MET cc_start: 0.6885 (tpp) cc_final: 0.6310 (tpt) REVERT: A 940 GLU cc_start: 0.8275 (tp30) cc_final: 0.7682 (tp30) REVERT: A 958 LEU cc_start: 0.9412 (tp) cc_final: 0.9129 (tp) REVERT: A 959 GLU cc_start: 0.8435 (pm20) cc_final: 0.8076 (pm20) REVERT: A 980 GLU cc_start: 0.8752 (tp30) cc_final: 0.8374 (tp30) REVERT: A 1078 ILE cc_start: 0.9224 (mm) cc_final: 0.8893 (mp) REVERT: B 1 MET cc_start: 0.7325 (tmm) cc_final: 0.6791 (tmm) REVERT: B 304 TYR cc_start: 0.8578 (t80) cc_final: 0.8121 (t80) REVERT: B 366 GLU cc_start: 0.9192 (pt0) cc_final: 0.8292 (tm-30) REVERT: B 430 ASP cc_start: 0.8061 (t0) cc_final: 0.7363 (t0) REVERT: C 7 LEU cc_start: 0.9131 (mt) cc_final: 0.8512 (mt) REVERT: C 8 GLU cc_start: 0.8709 (tp30) cc_final: 0.8436 (mm-30) REVERT: C 11 ASP cc_start: 0.8604 (m-30) cc_final: 0.6685 (m-30) REVERT: C 68 ILE cc_start: 0.8697 (mt) cc_final: 0.8341 (tt) REVERT: C 120 ASP cc_start: 0.8568 (m-30) cc_final: 0.8311 (m-30) REVERT: D 67 LEU cc_start: 0.8956 (pt) cc_final: 0.8751 (pp) REVERT: E 68 MET cc_start: 0.4510 (mpp) cc_final: 0.3165 (mpp) REVERT: E 75 MET cc_start: 0.8223 (mmp) cc_final: 0.8002 (mmm) REVERT: E 84 ASN cc_start: 0.8000 (t0) cc_final: 0.7605 (t0) REVERT: E 179 ASN cc_start: 0.8151 (p0) cc_final: 0.7630 (t0) REVERT: E 199 MET cc_start: 0.3548 (ptp) cc_final: 0.2007 (ttt) REVERT: E 215 PHE cc_start: 0.6941 (m-10) cc_final: 0.6668 (m-80) REVERT: F 1 MET cc_start: 0.7807 (mmt) cc_final: 0.7128 (mmt) REVERT: F 20 LYS cc_start: 0.8862 (ptmm) cc_final: 0.8635 (pptt) REVERT: F 24 ASN cc_start: 0.7941 (t0) cc_final: 0.7731 (t0) REVERT: F 44 HIS cc_start: 0.7930 (m90) cc_final: 0.7400 (m-70) REVERT: F 116 MET cc_start: 0.7384 (ppp) cc_final: 0.7002 (ppp) REVERT: F 182 LEU cc_start: 0.9341 (mt) cc_final: 0.9106 (mt) REVERT: F 193 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8361 (mp0) REVERT: F 211 TYR cc_start: 0.8991 (m-80) cc_final: 0.8746 (m-10) REVERT: F 249 TYR cc_start: 0.8544 (m-80) cc_final: 0.8319 (m-80) REVERT: G 79 LEU cc_start: 0.8810 (tp) cc_final: 0.8481 (tp) REVERT: G 114 TYR cc_start: 0.8727 (m-80) cc_final: 0.8334 (m-80) REVERT: G 149 ARG cc_start: 0.9199 (ptp-170) cc_final: 0.8847 (ptm160) REVERT: G 249 TYR cc_start: 0.3674 (m-80) cc_final: 0.3208 (m-80) outliers start: 1 outliers final: 0 residues processed: 396 average time/residue: 0.1282 time to fit residues: 79.7654 Evaluate side-chains 308 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 33 optimal weight: 0.0010 chunk 2 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 189 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 232 optimal weight: 2.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN A 558 GLN A 948 HIS ** A 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 52 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 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 = 0.3973 r_free = 0.3973 target = 0.109618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.085993 restraints weight = 71878.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.088381 restraints weight = 42206.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.090012 restraints weight = 28250.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.091088 restraints weight = 20731.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.091869 restraints weight = 16410.556| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.7471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20219 Z= 0.161 Angle : 0.784 29.057 27627 Z= 0.369 Chirality : 0.046 0.181 3152 Planarity : 0.005 0.098 3387 Dihedral : 14.553 87.211 3194 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 0.05 % Allowed : 0.15 % Favored : 99.81 % 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: -0.74 (0.17), residues: 2370 helix: 0.42 (0.20), residues: 679 sheet: 0.31 (0.21), residues: 613 loop : -1.58 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 141 TYR 0.052 0.002 TYR A 801 PHE 0.030 0.002 PHE G 144 TRP 0.022 0.002 TRP A 79 HIS 0.006 0.001 HIS A1021 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (20210) covalent geometry : angle 0.71862 / 0.37 (27609) hydrogen bonds : bond 0.03871 / 2.55 ( 848) hydrogen bonds : angle 5.26176 / 3.62 ( 2363) metal coordination : bond 0.01488 / 1.07 ( 8) metal coordination : angle 12.25833 / 7.49 ( 18) Misc. bond : bond 0.00004 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3878.44 seconds wall clock time: 67 minutes 37.78 seconds (4057.78 seconds total)