Starting phenix.real_space_refine on Mon Oct 26 05:31:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s1n_10081/10_2026/6s1n_10081_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s1n_10081/10_2026/6s1n_10081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6s1n_10081/10_2026/6s1n_10081_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s1n_10081/10_2026/6s1n_10081_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6s1n_10081/10_2026/6s1n_10081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s1n_10081/10_2026/6s1n_10081.map" } resolution = 4.86 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 64 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 98.895 98.577 74.641 1.00 40.62 S ATOM 7175 SG CYS A1015 101.836 96.664 76.373 1.00 40.62 S ATOM 7248 SG CYS A1026 102.565 100.377 75.449 1.00 40.62 S ATOM 7264 SG CYS A1029 101.561 98.148 72.827 1.00 40.62 S ATOM 7616 SG CYS A1071 59.269 81.282 75.051 1.00 40.62 S ATOM 7654 SG CYS A1076 63.753 77.569 73.723 1.00 30.94 S ATOM 7515 SG CYS A1058 63.215 83.861 70.771 1.00 40.62 S ATOM 7541 SG CYS A1061 59.419 78.748 69.874 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: 5.65, per 1000 atoms: 0.29 Number of scatterers: 19726 At special positions: 0 Unit cell: (154.44, 129.6, 172.8, 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: 1.75 Conformation dependent library (CDL) restraints added in 967.6 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1202 " pdb="FE1 SF4 A1202 " - pdb=" SG CYS A1071 " pdb="FE2 SF4 A1202 " - pdb=" SG CYS A1076 " pdb="FE3 SF4 A1202 " - pdb=" SG CYS A1058 " pdb="FE4 SF4 A1202 " - pdb=" SG CYS A1061 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1029 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1015 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1012 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1026 " Number of angles added : 6 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4502 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 19 sheets defined 31.0% alpha, 22.3% beta 18 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.640A pdb=" N SER A 176 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 3.628A 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: 3.926A 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: 3.593A 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: 3.582A pdb=" N ASP A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 413 Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 473 through 482 Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 501 through 526 Proline residue: A 519 - end of helix Processing helix chain 'A' and resid 527 through 540 removed outlier: 3.590A pdb=" N ASN A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 removed outlier: 3.640A 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: 4.068A 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: 4.037A 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: 3.629A 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: 3.562A 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: 3.794A pdb=" N ALA A1004 " --> pdb=" O GLY A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1056 removed outlier: 4.885A pdb=" N GLU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A1041 " --> pdb=" O TYR A1037 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER A1042 " --> pdb=" O GLN A1038 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS A1043 " --> pdb=" O LYS A1039 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 3.668A 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: 3.564A pdb=" N LEU A1054 " --> pdb=" O ARG A1050 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1063 removed outlier: 3.573A pdb=" N ARG A1060 " --> pdb=" O THR A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1096 removed outlier: 3.691A pdb=" N MET A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.922A 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: 4.280A 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: 3.543A pdb=" N THR B 56 " --> pdb=" O HIS B 52 " (cutoff:3.500A) Proline residue: B 63 - end of helix removed outlier: 3.901A 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: 3.719A 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: 3.803A pdb=" N TYR B 322 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 355 removed outlier: 3.558A 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: 3.895A pdb=" N LEU C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 52 removed outlier: 3.888A pdb=" N ASN C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 92 removed outlier: 3.507A pdb=" N VAL C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 124 removed outlier: 3.821A pdb=" N ASN C 116 " --> pdb=" O GLY C 112 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 124 " --> pdb=" O ASP C 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 53 removed outlier: 3.597A 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: 3.855A pdb=" N ARG D 69 " --> pdb=" O THR D 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 18 removed outlier: 4.176A pdb=" N LYS E 13 " --> pdb=" O GLY E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 72 through 80 Processing helix chain 'E' and resid 141 through 153 removed outlier: 3.811A pdb=" N HIS E 153 " --> pdb=" O ARG E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 216 Processing helix chain 'E' and resid 217 through 222 Proline residue: E 220 - end of helix No H-bonds generated for 'chain 'E' and resid 217 through 222' Processing helix chain 'F' and resid 8 through 20 removed outlier: 4.058A pdb=" N LEU F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 79 Processing helix chain 'F' and resid 141 through 152 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 222 Proline residue: F 220 - end of helix No H-bonds generated for 'chain 'F' and resid 217 through 222' Processing helix chain 'G' and resid 8 through 20 removed outlier: 4.016A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 79 Processing helix chain 'G' and resid 141 through 155 removed outlier: 3.591A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY G 155 " --> pdb=" O LEU G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 222 Proline residue: G 220 - end of helix No H-bonds generated for 'chain 'G' and resid 217 through 222' Processing sheet with id=AA1, first strand: chain 'A' and resid 286 through 291 removed outlier: 6.564A pdb=" N SER A 136 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ALA A 288 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N CYS A 138 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL A 290 " --> pdb=" O CYS A 138 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS A 140 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 100 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A 130 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLN A 98 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP A 265 " --> pdb=" O HIS A 298 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 151 Processing sheet with id=AA3, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.531A pdb=" N GLN A 369 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.715A 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: 6.473A pdb=" N LEU A 313 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 393 " --> pdb=" O MET A 457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 431 through 438 Processing sheet with id=AA5, first strand: chain 'A' and resid 592 through 594 removed outlier: 5.417A pdb=" N PHE A 794 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 6.131A 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: 3.797A pdb=" N TYR A 753 " --> pdb=" O MET A 760 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG A 762 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL A 751 " --> pdb=" O ARG A 762 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 592 through 594 removed outlier: 6.208A pdb=" N TYR A 798 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 7.436A 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: 6.982A 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 'B' and resid 141 through 143 removed outlier: 3.653A pdb=" N GLU B 132 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA B 160 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR B 176 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHE B 162 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 325 through 327 removed outlier: 7.701A pdb=" N PHE B 195 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 241 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU B 197 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU B 243 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL B 199 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N SER C 73 " --> pdb=" O CYS B 447 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS C 75 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL C 79 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS C 58 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE C 103 " --> pdb=" O HIS C 58 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR C 60 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS C 99 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 97 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE C 103 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL C 21 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 332 through 336 removed outlier: 6.614A pdb=" N ARG B 340 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N PHE B 403 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 342 " --> pdb=" O PHE B 403 " (cutoff:3.500A) removed outlier: 3.553A 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=AB3, first strand: chain 'E' and resid 60 through 61 Processing sheet with id=AB4, first strand: chain 'E' and resid 66 through 71 removed outlier: 7.299A pdb=" N GLU E 25 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N MET E 40 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N CYS E 27 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS E 240 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR E 224 " --> pdb=" O LYS E 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 178 through 183 Processing sheet with id=AB6, first strand: chain 'F' and resid 59 through 62 removed outlier: 4.359A pdb=" N VAL F 111 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS G 181 " --> pdb=" O VAL F 111 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP F 113 " --> pdb=" O ASN G 179 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN G 179 " --> pdb=" O ASP F 113 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN G 177 " --> pdb=" O GLU F 115 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 68 through 71 removed outlier: 7.287A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN F 36 " --> pdb=" O ASP F 29 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 178 through 183 Processing sheet with id=AB9, first strand: chain 'G' and resid 59 through 62 removed outlier: 3.646A pdb=" N THR G 59 " --> pdb=" O ARG G 5 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 66 through 71 removed outlier: 7.093A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) 787 hydrogen bonds defined for protein. 2205 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue (no planarity definition) Restraints generated for nucleic acids: 41 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 4.71 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 7991 1.40 - 1.63: 12020 1.63 - 1.85: 187 1.85 - 2.08: 0 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 1.216 0.306 2.00e-02 2.50e+03 2.34e+02 bond pdb=" C4' TTP T 101 " pdb=" O4' TTP T 101 " ideal model delta sigma weight residual 1.426 1.269 0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" C1' DC P 9 " pdb=" N1 DC P 9 " ideal model delta sigma weight residual 1.468 1.567 -0.099 1.40e-02 5.10e+03 5.03e+01 bond pdb=" C1' DC P 3 " pdb=" N1 DC P 3 " ideal model delta sigma weight residual 1.468 1.567 -0.099 1.40e-02 5.10e+03 4.99e+01 bond pdb=" C5 TTP T 101 " pdb=" C6 TTP T 101 " ideal model delta sigma weight residual 1.344 1.477 -0.133 2.00e-02 2.50e+03 4.42e+01 ... (remaining 20205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 26763 2.83 - 5.66: 698 5.66 - 8.50: 125 8.50 - 11.33: 18 11.33 - 14.16: 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 111.28 119.50 -8.22 1.09e+00 8.42e-01 5.69e+01 angle pdb=" N ARG A1098 " pdb=" CA ARG A1098 " pdb=" C ARG A1098 " ideal model delta sigma weight residual 111.36 103.66 7.70 1.09e+00 8.42e-01 4.98e+01 angle pdb=" N GLY A 592 " pdb=" CA GLY A 592 " pdb=" C GLY A 592 " ideal model delta sigma weight residual 110.20 119.03 -8.83 1.32e+00 5.74e-01 4.47e+01 angle pdb=" N ALA A1024 " pdb=" CA ALA A1024 " pdb=" C ALA A1024 " ideal model delta sigma weight residual 111.28 118.49 -7.21 1.09e+00 8.42e-01 4.38e+01 angle pdb=" C PRO A 82 " pdb=" N THR A 83 " pdb=" CA THR A 83 " ideal model delta sigma weight residual 120.94 132.43 -11.49 1.90e+00 2.77e-01 3.66e+01 ... (remaining 27604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.43: 10700 20.43 - 40.87: 1140 40.87 - 61.30: 329 61.30 - 81.74: 26 81.74 - 102.17: 14 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 122.80 137.60 -14.80 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 122.80 136.32 -13.52 0 2.50e+00 1.60e-01 2.93e+01 ... (remaining 12206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2819 0.100 - 0.200: 311 0.200 - 0.299: 18 0.299 - 0.399: 0 0.399 - 0.499: 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 6.22e+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 6.05e+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 -0.41 2.00e-01 2.50e+01 4.10e+00 ... (remaining 3149 not shown) Planarity restraints: 3387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1099 " -0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C PHE A1099 " 0.079 2.00e-02 2.50e+03 pdb=" O PHE A1099 " -0.029 2.00e-02 2.50e+03 pdb=" N AGLY A1100 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1099 " -0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C PHE A1099 " 0.079 2.00e-02 2.50e+03 pdb=" O PHE A1099 " -0.029 2.00e-02 2.50e+03 pdb=" N BGLY A1100 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG T 1 " 0.015 2.00e-02 2.50e+03 1.81e-02 9.80e+00 pdb=" N9 DG T 1 " -0.004 2.00e-02 2.50e+03 pdb=" C8 DG T 1 " 0.017 2.00e-02 2.50e+03 pdb=" N7 DG T 1 " -0.020 2.00e-02 2.50e+03 pdb=" C5 DG T 1 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DG T 1 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG T 1 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG T 1 " 0.011 2.00e-02 2.50e+03 pdb=" C2 DG T 1 " 0.010 2.00e-02 2.50e+03 pdb=" N2 DG T 1 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DG T 1 " -0.051 2.00e-02 2.50e+03 pdb=" C4 DG T 1 " 0.005 2.00e-02 2.50e+03 ... (remaining 3384 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 104 2.52 - 3.12: 12733 3.12 - 3.71: 28833 3.71 - 4.31: 40438 4.31 - 4.90: 67391 Nonbonded interactions: 149499 Sorted by model distance: nonbonded pdb=" C2' DA T 4 " pdb=" C7 DT T 5 " model vdw 1.929 3.860 nonbonded pdb=" CG1 VAL A 861 " pdb=" CD ARG A 985 " model vdw 1.930 3.860 nonbonded pdb=" OE1 GLN B 308 " pdb=" ND2 ASN B 330 " model vdw 1.954 3.120 nonbonded pdb=" O GLN B 308 " pdb=" CB THR B 329 " model vdw 2.044 3.470 nonbonded pdb=" CG1 VAL A 861 " pdb=" NE ARG A 985 " model vdw 2.074 3.540 ... (remaining 149494 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 26.820 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5280 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.306 20219 Z= 0.451 Angle : 1.203 39.355 27627 Z= 0.656 Chirality : 0.063 0.499 3152 Planarity : 0.009 0.075 3387 Dihedral : 18.003 102.172 7707 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.25 % Favored : 93.37 % Rotamer: Outliers : 0.83 % Allowed : 8.79 % Favored : 90.38 % 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: -3.47 (0.15), residues: 2370 helix: -2.39 (0.16), residues: 670 sheet: -0.89 (0.20), residues: 604 loop : -3.09 (0.15), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 276 TYR 0.025 0.003 TYR A 618 PHE 0.032 0.003 PHE A 637 TRP 0.036 0.003 TRP A 344 HIS 0.011 0.002 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00854 / 0.44 (20210) covalent geometry : angle 1.14467 / 0.66 (27609) hydrogen bonds : bond 0.14291 / 9.65 ( 824) hydrogen bonds : angle 6.95882 / 4.87 ( 2287) metal coordination : bond 0.14388 / 7.09 ( 8) metal coordination : angle 14.55625 / 8.22 ( 18) Misc. bond : bond 0.04185 / 2.20 ( 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 673 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 656 time to evaluate : 0.710 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: A 264 ASN cc_start: 0.7196 (t0) cc_final: 0.6911 (t0) REVERT: A 335 ILE cc_start: 0.7523 (pt) cc_final: 0.7234 (pt) REVERT: A 493 ILE cc_start: 0.8616 (mt) cc_final: 0.7646 (pt) REVERT: A 512 CYS cc_start: 0.8192 (t) cc_final: 0.7556 (t) REVERT: A 546 LEU cc_start: 0.6808 (mt) cc_final: 0.6394 (mt) REVERT: A 552 GLN cc_start: 0.7151 (mt0) cc_final: 0.6057 (mt0) REVERT: A 612 MET cc_start: 0.7141 (mtt) cc_final: 0.6712 (mmt) REVERT: A 693 LEU cc_start: 0.8584 (mt) cc_final: 0.8154 (mt) REVERT: A 696 SER cc_start: 0.8531 (m) cc_final: 0.7952 (p) REVERT: A 1010 ASN cc_start: 0.5764 (m110) cc_final: 0.5464 (m-40) REVERT: A 1088 ASP cc_start: 0.8332 (m-30) cc_final: 0.7941 (t0) REVERT: B 46 PHE cc_start: 0.7001 (m-80) cc_final: 0.6597 (m-80) REVERT: B 52 HIS cc_start: 0.8104 (m-70) cc_final: 0.7807 (m-70) REVERT: B 53 ILE cc_start: 0.8781 (mp) cc_final: 0.8323 (mm) REVERT: B 98 PHE cc_start: 0.8060 (t80) cc_final: 0.7856 (t80) REVERT: B 167 ASP cc_start: 0.7828 (m-30) cc_final: 0.7532 (p0) REVERT: B 192 THR cc_start: 0.5882 (m) cc_final: 0.5601 (t) REVERT: B 296 PRO cc_start: 0.7507 (Cg_endo) cc_final: 0.7005 (Cg_exo) REVERT: B 394 ILE cc_start: 0.7729 (mt) cc_final: 0.7472 (pt) REVERT: D 49 LEU cc_start: 0.8526 (mt) cc_final: 0.8181 (mm) REVERT: D 69 ARG cc_start: 0.7825 (ttt90) cc_final: 0.7534 (ttt180) REVERT: E 47 LEU cc_start: 0.7176 (tt) cc_final: 0.6414 (tt) REVERT: E 75 MET cc_start: 0.7607 (tpp) cc_final: 0.7104 (mmm) REVERT: E 116 MET cc_start: 0.5758 (ttt) cc_final: 0.4679 (tpt) REVERT: F 52 LEU cc_start: 0.8779 (mt) cc_final: 0.8564 (mt) REVERT: F 87 ILE cc_start: 0.8266 (mt) cc_final: 0.7877 (mm) REVERT: F 88 ILE cc_start: 0.7034 (mt) cc_final: 0.6292 (mp) REVERT: F 146 ARG cc_start: 0.7327 (mmp80) cc_final: 0.6946 (mmm160) REVERT: G 121 LEU cc_start: 0.4821 (pt) cc_final: 0.4226 (tp) outliers start: 17 outliers final: 2 residues processed: 670 average time/residue: 0.1571 time to fit residues: 153.7882 Evaluate side-chains 351 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 349 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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: 10.0000 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 6.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN A 165 GLN A 285 GLN ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN A 480 HIS A 558 GLN A 565 HIS ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN A 842 ASN A 865 GLN A 880 GLN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 GLN A1094 GLN B 21 ASN B 70 GLN B 184 GLN B 225 GLN B 232 GLN B 285 GLN C 4 GLN C 58 HIS E 246 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN F 125 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN G 204 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.117551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.097669 restraints weight = 107109.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.100071 restraints weight = 73712.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.101782 restraints weight = 53999.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.103024 restraints weight = 41855.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.104028 restraints weight = 33717.959| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3987 r_free = 0.3987 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3987 r_free = 0.3987 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20219 Z= 0.176 Angle : 0.883 30.486 27627 Z= 0.427 Chirality : 0.050 0.236 3152 Planarity : 0.007 0.082 3387 Dihedral : 16.095 86.743 3194 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.63 % Rotamer: Outliers : 0.19 % Allowed : 3.89 % Favored : 95.92 % 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: -2.44 (0.16), residues: 2370 helix: -1.05 (0.19), residues: 665 sheet: -0.39 (0.21), residues: 604 loop : -2.74 (0.16), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 443 TYR 0.022 0.002 TYR A 956 PHE 0.028 0.002 PHE F 215 TRP 0.023 0.002 TRP A1055 HIS 0.007 0.001 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (20210) covalent geometry : angle 0.81709 / 0.43 (27609) hydrogen bonds : bond 0.05401 / 3.59 ( 824) hydrogen bonds : angle 5.87445 / 4.08 ( 2287) metal coordination : bond 0.01971 / 0.98 ( 8) metal coordination : angle 13.11229 / 8.14 ( 18) Misc. bond : bond 0.00173 / 0.09 ( 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 428 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 424 time to evaluate : 0.634 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: A 264 ASN cc_start: 0.7441 (t0) cc_final: 0.6719 (t0) REVERT: A 340 LEU cc_start: 0.8398 (mm) cc_final: 0.8043 (mp) REVERT: A 508 LEU cc_start: 0.9618 (tp) cc_final: 0.9017 (tp) REVERT: A 512 CYS cc_start: 0.8787 (t) cc_final: 0.8402 (m) REVERT: A 612 MET cc_start: 0.7503 (mtt) cc_final: 0.7189 (mmt) REVERT: A 687 ASP cc_start: 0.8579 (t0) cc_final: 0.8249 (m-30) REVERT: A 696 SER cc_start: 0.8395 (m) cc_final: 0.8069 (p) REVERT: A 718 GLN cc_start: 0.8973 (mt0) cc_final: 0.8704 (pt0) REVERT: A 729 GLU cc_start: 0.8699 (mp0) cc_final: 0.8016 (mp0) REVERT: A 760 MET cc_start: 0.7863 (mmp) cc_final: 0.7655 (mmp) REVERT: A 798 TYR cc_start: 0.7917 (m-10) cc_final: 0.7052 (m-10) REVERT: A 848 LEU cc_start: 0.8876 (mp) cc_final: 0.8562 (mp) REVERT: A 1047 LEU cc_start: 0.8812 (mm) cc_final: 0.8476 (mm) REVERT: B 1 MET cc_start: 0.7941 (mmm) cc_final: 0.7549 (mmm) REVERT: B 52 HIS cc_start: 0.8492 (m-70) cc_final: 0.8069 (m170) REVERT: B 92 CYS cc_start: 0.6289 (m) cc_final: 0.5829 (m) REVERT: B 131 ASP cc_start: 0.7303 (p0) cc_final: 0.7004 (p0) REVERT: B 162 PHE cc_start: 0.8447 (t80) cc_final: 0.7770 (t80) REVERT: B 167 ASP cc_start: 0.8418 (m-30) cc_final: 0.7726 (p0) REVERT: B 180 ASP cc_start: 0.5296 (m-30) cc_final: 0.4860 (m-30) REVERT: B 248 LEU cc_start: 0.8198 (pt) cc_final: 0.7877 (pt) REVERT: B 342 LEU cc_start: 0.7561 (tt) cc_final: 0.6848 (mp) REVERT: C 11 ASP cc_start: 0.8745 (t0) cc_final: 0.8375 (t0) REVERT: D 47 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8395 (tm-30) REVERT: D 49 LEU cc_start: 0.8370 (mt) cc_final: 0.8143 (mm) REVERT: D 102 TRP cc_start: 0.8425 (m-10) cc_final: 0.8172 (m-10) REVERT: E 47 LEU cc_start: 0.7281 (tt) cc_final: 0.6566 (tt) REVERT: E 75 MET cc_start: 0.7400 (tpp) cc_final: 0.6794 (tpp) REVERT: E 84 ASN cc_start: 0.7450 (p0) cc_final: 0.7058 (p0) REVERT: E 116 MET cc_start: 0.7363 (ttt) cc_final: 0.6206 (tpt) REVERT: F 70 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7337 (m) REVERT: F 146 ARG cc_start: 0.7484 (mmp80) cc_final: 0.6830 (mmm160) REVERT: F 199 MET cc_start: 0.6302 (tpp) cc_final: 0.5101 (mmm) REVERT: G 17 GLU cc_start: 0.3417 (mm-30) cc_final: 0.2954 (mt-10) outliers start: 4 outliers final: 0 residues processed: 428 average time/residue: 0.1396 time to fit residues: 91.0252 Evaluate side-chains 316 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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: 8.9990 chunk 97 optimal weight: 0.9990 chunk 1 optimal weight: 0.0470 chunk 118 optimal weight: 8.9990 chunk 149 optimal weight: 0.0030 chunk 81 optimal weight: 0.6980 chunk 186 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 182 optimal weight: 8.9990 chunk 6 optimal weight: 0.0980 overall best weight: 0.3488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 GLN A 880 GLN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 HIS D 103 HIS ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 HIS ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.117328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.096665 restraints weight = 108895.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.099137 restraints weight = 74636.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.100890 restraints weight = 54796.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.102277 restraints weight = 42411.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.103306 restraints weight = 34092.752| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3975 r_free = 0.3975 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3975 r_free = 0.3975 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20219 Z= 0.150 Angle : 0.801 27.869 27627 Z= 0.385 Chirality : 0.048 0.402 3152 Planarity : 0.006 0.125 3387 Dihedral : 15.564 79.952 3194 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.86 % Favored : 95.10 % Rotamer: Outliers : 0.10 % Allowed : 3.06 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.16), residues: 2370 helix: -0.48 (0.19), residues: 669 sheet: -0.13 (0.21), residues: 606 loop : -2.43 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 149 TYR 0.023 0.002 TYR C 6 PHE 0.025 0.002 PHE A 479 TRP 0.019 0.001 TRP A1055 HIS 0.011 0.001 HIS E 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (20210) covalent geometry : angle 0.74446 / 0.38 (27609) hydrogen bonds : bond 0.04591 / 3.05 ( 824) hydrogen bonds : angle 5.49743 / 3.81 ( 2287) metal coordination : bond 0.02001 / 1.48 ( 8) metal coordination : angle 11.65622 / 6.97 ( 18) Misc. bond : bond 0.00023 / 0.01 ( 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 395 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 393 time to evaluate : 0.733 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: A 264 ASN cc_start: 0.7396 (t0) cc_final: 0.6652 (t0) REVERT: A 512 CYS cc_start: 0.8849 (t) cc_final: 0.8450 (t) REVERT: A 612 MET cc_start: 0.7810 (mtt) cc_final: 0.7330 (mmt) REVERT: A 687 ASP cc_start: 0.8689 (t0) cc_final: 0.8307 (m-30) REVERT: A 696 SER cc_start: 0.8500 (m) cc_final: 0.8153 (p) REVERT: A 718 GLN cc_start: 0.8927 (mt0) cc_final: 0.8624 (pt0) REVERT: A 801 TYR cc_start: 0.7238 (t80) cc_final: 0.6760 (t80) REVERT: A 867 VAL cc_start: 0.8936 (t) cc_final: 0.8657 (p) REVERT: A 944 PHE cc_start: 0.8587 (t80) cc_final: 0.8108 (t80) REVERT: B 52 HIS cc_start: 0.8467 (m-70) cc_final: 0.7976 (m170) REVERT: B 61 MET cc_start: 0.8345 (mtp) cc_final: 0.8083 (mtp) REVERT: B 90 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8459 (mmmt) REVERT: B 92 CYS cc_start: 0.6433 (m) cc_final: 0.6164 (m) REVERT: B 131 ASP cc_start: 0.7502 (p0) cc_final: 0.6454 (p0) REVERT: B 162 PHE cc_start: 0.8374 (t80) cc_final: 0.7986 (t80) REVERT: B 167 ASP cc_start: 0.8426 (m-30) cc_final: 0.7719 (p0) REVERT: B 200 SER cc_start: 0.7528 (p) cc_final: 0.7025 (t) REVERT: B 243 LEU cc_start: 0.7639 (tp) cc_final: 0.7370 (tp) REVERT: B 249 SER cc_start: 0.8659 (t) cc_final: 0.8456 (p) REVERT: B 342 LEU cc_start: 0.7539 (tt) cc_final: 0.6887 (mp) REVERT: B 360 ASP cc_start: 0.8094 (t70) cc_final: 0.7870 (t70) REVERT: C 11 ASP cc_start: 0.8574 (t0) cc_final: 0.8341 (t0) REVERT: D 47 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8360 (tm-30) REVERT: D 49 LEU cc_start: 0.8409 (mt) cc_final: 0.8166 (mm) REVERT: E 47 LEU cc_start: 0.7110 (tt) cc_final: 0.6647 (tt) REVERT: E 75 MET cc_start: 0.7426 (tpp) cc_final: 0.6529 (ttt) REVERT: E 84 ASN cc_start: 0.7248 (p0) cc_final: 0.6385 (p0) REVERT: E 199 MET cc_start: 0.3128 (mmm) cc_final: 0.2859 (mmt) REVERT: E 226 THR cc_start: 0.4395 (m) cc_final: 0.4187 (m) REVERT: F 139 MET cc_start: 0.7934 (mmt) cc_final: 0.7608 (mmm) REVERT: F 146 ARG cc_start: 0.7437 (mmp80) cc_final: 0.6828 (mmm160) REVERT: F 199 MET cc_start: 0.5159 (tpp) cc_final: 0.4712 (mmm) REVERT: G 38 GLN cc_start: 0.8328 (pm20) cc_final: 0.6918 (tp40) outliers start: 2 outliers final: 1 residues processed: 395 average time/residue: 0.1309 time to fit residues: 80.0789 Evaluate side-chains 304 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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: 7.9990 chunk 202 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 201 optimal weight: 0.0270 chunk 140 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 161 optimal weight: 0.0570 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN A 400 ASN A 411 GLN A 880 GLN ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 GLN A1094 GLN B 250 HIS B 285 GLN ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.113861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.093157 restraints weight = 107682.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.095541 restraints weight = 73945.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.097282 restraints weight = 54477.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.098587 restraints weight = 42399.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.099555 restraints weight = 34364.433| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3914 r_free = 0.3914 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3914 r_free = 0.3914 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 20219 Z= 0.162 Angle : 0.786 27.367 27627 Z= 0.380 Chirality : 0.047 0.204 3152 Planarity : 0.006 0.054 3387 Dihedral : 15.416 81.146 3194 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.90 % Favored : 95.06 % Rotamer: Outliers : 0.10 % Allowed : 3.26 % Favored : 96.65 % 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: -1.51 (0.17), residues: 2370 helix: -0.09 (0.20), residues: 677 sheet: 0.04 (0.21), residues: 605 loop : -2.26 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A 808 TYR 0.022 0.002 TYR A 956 PHE 0.030 0.002 PHE A 479 TRP 0.012 0.002 TRP D 102 HIS 0.009 0.001 HIS E 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (20210) covalent geometry : angle 0.72976 / 0.38 (27609) hydrogen bonds : bond 0.04216 / 2.77 ( 824) hydrogen bonds : angle 5.33246 / 3.69 ( 2287) metal coordination : bond 0.01454 / 1.02 ( 8) metal coordination : angle 11.45964 / 6.85 ( 18) Misc. bond : bond 0.00053 / 0.03 ( 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 374 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 372 time to evaluate : 0.724 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 247 ASN cc_start: 0.7989 (p0) cc_final: 0.7381 (m110) REVERT: A 264 ASN cc_start: 0.7594 (t0) cc_final: 0.6763 (t0) REVERT: A 512 CYS cc_start: 0.8803 (t) cc_final: 0.8399 (t) REVERT: A 612 MET cc_start: 0.8025 (mtt) cc_final: 0.7389 (mmt) REVERT: A 687 ASP cc_start: 0.8738 (t0) cc_final: 0.8285 (m-30) REVERT: A 696 SER cc_start: 0.8418 (m) cc_final: 0.7999 (p) REVERT: A 718 GLN cc_start: 0.8942 (mt0) cc_final: 0.8641 (pt0) REVERT: A 729 GLU cc_start: 0.8702 (mp0) cc_final: 0.8034 (mp0) REVERT: A 801 TYR cc_start: 0.7194 (t80) cc_final: 0.6724 (t80) REVERT: A 944 PHE cc_start: 0.8727 (t80) cc_final: 0.8228 (t80) REVERT: A 1062 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8239 (tm-30) REVERT: B 52 HIS cc_start: 0.8596 (m-70) cc_final: 0.8184 (m170) REVERT: B 61 MET cc_start: 0.8250 (mtp) cc_final: 0.7996 (mtp) REVERT: B 92 CYS cc_start: 0.6700 (m) cc_final: 0.6280 (m) REVERT: B 94 VAL cc_start: 0.7433 (p) cc_final: 0.7223 (p) REVERT: B 162 PHE cc_start: 0.8623 (t80) cc_final: 0.7972 (t80) REVERT: B 167 ASP cc_start: 0.8552 (m-30) cc_final: 0.7880 (p0) REVERT: B 180 ASP cc_start: 0.5491 (m-30) cc_final: 0.5225 (m-30) REVERT: B 200 SER cc_start: 0.7963 (p) cc_final: 0.7515 (t) REVERT: B 243 LEU cc_start: 0.7488 (tp) cc_final: 0.7245 (tp) REVERT: B 278 MET cc_start: 0.9228 (mtm) cc_final: 0.9014 (mtm) REVERT: B 342 LEU cc_start: 0.7713 (tt) cc_final: 0.6841 (mp) REVERT: B 385 TYR cc_start: 0.8749 (t80) cc_final: 0.8382 (t80) REVERT: C 11 ASP cc_start: 0.8676 (t0) cc_final: 0.8321 (t0) REVERT: C 61 TYR cc_start: 0.7306 (m-80) cc_final: 0.6983 (m-80) REVERT: D 47 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8472 (tm-30) REVERT: E 16 LEU cc_start: 0.6712 (tp) cc_final: 0.6449 (pp) REVERT: E 47 LEU cc_start: 0.7146 (tt) cc_final: 0.6150 (tp) REVERT: E 71 ASN cc_start: 0.6630 (m-40) cc_final: 0.5987 (p0) REVERT: E 79 LEU cc_start: 0.8583 (mm) cc_final: 0.8313 (mm) REVERT: E 84 ASN cc_start: 0.6941 (p0) cc_final: 0.6531 (p0) REVERT: E 199 MET cc_start: 0.3218 (mmm) cc_final: 0.2878 (mmt) REVERT: F 124 GLU cc_start: 0.7953 (tp30) cc_final: 0.7398 (tm-30) REVERT: F 146 ARG cc_start: 0.7567 (mmp80) cc_final: 0.7062 (mmm160) REVERT: F 199 MET cc_start: 0.5591 (tpp) cc_final: 0.4550 (mmm) outliers start: 2 outliers final: 0 residues processed: 373 average time/residue: 0.1309 time to fit residues: 76.1529 Evaluate side-chains 286 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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: 8.9990 chunk 75 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS A 283 GLN A 684 GLN A 743 ASN A 948 HIS A 988 HIS ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1066 HIS ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN F 184 GLN F 213 ASN ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.104670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.085570 restraints weight = 110695.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.087522 restraints weight = 78207.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.089003 restraints weight = 58901.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.090093 restraints weight = 46314.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.090971 restraints weight = 37903.554| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.6015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 20219 Z= 0.247 Angle : 0.927 34.502 27627 Z= 0.446 Chirality : 0.051 0.226 3152 Planarity : 0.007 0.098 3387 Dihedral : 15.560 76.361 3194 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.83 % Favored : 94.13 % Rotamer: Outliers : 0.05 % Allowed : 3.79 % Favored : 96.16 % 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: -1.48 (0.17), residues: 2370 helix: -0.20 (0.19), residues: 680 sheet: 0.08 (0.21), residues: 596 loop : -2.14 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 791 TYR 0.026 0.003 TYR A1080 PHE 0.033 0.004 PHE F 144 TRP 0.025 0.003 TRP A 79 HIS 0.012 0.002 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.25 (20210) covalent geometry : angle 0.86400 / 0.45 (27609) hydrogen bonds : bond 0.05130 / 3.38 ( 824) hydrogen bonds : angle 5.58683 / 3.84 ( 2287) metal coordination : bond 0.01537 / 0.95 ( 8) metal coordination : angle 13.21617 / 7.87 ( 18) Misc. bond : bond 0.00069 / 0.04 ( 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 363 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 362 time to evaluate : 0.702 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: A 255 MET cc_start: 0.8818 (ptp) cc_final: 0.8146 (mtm) REVERT: A 264 ASN cc_start: 0.7844 (t0) cc_final: 0.7144 (t0) REVERT: A 316 ASP cc_start: 0.6316 (t0) cc_final: 0.6056 (t0) REVERT: A 340 LEU cc_start: 0.8810 (mm) cc_final: 0.8432 (mp) REVERT: A 512 CYS cc_start: 0.8756 (t) cc_final: 0.8490 (m) REVERT: A 612 MET cc_start: 0.8399 (mtt) cc_final: 0.7774 (mmm) REVERT: A 637 PHE cc_start: 0.6279 (p90) cc_final: 0.5577 (p90) REVERT: A 687 ASP cc_start: 0.8682 (t0) cc_final: 0.8269 (m-30) REVERT: A 696 SER cc_start: 0.8599 (m) cc_final: 0.8165 (p) REVERT: A 867 VAL cc_start: 0.9265 (t) cc_final: 0.9029 (m) REVERT: A 884 THR cc_start: 0.6600 (t) cc_final: 0.6396 (t) REVERT: A 928 SER cc_start: 0.8305 (t) cc_final: 0.8026 (t) REVERT: A 944 PHE cc_start: 0.8814 (t80) cc_final: 0.8420 (t80) REVERT: A 955 GLN cc_start: 0.9300 (mm110) cc_final: 0.8736 (pm20) REVERT: A 1050 ARG cc_start: 0.8709 (mtm-85) cc_final: 0.8382 (ptp90) REVERT: B 52 HIS cc_start: 0.8716 (m-70) cc_final: 0.8218 (m170) REVERT: B 61 MET cc_start: 0.8500 (mtp) cc_final: 0.8252 (mtp) REVERT: B 92 CYS cc_start: 0.6885 (m) cc_final: 0.6313 (m) REVERT: B 94 VAL cc_start: 0.7802 (p) cc_final: 0.7537 (p) REVERT: B 99 LYS cc_start: 0.9187 (tttp) cc_final: 0.8932 (tptt) REVERT: B 101 MET cc_start: 0.7652 (mmm) cc_final: 0.6775 (mmm) REVERT: B 131 ASP cc_start: 0.8553 (p0) cc_final: 0.7889 (p0) REVERT: B 162 PHE cc_start: 0.8627 (t80) cc_final: 0.7902 (t80) REVERT: B 167 ASP cc_start: 0.8424 (m-30) cc_final: 0.8082 (t0) REVERT: B 180 ASP cc_start: 0.5277 (m-30) cc_final: 0.4875 (m-30) REVERT: B 200 SER cc_start: 0.8353 (p) cc_final: 0.7784 (t) REVERT: B 278 MET cc_start: 0.9258 (mtm) cc_final: 0.8862 (mpp) REVERT: B 342 LEU cc_start: 0.7827 (tt) cc_final: 0.7075 (mp) REVERT: B 360 ASP cc_start: 0.8794 (t0) cc_final: 0.8523 (t0) REVERT: B 385 TYR cc_start: 0.8902 (t80) cc_final: 0.8380 (t80) REVERT: C 11 ASP cc_start: 0.8702 (t0) cc_final: 0.8313 (t0) REVERT: C 36 GLN cc_start: 0.8923 (tt0) cc_final: 0.8600 (tp40) REVERT: D 107 LEU cc_start: 0.8720 (pp) cc_final: 0.8384 (mp) REVERT: E 84 ASN cc_start: 0.6895 (p0) cc_final: 0.6537 (p0) REVERT: E 199 MET cc_start: 0.3256 (mmm) cc_final: 0.2988 (mmt) REVERT: F 146 ARG cc_start: 0.7662 (mmp80) cc_final: 0.7024 (mmm160) outliers start: 1 outliers final: 0 residues processed: 362 average time/residue: 0.1360 time to fit residues: 76.3467 Evaluate side-chains 272 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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: 2.9990 chunk 104 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 236 optimal weight: 0.7980 chunk 179 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN B 285 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN F 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.102001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.082478 restraints weight = 111076.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.084418 restraints weight = 78251.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.085893 restraints weight = 58765.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.086981 restraints weight = 46303.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.087865 restraints weight = 37927.119| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 20219 Z= 0.202 Angle : 0.845 34.269 27627 Z= 0.405 Chirality : 0.048 0.238 3152 Planarity : 0.006 0.086 3387 Dihedral : 15.619 82.366 3194 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.10 % Allowed : 1.99 % Favored : 97.91 % 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: -1.36 (0.17), residues: 2370 helix: -0.06 (0.19), residues: 672 sheet: 0.07 (0.21), residues: 598 loop : -2.03 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 985 TYR 0.027 0.002 TYR C 6 PHE 0.038 0.003 PHE B 299 TRP 0.020 0.002 TRP A 79 HIS 0.010 0.002 HIS E 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (20210) covalent geometry : angle 0.78495 / 0.40 (27609) hydrogen bonds : bond 0.04351 / 2.91 ( 824) hydrogen bonds : angle 5.42499 / 3.74 ( 2287) metal coordination : bond 0.01412 / 0.83 ( 8) metal coordination : angle 12.32691 / 7.22 ( 18) Misc. bond : bond 0.00087 / 0.05 ( 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 357 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 355 time to evaluate : 0.549 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 340 LEU cc_start: 0.8920 (mm) cc_final: 0.8521 (mp) REVERT: A 461 GLN cc_start: 0.6983 (mp10) cc_final: 0.6589 (mp10) REVERT: A 508 LEU cc_start: 0.9513 (tp) cc_final: 0.9290 (tp) REVERT: A 517 TYR cc_start: 0.9213 (t80) cc_final: 0.8727 (t80) REVERT: A 527 MET cc_start: 0.9271 (pmm) cc_final: 0.8762 (pmm) REVERT: A 564 MET cc_start: 0.7639 (ptm) cc_final: 0.7404 (ptm) REVERT: A 611 MET cc_start: 0.8709 (mtm) cc_final: 0.8152 (ppp) REVERT: A 612 MET cc_start: 0.8630 (mtt) cc_final: 0.7290 (mtt) REVERT: A 660 LEU cc_start: 0.9129 (mt) cc_final: 0.8747 (mt) REVERT: A 687 ASP cc_start: 0.8765 (t0) cc_final: 0.8217 (m-30) REVERT: A 696 SER cc_start: 0.8648 (m) cc_final: 0.8251 (p) REVERT: A 798 TYR cc_start: 0.7885 (m-10) cc_final: 0.7096 (m-80) REVERT: A 867 VAL cc_start: 0.9406 (t) cc_final: 0.9196 (m) REVERT: A 940 GLU cc_start: 0.8415 (tp30) cc_final: 0.8157 (tp30) REVERT: A 955 GLN cc_start: 0.9318 (mm110) cc_final: 0.8781 (pm20) REVERT: A 1050 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8383 (ptp90) REVERT: A 1054 LEU cc_start: 0.9321 (mt) cc_final: 0.9117 (mt) REVERT: A 1065 LEU cc_start: 0.9233 (mm) cc_final: 0.8540 (mm) REVERT: A 1066 HIS cc_start: 0.8413 (m90) cc_final: 0.7993 (t-90) REVERT: B 45 SER cc_start: 0.9484 (t) cc_final: 0.9158 (m) REVERT: B 52 HIS cc_start: 0.8556 (m-70) cc_final: 0.8172 (m170) REVERT: B 90 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8248 (mmmt) REVERT: B 92 CYS cc_start: 0.7140 (m) cc_final: 0.6529 (m) REVERT: B 99 LYS cc_start: 0.9396 (tttp) cc_final: 0.8511 (tppt) REVERT: B 131 ASP cc_start: 0.8230 (p0) cc_final: 0.7940 (m-30) REVERT: B 162 PHE cc_start: 0.8670 (t80) cc_final: 0.7923 (t80) REVERT: B 167 ASP cc_start: 0.8613 (m-30) cc_final: 0.8218 (t0) REVERT: B 180 ASP cc_start: 0.5443 (m-30) cc_final: 0.4934 (m-30) REVERT: B 200 SER cc_start: 0.8129 (p) cc_final: 0.7867 (t) REVERT: B 233 CYS cc_start: 0.9119 (t) cc_final: 0.8876 (m) REVERT: B 278 MET cc_start: 0.9382 (mtm) cc_final: 0.8956 (mtm) REVERT: B 333 GLN cc_start: 0.8065 (mt0) cc_final: 0.7693 (tp40) REVERT: B 342 LEU cc_start: 0.7548 (tt) cc_final: 0.7084 (mp) REVERT: B 360 ASP cc_start: 0.8866 (t0) cc_final: 0.8590 (t0) REVERT: B 385 TYR cc_start: 0.8889 (t80) cc_final: 0.8441 (t80) REVERT: C 11 ASP cc_start: 0.8740 (t0) cc_final: 0.8331 (t0) REVERT: C 32 VAL cc_start: 0.8205 (m) cc_final: 0.7912 (m) REVERT: C 36 GLN cc_start: 0.8994 (tt0) cc_final: 0.8576 (tp40) REVERT: E 47 LEU cc_start: 0.7069 (tp) cc_final: 0.6224 (tp) REVERT: E 75 MET cc_start: 0.6229 (tpp) cc_final: 0.6023 (mtt) REVERT: E 84 ASN cc_start: 0.6941 (p0) cc_final: 0.6624 (p0) REVERT: F 146 ARG cc_start: 0.7829 (mmp80) cc_final: 0.7260 (mmm160) REVERT: F 199 MET cc_start: 0.6226 (mmm) cc_final: 0.5180 (mmm) outliers start: 2 outliers final: 0 residues processed: 355 average time/residue: 0.1260 time to fit residues: 69.7186 Evaluate side-chains 267 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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: 10.0000 chunk 75 optimal weight: 0.5980 chunk 207 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 159 optimal weight: 0.2980 chunk 205 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN C 35 ASN C 116 ASN D 68 GLN ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN F 179 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.103272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.083596 restraints weight = 110222.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.085559 restraints weight = 77443.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.087017 restraints weight = 58227.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.088113 restraints weight = 45805.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.088981 restraints weight = 37840.977| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.6927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 20219 Z= 0.139 Angle : 0.782 35.414 27627 Z= 0.369 Chirality : 0.046 0.198 3152 Planarity : 0.006 0.082 3387 Dihedral : 15.444 82.670 3194 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.10 % Allowed : 1.60 % Favored : 98.30 % 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: -1.17 (0.17), residues: 2370 helix: 0.16 (0.20), residues: 674 sheet: 0.10 (0.21), residues: 593 loop : -1.90 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 218 TYR 0.028 0.002 TYR C 6 PHE 0.026 0.002 PHE A 135 TRP 0.017 0.001 TRP D 56 HIS 0.008 0.001 HIS E 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (20210) covalent geometry : angle 0.71991 / 0.37 (27609) hydrogen bonds : bond 0.04013 / 2.64 ( 824) hydrogen bonds : angle 5.21437 / 3.58 ( 2287) metal coordination : bond 0.01297 / 0.94 ( 8) metal coordination : angle 11.97667 / 7.17 ( 18) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 349 time to evaluate : 0.654 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: A 264 ASN cc_start: 0.8093 (t0) cc_final: 0.7569 (t0) REVERT: A 340 LEU cc_start: 0.8863 (mm) cc_final: 0.8584 (mt) REVERT: A 451 MET cc_start: 0.7070 (tpt) cc_final: 0.6433 (tpp) REVERT: A 459 MET cc_start: 0.8777 (pmm) cc_final: 0.8386 (pmm) REVERT: A 461 GLN cc_start: 0.7029 (mp10) cc_final: 0.6797 (mp10) REVERT: A 512 CYS cc_start: 0.8562 (t) cc_final: 0.8198 (t) REVERT: A 517 TYR cc_start: 0.8926 (t80) cc_final: 0.8483 (t80) REVERT: A 535 MET cc_start: 0.8842 (ttt) cc_final: 0.8101 (mmp) REVERT: A 611 MET cc_start: 0.8785 (mtm) cc_final: 0.8085 (ppp) REVERT: A 612 MET cc_start: 0.8595 (mtt) cc_final: 0.7267 (mtt) REVERT: A 660 LEU cc_start: 0.9134 (mt) cc_final: 0.8784 (mt) REVERT: A 687 ASP cc_start: 0.8704 (t0) cc_final: 0.8289 (m-30) REVERT: A 696 SER cc_start: 0.8701 (m) cc_final: 0.8274 (p) REVERT: A 711 LEU cc_start: 0.8881 (tp) cc_final: 0.8621 (tp) REVERT: A 729 GLU cc_start: 0.8704 (mp0) cc_final: 0.8050 (mp0) REVERT: A 738 LYS cc_start: 0.8601 (tptp) cc_final: 0.8272 (tttt) REVERT: A 801 TYR cc_start: 0.7369 (t80) cc_final: 0.6774 (t80) REVERT: A 867 VAL cc_start: 0.9401 (t) cc_final: 0.9091 (m) REVERT: A 889 ARG cc_start: 0.8406 (mmp-170) cc_final: 0.7825 (mtm180) REVERT: A 955 GLN cc_start: 0.9312 (mm110) cc_final: 0.8776 (pm20) REVERT: A 1065 LEU cc_start: 0.9143 (mm) cc_final: 0.8469 (mm) REVERT: A 1066 HIS cc_start: 0.8292 (m90) cc_final: 0.8081 (t-90) REVERT: B 45 SER cc_start: 0.9483 (t) cc_final: 0.9052 (p) REVERT: B 52 HIS cc_start: 0.8440 (m-70) cc_final: 0.8114 (m170) REVERT: B 92 CYS cc_start: 0.7138 (m) cc_final: 0.6617 (m) REVERT: B 162 PHE cc_start: 0.8567 (t80) cc_final: 0.8183 (t80) REVERT: B 167 ASP cc_start: 0.8683 (m-30) cc_final: 0.8256 (t0) REVERT: B 180 ASP cc_start: 0.5582 (m-30) cc_final: 0.5176 (m-30) REVERT: B 200 SER cc_start: 0.8098 (p) cc_final: 0.7690 (t) REVERT: B 233 CYS cc_start: 0.9111 (t) cc_final: 0.8865 (m) REVERT: B 246 ASN cc_start: 0.8362 (m-40) cc_final: 0.8150 (m-40) REVERT: B 333 GLN cc_start: 0.8164 (mt0) cc_final: 0.7933 (tp-100) REVERT: B 360 ASP cc_start: 0.8851 (t0) cc_final: 0.8614 (t0) REVERT: B 385 TYR cc_start: 0.8873 (t80) cc_final: 0.8418 (t80) REVERT: B 438 CYS cc_start: 0.8645 (m) cc_final: 0.7514 (t) REVERT: C 11 ASP cc_start: 0.8713 (t0) cc_final: 0.8256 (t0) REVERT: C 36 GLN cc_start: 0.8951 (tt0) cc_final: 0.8606 (tp40) REVERT: C 59 VAL cc_start: 0.6533 (m) cc_final: 0.6093 (p) REVERT: C 61 TYR cc_start: 0.7420 (m-80) cc_final: 0.7159 (m-80) REVERT: E 84 ASN cc_start: 0.7199 (p0) cc_final: 0.6900 (p0) REVERT: F 146 ARG cc_start: 0.7664 (mmp80) cc_final: 0.7362 (mmm160) REVERT: F 199 MET cc_start: 0.6235 (mmm) cc_final: 0.5218 (mmm) REVERT: G 57 PHE cc_start: 0.4286 (m-10) cc_final: 0.4061 (m-10) REVERT: G 229 MET cc_start: 0.3931 (pmm) cc_final: 0.2836 (pmm) outliers start: 2 outliers final: 0 residues processed: 350 average time/residue: 0.1297 time to fit residues: 70.7776 Evaluate side-chains 277 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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: 0.5980 chunk 11 optimal weight: 0.4980 chunk 145 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 138 optimal weight: 0.0370 chunk 232 optimal weight: 0.0030 chunk 156 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.3868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1021 HIS ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN G 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.103986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.084467 restraints weight = 109623.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.086448 restraints weight = 76684.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.087942 restraints weight = 57367.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.088997 restraints weight = 45101.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.089904 restraints weight = 36997.925| |-----------------------------------------------------------------------------| 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) = 0.089 | | 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) = 0.089 | | 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: 0.7007 moved from start: 0.7058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20219 Z= 0.133 Angle : 0.785 34.758 27627 Z= 0.369 Chirality : 0.046 0.266 3152 Planarity : 0.006 0.079 3387 Dihedral : 15.332 83.229 3194 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.05 % Allowed : 1.17 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.17), residues: 2370 helix: 0.24 (0.20), residues: 662 sheet: 0.09 (0.21), residues: 592 loop : -1.84 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 62 TYR 0.029 0.002 TYR A 956 PHE 0.028 0.002 PHE A 786 TRP 0.018 0.001 TRP D 56 HIS 0.010 0.001 HIS E 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (20210) covalent geometry : angle 0.72578 / 0.37 (27609) hydrogen bonds : bond 0.03841 / 2.54 ( 824) hydrogen bonds : angle 5.09849 / 3.49 ( 2287) metal coordination : bond 0.01402 / 1.00 ( 8) metal coordination : angle 11.70549 / 6.99 ( 18) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 352 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ASN cc_start: 0.7999 (t0) cc_final: 0.7496 (t0) REVERT: A 317 ILE cc_start: 0.7886 (pt) cc_final: 0.7556 (pt) REVERT: A 340 LEU cc_start: 0.8850 (mm) cc_final: 0.8649 (mt) REVERT: A 451 MET cc_start: 0.6913 (tpt) cc_final: 0.6237 (tpp) REVERT: A 459 MET cc_start: 0.8727 (pmm) cc_final: 0.8389 (pmm) REVERT: A 461 GLN cc_start: 0.7010 (mp10) cc_final: 0.6619 (mp10) REVERT: A 517 TYR cc_start: 0.9084 (t80) cc_final: 0.8649 (t80) REVERT: A 535 MET cc_start: 0.8844 (ttt) cc_final: 0.8081 (mmp) REVERT: A 611 MET cc_start: 0.8759 (mtm) cc_final: 0.8057 (ppp) REVERT: A 612 MET cc_start: 0.8540 (mtt) cc_final: 0.7186 (mtt) REVERT: A 660 LEU cc_start: 0.9111 (mt) cc_final: 0.8763 (mt) REVERT: A 687 ASP cc_start: 0.8722 (t0) cc_final: 0.8335 (m-30) REVERT: A 696 SER cc_start: 0.8703 (m) cc_final: 0.8261 (p) REVERT: A 711 LEU cc_start: 0.8873 (tp) cc_final: 0.8629 (tp) REVERT: A 729 GLU cc_start: 0.8816 (mp0) cc_final: 0.8212 (mp0) REVERT: A 738 LYS cc_start: 0.8516 (tptp) cc_final: 0.8225 (tttt) REVERT: A 801 TYR cc_start: 0.7273 (t80) cc_final: 0.6663 (t80) REVERT: A 867 VAL cc_start: 0.9382 (t) cc_final: 0.9027 (m) REVERT: A 889 ARG cc_start: 0.8317 (mmp-170) cc_final: 0.8025 (mtm180) REVERT: A 918 LEU cc_start: 0.8449 (mm) cc_final: 0.7830 (tp) REVERT: A 955 GLN cc_start: 0.9300 (mm110) cc_final: 0.8761 (pm20) REVERT: A 1065 LEU cc_start: 0.9121 (mm) cc_final: 0.8431 (mm) REVERT: A 1066 HIS cc_start: 0.8224 (m90) cc_final: 0.8014 (t-90) REVERT: B 45 SER cc_start: 0.9377 (t) cc_final: 0.9011 (p) REVERT: B 52 HIS cc_start: 0.8400 (m-70) cc_final: 0.8054 (m170) REVERT: B 92 CYS cc_start: 0.7134 (m) cc_final: 0.6525 (m) REVERT: B 162 PHE cc_start: 0.8481 (t80) cc_final: 0.8095 (t80) REVERT: B 167 ASP cc_start: 0.8630 (m-30) cc_final: 0.8246 (t0) REVERT: B 200 SER cc_start: 0.8008 (p) cc_final: 0.7724 (t) REVERT: B 233 CYS cc_start: 0.9032 (t) cc_final: 0.8830 (m) REVERT: B 278 MET cc_start: 0.9319 (mtm) cc_final: 0.8820 (mpp) REVERT: B 333 GLN cc_start: 0.8260 (mt0) cc_final: 0.7954 (tp-100) REVERT: B 360 ASP cc_start: 0.8872 (t0) cc_final: 0.8656 (t0) REVERT: B 385 TYR cc_start: 0.8835 (t80) cc_final: 0.8418 (t80) REVERT: B 438 CYS cc_start: 0.8612 (m) cc_final: 0.7497 (t) REVERT: C 11 ASP cc_start: 0.8688 (t0) cc_final: 0.8209 (t0) REVERT: C 36 GLN cc_start: 0.8930 (tt0) cc_final: 0.8627 (tp40) REVERT: C 59 VAL cc_start: 0.6572 (m) cc_final: 0.6117 (p) REVERT: C 61 TYR cc_start: 0.7432 (m-80) cc_final: 0.7224 (m-80) REVERT: E 16 LEU cc_start: 0.6904 (tp) cc_final: 0.6422 (pp) REVERT: E 84 ASN cc_start: 0.7030 (p0) cc_final: 0.6732 (p0) REVERT: F 146 ARG cc_start: 0.7668 (mmp80) cc_final: 0.7237 (mmm160) REVERT: F 199 MET cc_start: 0.6249 (mmm) cc_final: 0.5308 (mmm) REVERT: F 235 LEU cc_start: 0.8291 (tp) cc_final: 0.7990 (tp) REVERT: G 229 MET cc_start: 0.3935 (pmm) cc_final: 0.2869 (pmm) outliers start: 1 outliers final: 0 residues processed: 352 average time/residue: 0.1328 time to fit residues: 72.9741 Evaluate side-chains 274 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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: 3.9990 chunk 175 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 chunk 234 optimal weight: 0.4980 chunk 167 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 212 optimal weight: 8.9990 chunk 80 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 GLN C 35 ASN ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN G 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.101835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.082327 restraints weight = 110225.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.084287 restraints weight = 77030.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.085724 restraints weight = 57495.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.086830 restraints weight = 45325.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.087645 restraints weight = 37123.000| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.7416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20219 Z= 0.155 Angle : 0.797 34.547 27627 Z= 0.379 Chirality : 0.046 0.185 3152 Planarity : 0.006 0.071 3387 Dihedral : 15.280 86.836 3194 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.05 % Allowed : 0.87 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.17), residues: 2370 helix: 0.16 (0.20), residues: 675 sheet: 0.13 (0.21), residues: 604 loop : -1.89 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG B 354 TYR 0.033 0.002 TYR A 956 PHE 0.025 0.002 PHE B 316 TRP 0.019 0.002 TRP E 28 HIS 0.011 0.001 HIS A1021 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (20210) covalent geometry : angle 0.73770 / 0.38 (27609) hydrogen bonds : bond 0.04115 / 2.69 ( 824) hydrogen bonds : angle 5.20391 / 3.55 ( 2287) metal coordination : bond 0.01252 / 0.84 ( 8) metal coordination : angle 11.89236 / 7.05 ( 18) Misc. bond : bond 0.00056 / 0.03 ( 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 347 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 0.474 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: A 317 ILE cc_start: 0.8105 (pt) cc_final: 0.7898 (pt) REVERT: A 340 LEU cc_start: 0.8983 (mm) cc_final: 0.8588 (mp) REVERT: A 451 MET cc_start: 0.7117 (tpt) cc_final: 0.6356 (tpp) REVERT: A 461 GLN cc_start: 0.7553 (mp10) cc_final: 0.7053 (mp10) REVERT: A 517 TYR cc_start: 0.9210 (t80) cc_final: 0.8836 (t80) REVERT: A 523 LEU cc_start: 0.9554 (pp) cc_final: 0.9323 (pp) REVERT: A 535 MET cc_start: 0.8935 (ttt) cc_final: 0.8080 (mmp) REVERT: A 611 MET cc_start: 0.8898 (mtm) cc_final: 0.8182 (ppp) REVERT: A 612 MET cc_start: 0.8707 (mtt) cc_final: 0.7420 (mtt) REVERT: A 660 LEU cc_start: 0.9145 (mt) cc_final: 0.8806 (mt) REVERT: A 696 SER cc_start: 0.8677 (m) cc_final: 0.8194 (p) REVERT: A 711 LEU cc_start: 0.8929 (tp) cc_final: 0.8657 (tp) REVERT: A 729 GLU cc_start: 0.8881 (mp0) cc_final: 0.8303 (mp0) REVERT: A 738 LYS cc_start: 0.8636 (tptp) cc_final: 0.8280 (tttt) REVERT: A 801 TYR cc_start: 0.7272 (t80) cc_final: 0.6549 (t80) REVERT: A 867 VAL cc_start: 0.9400 (t) cc_final: 0.9063 (m) REVERT: A 889 ARG cc_start: 0.8364 (mmp-170) cc_final: 0.7958 (mtm180) REVERT: A 955 GLN cc_start: 0.9312 (mm110) cc_final: 0.8801 (pm20) REVERT: A 1044 LEU cc_start: 0.9008 (mt) cc_final: 0.8785 (mp) REVERT: A 1065 LEU cc_start: 0.9126 (mm) cc_final: 0.8385 (mm) REVERT: B 1 MET cc_start: 0.8716 (tpp) cc_final: 0.8440 (tpp) REVERT: B 45 SER cc_start: 0.9489 (t) cc_final: 0.9074 (p) REVERT: B 52 HIS cc_start: 0.8461 (m-70) cc_final: 0.8106 (m170) REVERT: B 92 CYS cc_start: 0.7331 (m) cc_final: 0.6816 (m) REVERT: B 167 ASP cc_start: 0.8663 (m-30) cc_final: 0.8304 (t0) REVERT: B 180 ASP cc_start: 0.5237 (m-30) cc_final: 0.4827 (m-30) REVERT: B 200 SER cc_start: 0.8227 (p) cc_final: 0.7951 (t) REVERT: B 278 MET cc_start: 0.9262 (mtm) cc_final: 0.8838 (mpp) REVERT: B 296 PRO cc_start: 0.8189 (Cg_exo) cc_final: 0.7917 (Cg_endo) REVERT: B 360 ASP cc_start: 0.8941 (t0) cc_final: 0.8659 (t0) REVERT: B 385 TYR cc_start: 0.8862 (t80) cc_final: 0.8403 (t80) REVERT: B 438 CYS cc_start: 0.8724 (m) cc_final: 0.7684 (t) REVERT: C 11 ASP cc_start: 0.8775 (t0) cc_final: 0.8311 (t0) REVERT: C 36 GLN cc_start: 0.8978 (tt0) cc_final: 0.8583 (tp40) REVERT: C 59 VAL cc_start: 0.7025 (m) cc_final: 0.6576 (p) REVERT: E 16 LEU cc_start: 0.6319 (tp) cc_final: 0.5861 (pp) REVERT: E 71 ASN cc_start: 0.6431 (m-40) cc_final: 0.6139 (p0) REVERT: E 84 ASN cc_start: 0.6909 (p0) cc_final: 0.6588 (p0) REVERT: F 146 ARG cc_start: 0.7719 (mmp80) cc_final: 0.7321 (mmm160) REVERT: F 199 MET cc_start: 0.6315 (mmm) cc_final: 0.5461 (mmm) REVERT: G 229 MET cc_start: 0.3865 (pmm) cc_final: 0.2807 (pmm) outliers start: 1 outliers final: 0 residues processed: 346 average time/residue: 0.1265 time to fit residues: 69.1055 Evaluate side-chains 268 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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: 0.0050 chunk 190 optimal weight: 0.3980 chunk 233 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 240 optimal weight: 10.0000 chunk 223 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 overall best weight: 1.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 333 GLN C 35 ASN ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 HIS F 38 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.100161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.080748 restraints weight = 111052.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.082681 restraints weight = 77479.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.084089 restraints weight = 57959.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.085164 restraints weight = 45790.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.086016 restraints weight = 37580.960| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3673 r_free = 0.3673 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3673 r_free = 0.3673 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.7792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20219 Z= 0.159 Angle : 0.802 34.027 27627 Z= 0.382 Chirality : 0.047 0.181 3152 Planarity : 0.006 0.074 3387 Dihedral : 15.304 89.690 3194 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.10 % Allowed : 0.19 % Favored : 99.71 % 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: -1.14 (0.17), residues: 2370 helix: 0.23 (0.20), residues: 669 sheet: 0.04 (0.21), residues: 604 loop : -1.88 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 66 TYR 0.034 0.002 TYR A 956 PHE 0.025 0.002 PHE B 316 TRP 0.023 0.002 TRP E 28 HIS 0.011 0.002 HIS A1021 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (20210) covalent geometry : angle 0.74502 / 0.38 (27609) hydrogen bonds : bond 0.04090 / 2.66 ( 824) hydrogen bonds : angle 5.22533 / 3.56 ( 2287) metal coordination : bond 0.01305 / 0.86 ( 8) metal coordination : angle 11.63147 / 6.87 ( 18) Misc. bond : bond 0.00080 / 0.04 ( 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 345 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 343 time to evaluate : 0.771 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: A 98 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8350 (pp30) REVERT: A 340 LEU cc_start: 0.8984 (mm) cc_final: 0.8625 (mp) REVERT: A 396 TYR cc_start: 0.5370 (t80) cc_final: 0.5046 (t80) REVERT: A 451 MET cc_start: 0.7102 (tpt) cc_final: 0.6385 (tpp) REVERT: A 459 MET cc_start: 0.8756 (pmm) cc_final: 0.8455 (pmm) REVERT: A 461 GLN cc_start: 0.7582 (mp10) cc_final: 0.7235 (mp10) REVERT: A 508 LEU cc_start: 0.9486 (tp) cc_final: 0.9262 (tp) REVERT: A 517 TYR cc_start: 0.9237 (t80) cc_final: 0.8880 (t80) REVERT: A 535 MET cc_start: 0.8957 (ttt) cc_final: 0.8089 (mmp) REVERT: A 611 MET cc_start: 0.8854 (mtm) cc_final: 0.8206 (ppp) REVERT: A 612 MET cc_start: 0.8859 (mtt) cc_final: 0.7533 (mtt) REVERT: A 660 LEU cc_start: 0.9162 (mt) cc_final: 0.8676 (mt) REVERT: A 711 LEU cc_start: 0.8942 (tp) cc_final: 0.8663 (tp) REVERT: A 729 GLU cc_start: 0.8902 (mp0) cc_final: 0.8349 (mp0) REVERT: A 738 LYS cc_start: 0.8675 (tptp) cc_final: 0.8302 (tttt) REVERT: A 801 TYR cc_start: 0.7380 (t80) cc_final: 0.6663 (t80) REVERT: A 867 VAL cc_start: 0.9423 (t) cc_final: 0.9086 (m) REVERT: A 955 GLN cc_start: 0.9331 (mm110) cc_final: 0.8825 (pm20) REVERT: A 1050 ARG cc_start: 0.8688 (mtm-85) cc_final: 0.8361 (mtp180) REVERT: A 1054 LEU cc_start: 0.9300 (mt) cc_final: 0.9053 (mt) REVERT: A 1067 GLU cc_start: 0.7739 (mp0) cc_final: 0.6940 (tp30) REVERT: B 45 SER cc_start: 0.9399 (t) cc_final: 0.9058 (p) REVERT: B 52 HIS cc_start: 0.8589 (m-70) cc_final: 0.8054 (m170) REVERT: B 162 PHE cc_start: 0.8670 (t80) cc_final: 0.8189 (t80) REVERT: B 167 ASP cc_start: 0.8725 (m-30) cc_final: 0.8385 (t0) REVERT: B 180 ASP cc_start: 0.5741 (m-30) cc_final: 0.5366 (m-30) REVERT: B 249 SER cc_start: 0.8967 (t) cc_final: 0.8593 (p) REVERT: B 278 MET cc_start: 0.9214 (mtm) cc_final: 0.8829 (mtm) REVERT: B 360 ASP cc_start: 0.8934 (t0) cc_final: 0.8667 (t0) REVERT: B 385 TYR cc_start: 0.8907 (t80) cc_final: 0.8472 (t80) REVERT: B 393 PHE cc_start: 0.8642 (m-80) cc_final: 0.8421 (m-80) REVERT: C 11 ASP cc_start: 0.8805 (t0) cc_final: 0.8341 (t0) REVERT: C 36 GLN cc_start: 0.9003 (tt0) cc_final: 0.8641 (tp40) REVERT: E 71 ASN cc_start: 0.6429 (m-40) cc_final: 0.6119 (p0) REVERT: E 84 ASN cc_start: 0.7035 (p0) cc_final: 0.6748 (p0) REVERT: F 97 ASP cc_start: 0.8297 (p0) cc_final: 0.8095 (p0) REVERT: F 144 PHE cc_start: 0.7020 (m-80) cc_final: 0.6800 (m-80) REVERT: F 146 ARG cc_start: 0.7752 (mmp80) cc_final: 0.7359 (mmm160) REVERT: F 199 MET cc_start: 0.6478 (mmm) cc_final: 0.5687 (mmm) outliers start: 2 outliers final: 0 residues processed: 344 average time/residue: 0.1289 time to fit residues: 69.7077 Evaluate side-chains 270 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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: 7.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 168 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 212 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 232 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 GLN B 8 GLN ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN ** E 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 HIS F 38 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.100075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.080981 restraints weight = 112165.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.082834 restraints weight = 78692.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.084222 restraints weight = 59172.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.085280 restraints weight = 46676.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.086150 restraints weight = 38326.348| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.8006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20219 Z= 0.147 Angle : 0.790 34.592 27627 Z= 0.375 Chirality : 0.047 0.227 3152 Planarity : 0.006 0.075 3387 Dihedral : 15.279 89.747 3194 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % 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: -1.16 (0.17), residues: 2370 helix: 0.14 (0.20), residues: 670 sheet: 0.05 (0.21), residues: 603 loop : -1.84 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 354 TYR 0.036 0.002 TYR A 956 PHE 0.024 0.002 PHE B 162 TRP 0.021 0.002 TRP D 102 HIS 0.011 0.001 HIS A1021 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (20210) covalent geometry : angle 0.73242 / 0.37 (27609) hydrogen bonds : bond 0.04015 / 2.61 ( 824) hydrogen bonds : angle 5.21995 / 3.56 ( 2287) metal coordination : bond 0.01242 / 0.86 ( 8) metal coordination : angle 11.63992 / 6.89 ( 18) Misc. bond : bond 0.00072 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3755.43 seconds wall clock time: 65 minutes 34.77 seconds (3934.77 seconds total)