Starting phenix.real_space_refine on Thu Aug 6 11:35:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h0i_34412/08_2026/8h0i_34412.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h0i_34412/08_2026/8h0i_34412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h0i_34412/08_2026/8h0i_34412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h0i_34412/08_2026/8h0i_34412.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h0i_34412/08_2026/8h0i_34412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h0i_34412/08_2026/8h0i_34412.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8h0i_34412/08_2026/8h0i_34412.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h0i_34412/08_2026/8h0i_34412.cif" } resolution = 2.8 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 36 5.49 5 S 80 5.16 5 Cl 2 4.86 5 C 9428 2.51 5 N 2686 2.21 5 O 2782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15018 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2797 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 14, 'TRANS': 330} Chain breaks: 3 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 5, 'ARG:plan': 4, 'TYR:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1117 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1076 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain breaks: 2 Chain: "E" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1102 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1023 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'RNAv2': 19} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 14, 'rna3p': 4} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 760 SG CYS A 84 62.480 55.613 51.523 1.00 28.54 S ATOM 782 SG CYS A 87 64.206 53.365 53.738 1.00 29.65 S ATOM 2190 SG CYS A 271 22.526 52.111 59.584 1.00152.44 S ATOM 2213 SG CYS A 274 25.489 52.841 58.094 1.00145.84 S Restraints were copied for chains: B, G, H, I, J, Y Time building chain proxies: 3.44, per 1000 atoms: 0.23 Number of scatterers: 15018 At special positions: 0 Unit cell: (147, 113.4, 112.56, 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 4 29.99 Cl 2 17.00 S 80 16.00 P 36 15.00 O 2782 8.00 N 2686 7.00 C 9428 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=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 681.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" ND1 HIS A 53 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 87 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 84 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" ND1 HIS A 240 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 274 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 271 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" ND1 HIS B 53 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 84 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 87 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" ND1 HIS B 240 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 271 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 274 " 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3248 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 15 sheets defined 38.4% alpha, 30.9% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.525A pdb=" N ARG A 57 " --> pdb=" O HIS A 53 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 98 removed outlier: 3.539A pdb=" N GLU A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 136 through 148 removed outlier: 3.773A pdb=" N VAL A 148 " --> pdb=" O TRP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 177 Processing helix chain 'A' and resid 181 through 189 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.606A pdb=" N CYS A 244 " --> pdb=" O HIS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 271 through 285 Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.622A pdb=" N GLY A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 334 removed outlier: 3.808A pdb=" N VAL A 334 " --> pdb=" O TRP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.525A pdb=" N ARG B 57 " --> pdb=" O HIS B 53 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 98 removed outlier: 3.539A pdb=" N GLU B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 128 Processing helix chain 'B' and resid 136 through 148 removed outlier: 3.773A pdb=" N VAL B 148 " --> pdb=" O TRP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 177 Processing helix chain 'B' and resid 181 through 189 Processing helix chain 'B' and resid 240 through 249 removed outlier: 3.607A pdb=" N CYS B 244 " --> pdb=" O HIS B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 253 Processing helix chain 'B' and resid 271 through 285 Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.622A pdb=" N GLY B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.808A pdb=" N VAL B 334 " --> pdb=" O TRP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 362 Processing helix chain 'C' and resid 14 through 31 removed outlier: 3.514A pdb=" N ILE C 18 " --> pdb=" O ASP C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 Processing helix chain 'C' and resid 165 through 171 removed outlier: 3.737A pdb=" N LEU C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 15 through 24 removed outlier: 4.087A pdb=" N GLU D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 51 removed outlier: 3.664A pdb=" N GLY D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'E' and resid 14 through 31 removed outlier: 3.576A pdb=" N LYS E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.712A pdb=" N GLU E 45 " --> pdb=" O HIS E 42 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER E 46 " --> pdb=" O HIS E 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 42 through 46' Processing helix chain 'E' and resid 99 through 111 Processing helix chain 'E' and resid 165 through 171 removed outlier: 3.684A pdb=" N LEU E 169 " --> pdb=" O SER E 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 21 Processing helix chain 'F' and resid 36 through 51 Processing helix chain 'F' and resid 70 through 74 Processing helix chain 'F' and resid 139 through 150 Processing helix chain 'G' and resid 14 through 31 removed outlier: 3.515A pdb=" N ILE G 18 " --> pdb=" O ASP G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 111 Processing helix chain 'G' and resid 165 through 171 removed outlier: 3.738A pdb=" N LEU G 169 " --> pdb=" O SER G 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 15 Processing helix chain 'H' and resid 15 through 24 removed outlier: 4.088A pdb=" N GLU H 24 " --> pdb=" O LYS H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 51 removed outlier: 3.664A pdb=" N GLY H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 140 through 151 Processing helix chain 'I' and resid 14 through 31 removed outlier: 3.576A pdb=" N LYS I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 46 removed outlier: 3.712A pdb=" N GLU I 45 " --> pdb=" O HIS I 42 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER I 46 " --> pdb=" O HIS I 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 42 through 46' Processing helix chain 'I' and resid 99 through 111 Processing helix chain 'I' and resid 165 through 171 removed outlier: 3.684A pdb=" N LEU I 169 " --> pdb=" O SER I 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 21 Processing helix chain 'J' and resid 36 through 51 Processing helix chain 'J' and resid 70 through 74 Processing helix chain 'J' and resid 139 through 150 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 47 removed outlier: 5.028A pdb=" N VAL A 28 " --> pdb=" O MET A 39 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N GLN A 41 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 10.058A pdb=" N TYR A 26 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ARG A 43 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N LEU A 24 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TRP A 23 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TRP A 81 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 225 removed outlier: 10.451A pdb=" N ASN A 219 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N ARG A 209 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG A 221 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR A 260 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N CYS A 291 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 262 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LYS A 293 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS A 264 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N LYS A 317 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU A 290 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N SER A 319 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE A 292 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 35 through 47 removed outlier: 5.029A pdb=" N VAL B 28 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N GLN B 41 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 10.058A pdb=" N TYR B 26 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ARG B 43 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 11.541A pdb=" N LEU B 24 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TRP B 23 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TRP B 81 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 215 through 225 removed outlier: 10.451A pdb=" N ASN B 219 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N ARG B 209 " --> pdb=" O ASN B 219 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG B 221 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TYR B 260 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N CYS B 291 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 262 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LYS B 293 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS B 264 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N LYS B 317 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU B 290 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N SER B 319 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE B 292 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 39 through 41 removed outlier: 3.505A pdb=" N GLU C 54 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 53 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 39 through 41 removed outlier: 3.505A pdb=" N GLU C 54 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 53 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE C 87 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE C 9 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 11.572A pdb=" N TRP C 89 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 14.274A pdb=" N VAL C 7 " --> pdb=" O TRP C 89 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU D 64 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 55 " --> pdb=" O PHE D 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 85 through 87 removed outlier: 3.766A pdb=" N ILE D 109 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP D 120 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 39 through 41 removed outlier: 6.471A pdb=" N THR E 68 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU E 54 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE E 66 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU E 64 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY E 71 " --> pdb=" O GLY E 82 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLY E 82 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN E 83 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE E 87 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE E 9 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 11.329A pdb=" N TRP E 89 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 13.932A pdb=" N VAL E 7 " --> pdb=" O TRP E 89 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU F 64 " --> pdb=" O ALA F 59 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL F 58 " --> pdb=" O LYS F 28 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS F 28 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP F 120 " --> pdb=" O ASP F 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 39 through 41 removed outlier: 6.471A pdb=" N THR E 68 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU E 54 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE E 66 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU E 64 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY E 71 " --> pdb=" O GLY E 82 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLY E 82 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 11.394A pdb=" N SER E 95 " --> pdb=" O PRO F 100 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE F 102 " --> pdb=" O SER E 95 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 39 through 41 removed outlier: 3.505A pdb=" N GLU G 54 " --> pdb=" O ARG G 41 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER G 53 " --> pdb=" O THR G 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 39 through 41 removed outlier: 3.505A pdb=" N GLU G 54 " --> pdb=" O ARG G 41 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER G 53 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE G 87 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE G 9 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 11.572A pdb=" N TRP G 89 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 14.274A pdb=" N VAL G 7 " --> pdb=" O TRP G 89 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU H 64 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE H 55 " --> pdb=" O PHE H 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 85 through 87 removed outlier: 3.766A pdb=" N ILE H 109 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP H 120 " --> pdb=" O ASP H 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 6 through 9 removed outlier: 3.514A pdb=" N VAL J 58 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS J 28 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP J 120 " --> pdb=" O ASP J 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 11 through 13 removed outlier: 4.245A pdb=" N GLN I 83 " --> pdb=" O VAL I 13 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLY I 82 " --> pdb=" O GLY I 71 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY I 71 " --> pdb=" O GLY I 82 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU I 64 " --> pdb=" O HIS I 56 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS I 56 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE I 66 " --> pdb=" O GLU I 54 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU I 54 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR I 68 " --> pdb=" O SER I 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 11 through 13 removed outlier: 4.245A pdb=" N GLN I 83 " --> pdb=" O VAL I 13 " (cutoff:3.500A) 740 hydrogen bonds defined for protein. 2091 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2328 1.31 - 1.44: 4902 1.44 - 1.56: 8076 1.56 - 1.69: 72 1.69 - 1.81: 122 Bond restraints: 15500 Sorted by residual: bond pdb=" C ILE G 51 " pdb=" O ILE G 51 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.19e-02 7.06e+03 1.63e+01 bond pdb=" C ILE C 51 " pdb=" O ILE C 51 " ideal model delta sigma weight residual 1.236 1.190 0.047 1.19e-02 7.06e+03 1.53e+01 bond pdb=" C TYR C 69 " pdb=" O TYR C 69 " ideal model delta sigma weight residual 1.234 1.186 0.048 1.26e-02 6.30e+03 1.44e+01 bond pdb=" C TYR G 69 " pdb=" O TYR G 69 " ideal model delta sigma weight residual 1.234 1.186 0.047 1.26e-02 6.30e+03 1.42e+01 bond pdb=" C TRP G 70 " pdb=" O TRP G 70 " ideal model delta sigma weight residual 1.234 1.190 0.044 1.18e-02 7.18e+03 1.42e+01 ... (remaining 15495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 20570 2.05 - 4.09: 460 4.09 - 6.14: 81 6.14 - 8.19: 9 8.19 - 10.23: 4 Bond angle restraints: 21124 Sorted by residual: angle pdb=" N SER C 52 " pdb=" CA SER C 52 " pdb=" C SER C 52 " ideal model delta sigma weight residual 111.28 118.22 -6.94 1.09e+00 8.42e-01 4.05e+01 angle pdb=" N SER G 52 " pdb=" CA SER G 52 " pdb=" C SER G 52 " ideal model delta sigma weight residual 111.28 118.20 -6.92 1.09e+00 8.42e-01 4.03e+01 angle pdb=" N ILE G 51 " pdb=" CA ILE G 51 " pdb=" C ILE G 51 " ideal model delta sigma weight residual 109.34 102.93 6.41 2.08e+00 2.31e-01 9.50e+00 angle pdb=" N ILE C 51 " pdb=" CA ILE C 51 " pdb=" C ILE C 51 " ideal model delta sigma weight residual 109.34 102.98 6.36 2.08e+00 2.31e-01 9.36e+00 angle pdb=" C ILE G 51 " pdb=" CA ILE G 51 " pdb=" CB ILE G 51 " ideal model delta sigma weight residual 111.29 106.29 5.00 1.64e+00 3.72e-01 9.29e+00 ... (remaining 21119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 7979 15.55 - 31.10: 681 31.10 - 46.64: 162 46.64 - 62.19: 150 62.19 - 77.74: 44 Dihedral angle restraints: 9016 sinusoidal: 4018 harmonic: 4998 Sorted by residual: dihedral pdb=" C4' U Y 13 " pdb=" C3' U Y 13 " pdb=" C2' U Y 13 " pdb=" C1' U Y 13 " ideal model delta sinusoidal sigma weight residual 36.35 -36.09 72.43 1 3.10e+00 1.04e-01 6.97e+02 dihedral pdb=" C4' U X 13 " pdb=" C3' U X 13 " pdb=" C2' U X 13 " pdb=" C1' U X 13 " ideal model delta sinusoidal sigma weight residual 36.35 -36.09 72.43 1 3.10e+00 1.04e-01 6.97e+02 dihedral pdb=" C4' A X 15 " pdb=" C3' A X 15 " pdb=" C2' A X 15 " pdb=" C1' A X 15 " ideal model delta sinusoidal sigma weight residual 36.34 -35.63 71.98 1 3.10e+00 1.04e-01 6.90e+02 ... (remaining 9013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2056 0.110 - 0.220: 40 0.220 - 0.329: 98 0.329 - 0.439: 0 0.439 - 0.549: 2 Chirality restraints: 2196 Sorted by residual: chirality pdb=" CA SER C 52 " pdb=" N SER C 52 " pdb=" C SER C 52 " pdb=" CB SER C 52 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.53e+00 chirality pdb=" CA SER G 52 " pdb=" N SER G 52 " pdb=" C SER G 52 " pdb=" CB SER G 52 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.46e+00 chirality pdb=" C2' U X 12 " pdb=" C3' U X 12 " pdb=" O2' U X 12 " pdb=" C1' U X 12 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 2193 not shown) Planarity restraints: 2562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 70 " 0.022 2.00e-02 2.50e+03 2.35e-02 1.39e+01 pdb=" CG TRP I 70 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP I 70 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP I 70 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 70 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP I 70 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 70 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 70 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 70 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP I 70 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 70 " 0.021 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP E 70 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP E 70 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP E 70 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 70 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP E 70 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 70 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 70 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 70 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 70 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 67 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C THR C 67 " -0.038 2.00e-02 2.50e+03 pdb=" O THR C 67 " 0.014 2.00e-02 2.50e+03 pdb=" N THR C 68 " 0.013 2.00e-02 2.50e+03 ... (remaining 2559 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 951 2.74 - 3.28: 13899 3.28 - 3.82: 24046 3.82 - 4.36: 28751 4.36 - 4.90: 51337 Nonbonded interactions: 118984 Sorted by model distance: nonbonded pdb=" OG1 THR B 322 " pdb=" OE1 GLU B 325 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR A 322 " pdb=" OE1 GLU A 325 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASN D 46 " pdb=" NH2 ARG D 49 " model vdw 2.261 3.120 nonbonded pdb=" OD1 ASN H 46 " pdb=" NH2 ARG H 49 " model vdw 2.261 3.120 nonbonded pdb=" OD1 ASN A 20 " pdb=" N2 G X 10 " model vdw 2.275 3.120 ... (remaining 118979 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 17.790 Find NCS groups from input model: 0.130 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:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.275 15512 Z= 0.218 Angle : 0.707 10.233 21124 Z= 0.369 Chirality : 0.070 0.549 2196 Planarity : 0.004 0.039 2562 Dihedral : 15.746 77.740 5768 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.81 % Allowed : 0.67 % Favored : 98.52 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.21), residues: 1654 helix: 1.68 (0.23), residues: 582 sheet: -0.07 (0.26), residues: 404 loop : -0.75 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 222 TYR 0.011 0.001 TYR B 118 PHE 0.013 0.001 PHE A 245 TRP 0.061 0.001 TRP I 70 HIS 0.002 0.001 HIS E 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.19 (15500) covalent geometry : angle 0.70655 / 0.37 (21124) hydrogen bonds : bond 0.14274 / 9.43 ( 684) hydrogen bonds : angle 6.46546 / 4.64 ( 2091) metal coordination : bond 0.11430 / 6.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 275 time to evaluate : 0.631 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 outliers start: 12 outliers final: 0 residues processed: 281 average time/residue: 0.6265 time to fit residues: 194.0715 Evaluate side-chains 166 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 ASN A 199 HIS B 9 ASN B 199 HIS ** C 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 HIS ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.072662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.049333 restraints weight = 56203.565| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.92 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15512 Z= 0.288 Angle : 1.041 17.389 21124 Z= 0.458 Chirality : 0.087 0.894 2196 Planarity : 0.005 0.050 2562 Dihedral : 13.467 138.544 2336 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.95 % Allowed : 12.42 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.21), residues: 1654 helix: 1.80 (0.22), residues: 578 sheet: 0.15 (0.26), residues: 410 loop : -0.73 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 19 TYR 0.015 0.002 TYR F 85 PHE 0.020 0.002 PHE H 127 TRP 0.036 0.002 TRP E 70 HIS 0.006 0.001 HIS E 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.29 (15500) covalent geometry : angle 1.04053 / 0.46 (21124) hydrogen bonds : bond 0.04253 / 2.86 ( 684) hydrogen bonds : angle 5.04320 / 3.62 ( 2091) metal coordination : bond 0.00864 / 0.55 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 TYR cc_start: 0.8272 (m-80) cc_final: 0.8060 (m-80) REVERT: B 202 TYR cc_start: 0.8266 (m-80) cc_final: 0.8055 (m-80) REVERT: C 36 LYS cc_start: 0.9564 (OUTLIER) cc_final: 0.9019 (mtmm) REVERT: C 172 ASP cc_start: 0.8959 (p0) cc_final: 0.8672 (p0) REVERT: C 176 LYS cc_start: 0.8978 (pttt) cc_final: 0.8717 (pttt) REVERT: E 14 ASP cc_start: 0.8797 (t0) cc_final: 0.8267 (t0) REVERT: E 37 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8131 (p0) REVERT: E 105 GLN cc_start: 0.9513 (mm110) cc_final: 0.9283 (mm-40) REVERT: E 171 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: F 114 ILE cc_start: 0.9405 (pt) cc_final: 0.9056 (mt) REVERT: G 36 LYS cc_start: 0.9557 (OUTLIER) cc_final: 0.9011 (mtmm) REVERT: G 172 ASP cc_start: 0.8951 (p0) cc_final: 0.8656 (p0) REVERT: G 176 LYS cc_start: 0.8971 (pttt) cc_final: 0.8711 (pttt) REVERT: I 14 ASP cc_start: 0.8806 (t0) cc_final: 0.8270 (t0) REVERT: I 105 GLN cc_start: 0.9487 (mm110) cc_final: 0.9256 (mm-40) REVERT: I 171 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7939 (pm20) outliers start: 29 outliers final: 10 residues processed: 191 average time/residue: 0.6304 time to fit residues: 132.4176 Evaluate side-chains 170 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 171 GLU Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 139 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 chunk 62 optimal weight: 30.0000 chunk 53 optimal weight: 0.8980 chunk 145 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 149 optimal weight: 0.0470 chunk 52 optimal weight: 3.9990 overall best weight: 1.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 97 GLN F 45 GLN F 117 GLN G 97 GLN J 45 GLN J 74 GLN J 117 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.074288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.051508 restraints weight = 55854.505| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 4.16 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15512 Z= 0.141 Angle : 0.787 10.359 21124 Z= 0.363 Chirality : 0.063 0.500 2196 Planarity : 0.004 0.055 2562 Dihedral : 13.858 149.195 2336 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.15 % Allowed : 14.09 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.21), residues: 1654 helix: 1.89 (0.22), residues: 578 sheet: 0.30 (0.26), residues: 408 loop : -0.69 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 198 TYR 0.009 0.001 TYR B 202 PHE 0.017 0.001 PHE J 143 TRP 0.018 0.001 TRP E 70 HIS 0.021 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (15500) covalent geometry : angle 0.78699 / 0.36 (21124) hydrogen bonds : bond 0.03217 / 2.18 ( 684) hydrogen bonds : angle 4.61687 / 3.32 ( 2091) metal coordination : bond 0.00265 / 0.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.9466 (OUTLIER) cc_final: 0.9254 (ttp) REVERT: A 202 TYR cc_start: 0.8262 (m-80) cc_final: 0.7908 (m-80) REVERT: B 135 MET cc_start: 0.9470 (OUTLIER) cc_final: 0.9258 (ttp) REVERT: B 202 TYR cc_start: 0.8248 (m-80) cc_final: 0.7900 (m-80) REVERT: C 36 LYS cc_start: 0.9593 (OUTLIER) cc_final: 0.9039 (mtmm) REVERT: D 98 LYS cc_start: 0.8880 (ttmt) cc_final: 0.8599 (ttmm) REVERT: D 149 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8258 (ttp-170) REVERT: E 14 ASP cc_start: 0.8649 (t0) cc_final: 0.8416 (t0) REVERT: E 105 GLN cc_start: 0.9543 (mm110) cc_final: 0.9258 (mm-40) REVERT: F 114 ILE cc_start: 0.9460 (pt) cc_final: 0.9044 (mt) REVERT: G 36 LYS cc_start: 0.9590 (OUTLIER) cc_final: 0.9038 (mtmm) REVERT: H 98 LYS cc_start: 0.8894 (ttmt) cc_final: 0.8612 (ttmm) REVERT: H 149 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8237 (ttp-170) REVERT: I 14 ASP cc_start: 0.8609 (t0) cc_final: 0.8366 (t0) REVERT: I 105 GLN cc_start: 0.9526 (mm110) cc_final: 0.9312 (mm-40) REVERT: J 122 MET cc_start: 0.8385 (tpp) cc_final: 0.8181 (tpp) outliers start: 32 outliers final: 7 residues processed: 189 average time/residue: 0.6159 time to fit residues: 128.6051 Evaluate side-chains 167 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 149 ARG Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 149 ARG Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 57 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 158 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 GLN B 166 GLN D 8 GLN E 6 GLN F 77 GLN H 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.071332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.047774 restraints weight = 56111.322| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.96 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 15512 Z= 0.325 Angle : 0.825 9.377 21124 Z= 0.396 Chirality : 0.061 0.370 2196 Planarity : 0.004 0.053 2562 Dihedral : 14.272 147.093 2336 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.42 % Allowed : 14.97 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1654 helix: 1.83 (0.22), residues: 580 sheet: 0.23 (0.26), residues: 414 loop : -0.55 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 151 TYR 0.020 0.002 TYR F 85 PHE 0.021 0.002 PHE H 143 TRP 0.024 0.001 TRP I 70 HIS 0.005 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.33 (15500) covalent geometry : angle 0.82517 / 0.40 (21124) hydrogen bonds : bond 0.04045 / 2.76 ( 684) hydrogen bonds : angle 4.83492 / 3.45 ( 2091) metal coordination : bond 0.00959 / 0.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 TYR cc_start: 0.8259 (m-80) cc_final: 0.7994 (m-80) REVERT: A 321 MET cc_start: 0.8850 (mpp) cc_final: 0.8390 (mmm) REVERT: B 202 TYR cc_start: 0.8257 (m-80) cc_final: 0.7992 (m-80) REVERT: B 321 MET cc_start: 0.8843 (mpp) cc_final: 0.8387 (mmm) REVERT: C 2 GLU cc_start: 0.8604 (pm20) cc_final: 0.8356 (pm20) REVERT: C 36 LYS cc_start: 0.9570 (OUTLIER) cc_final: 0.9012 (mtmm) REVERT: D 98 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8680 (ttmm) REVERT: D 148 ARG cc_start: 0.9164 (tpm170) cc_final: 0.8187 (tpm170) REVERT: E 14 ASP cc_start: 0.8679 (t0) cc_final: 0.8347 (t0) REVERT: E 105 GLN cc_start: 0.9563 (mm110) cc_final: 0.9328 (mm-40) REVERT: F 114 ILE cc_start: 0.9434 (pt) cc_final: 0.8998 (mt) REVERT: G 2 GLU cc_start: 0.8597 (pm20) cc_final: 0.8349 (pm20) REVERT: G 36 LYS cc_start: 0.9569 (OUTLIER) cc_final: 0.9011 (mtmm) REVERT: H 98 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8679 (ttmm) REVERT: H 148 ARG cc_start: 0.9174 (tpm170) cc_final: 0.8196 (tpm170) REVERT: I 14 ASP cc_start: 0.8688 (t0) cc_final: 0.8370 (t0) REVERT: I 91 LYS cc_start: 0.8887 (tptp) cc_final: 0.8680 (tptp) REVERT: I 105 GLN cc_start: 0.9563 (mm110) cc_final: 0.9326 (mm-40) outliers start: 36 outliers final: 20 residues processed: 183 average time/residue: 0.6094 time to fit residues: 123.3038 Evaluate side-chains 172 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 132 optimal weight: 4.9990 chunk 50 optimal weight: 0.0570 chunk 87 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 159 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 8 GLN H 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.072592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.049171 restraints weight = 55958.422| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.99 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15512 Z= 0.158 Angle : 0.740 8.856 21124 Z= 0.349 Chirality : 0.056 0.278 2196 Planarity : 0.004 0.055 2562 Dihedral : 14.155 147.579 2336 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.42 % Allowed : 15.03 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.21), residues: 1654 helix: 2.03 (0.22), residues: 578 sheet: 0.27 (0.25), residues: 416 loop : -0.48 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 149 TYR 0.009 0.001 TYR C 69 PHE 0.010 0.001 PHE H 143 TRP 0.014 0.001 TRP E 70 HIS 0.003 0.001 HIS I 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (15500) covalent geometry : angle 0.73966 / 0.35 (21124) hydrogen bonds : bond 0.03214 / 2.19 ( 684) hydrogen bonds : angle 4.49308 / 3.22 ( 2091) metal coordination : bond 0.00316 / 0.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 TYR cc_start: 0.8251 (m-80) cc_final: 0.7948 (m-80) REVERT: A 321 MET cc_start: 0.8866 (mpp) cc_final: 0.8430 (mmm) REVERT: B 202 TYR cc_start: 0.8258 (m-80) cc_final: 0.7951 (m-80) REVERT: B 321 MET cc_start: 0.8861 (mpp) cc_final: 0.8427 (mmm) REVERT: C 2 GLU cc_start: 0.8622 (pm20) cc_final: 0.8357 (pm20) REVERT: C 36 LYS cc_start: 0.9573 (OUTLIER) cc_final: 0.9020 (mtmm) REVERT: D 98 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8685 (ttmm) REVERT: D 148 ARG cc_start: 0.9107 (tpm170) cc_final: 0.8842 (tpm170) REVERT: D 149 ARG cc_start: 0.9151 (mmm160) cc_final: 0.8907 (mmm160) REVERT: E 14 ASP cc_start: 0.8658 (t0) cc_final: 0.8384 (t0) REVERT: E 91 LYS cc_start: 0.8797 (tptp) cc_final: 0.8560 (tptp) REVERT: E 105 GLN cc_start: 0.9572 (mm110) cc_final: 0.9287 (mm-40) REVERT: F 114 ILE cc_start: 0.9457 (pt) cc_final: 0.9072 (mt) REVERT: G 2 GLU cc_start: 0.8626 (pm20) cc_final: 0.8361 (pm20) REVERT: G 36 LYS cc_start: 0.9569 (OUTLIER) cc_final: 0.9014 (mtmm) REVERT: H 98 LYS cc_start: 0.9002 (ttmt) cc_final: 0.8696 (ttmm) REVERT: H 148 ARG cc_start: 0.9106 (tpm170) cc_final: 0.8838 (tpm170) REVERT: H 149 ARG cc_start: 0.9149 (mmm160) cc_final: 0.8904 (mmm160) REVERT: I 14 ASP cc_start: 0.8650 (t0) cc_final: 0.8391 (t0) REVERT: I 91 LYS cc_start: 0.8908 (tptp) cc_final: 0.8698 (tptp) REVERT: I 105 GLN cc_start: 0.9561 (mm110) cc_final: 0.9273 (mm-40) outliers start: 36 outliers final: 14 residues processed: 187 average time/residue: 0.5821 time to fit residues: 122.6450 Evaluate side-chains 168 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 70 optimal weight: 10.0000 chunk 134 optimal weight: 0.6980 chunk 144 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 62 optimal weight: 0.0170 chunk 29 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 overall best weight: 4.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 20 ASN D 8 GLN H 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.071761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.047807 restraints weight = 56955.397| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 4.05 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15512 Z= 0.225 Angle : 0.765 8.733 21124 Z= 0.362 Chirality : 0.056 0.307 2196 Planarity : 0.004 0.053 2562 Dihedral : 14.170 147.017 2336 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.15 % Allowed : 16.44 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.21), residues: 1654 helix: 1.95 (0.22), residues: 580 sheet: 0.25 (0.25), residues: 418 loop : -0.41 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 23 TYR 0.012 0.001 TYR G 69 PHE 0.015 0.001 PHE D 143 TRP 0.015 0.001 TRP E 70 HIS 0.004 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (15500) covalent geometry : angle 0.76532 / 0.36 (21124) hydrogen bonds : bond 0.03443 / 2.34 ( 684) hydrogen bonds : angle 4.53899 / 3.24 ( 2091) metal coordination : bond 0.00544 / 0.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 TYR cc_start: 0.8273 (m-80) cc_final: 0.7939 (m-80) REVERT: A 321 MET cc_start: 0.8898 (mpp) cc_final: 0.8400 (mmm) REVERT: B 202 TYR cc_start: 0.8276 (m-80) cc_final: 0.7943 (m-80) REVERT: B 321 MET cc_start: 0.8894 (mpp) cc_final: 0.8398 (mmm) REVERT: C 36 LYS cc_start: 0.9567 (OUTLIER) cc_final: 0.8999 (mtmm) REVERT: D 149 ARG cc_start: 0.9206 (mmm160) cc_final: 0.8905 (tpm170) REVERT: E 105 GLN cc_start: 0.9588 (mm110) cc_final: 0.9290 (mm-40) REVERT: F 114 ILE cc_start: 0.9454 (pt) cc_final: 0.9024 (mt) REVERT: G 36 LYS cc_start: 0.9562 (OUTLIER) cc_final: 0.8994 (mtmm) REVERT: H 149 ARG cc_start: 0.9199 (mmm160) cc_final: 0.8905 (tpm170) REVERT: I 14 ASP cc_start: 0.8646 (t0) cc_final: 0.8436 (t0) REVERT: I 105 GLN cc_start: 0.9558 (mm110) cc_final: 0.9264 (mm110) REVERT: J 122 MET cc_start: 0.8333 (tpp) cc_final: 0.8098 (tpp) outliers start: 32 outliers final: 18 residues processed: 183 average time/residue: 0.5978 time to fit residues: 121.0845 Evaluate side-chains 174 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 134 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 106 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 ASN D 8 GLN H 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.071472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.048051 restraints weight = 56745.609| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.96 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15512 Z= 0.207 Angle : 0.781 9.869 21124 Z= 0.369 Chirality : 0.056 0.314 2196 Planarity : 0.004 0.053 2562 Dihedral : 14.184 146.892 2336 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.81 % Allowed : 18.59 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.21), residues: 1654 helix: 1.98 (0.22), residues: 580 sheet: 0.29 (0.25), residues: 418 loop : -0.34 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 93 TYR 0.011 0.001 TYR G 69 PHE 0.015 0.001 PHE D 143 TRP 0.013 0.001 TRP E 70 HIS 0.004 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 (15500) covalent geometry : angle 0.78058 / 0.37 (21124) hydrogen bonds : bond 0.03357 / 2.29 ( 684) hydrogen bonds : angle 4.49894 / 3.21 ( 2091) metal coordination : bond 0.00448 / 0.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 TYR cc_start: 0.8298 (m-80) cc_final: 0.7969 (m-80) REVERT: A 321 MET cc_start: 0.8838 (mpp) cc_final: 0.8494 (mmm) REVERT: B 202 TYR cc_start: 0.8301 (m-80) cc_final: 0.7971 (m-80) REVERT: B 321 MET cc_start: 0.8837 (mpp) cc_final: 0.8496 (mmm) REVERT: C 36 LYS cc_start: 0.9548 (OUTLIER) cc_final: 0.8997 (mtmm) REVERT: C 88 GLU cc_start: 0.7203 (pp20) cc_final: 0.6944 (pp20) REVERT: D 149 ARG cc_start: 0.9224 (mmm160) cc_final: 0.8873 (tpm170) REVERT: E 14 ASP cc_start: 0.8617 (t0) cc_final: 0.8386 (t0) REVERT: E 105 GLN cc_start: 0.9552 (mm110) cc_final: 0.9254 (mm-40) REVERT: F 114 ILE cc_start: 0.9475 (pt) cc_final: 0.9108 (mt) REVERT: G 36 LYS cc_start: 0.9537 (OUTLIER) cc_final: 0.8986 (mtmm) REVERT: H 149 ARG cc_start: 0.9218 (mmm160) cc_final: 0.8842 (tpm170) REVERT: I 14 ASP cc_start: 0.8656 (t0) cc_final: 0.8384 (t0) REVERT: I 91 LYS cc_start: 0.8738 (tptp) cc_final: 0.8479 (tptp) REVERT: I 101 ASP cc_start: 0.9464 (m-30) cc_final: 0.9262 (m-30) REVERT: I 105 GLN cc_start: 0.9534 (mm110) cc_final: 0.9242 (mm110) outliers start: 27 outliers final: 16 residues processed: 181 average time/residue: 0.5572 time to fit residues: 111.7377 Evaluate side-chains 173 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 29 MET Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 15 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 162 optimal weight: 20.0000 chunk 154 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 8 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN J 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.072074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.048635 restraints weight = 57224.708| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.99 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15512 Z= 0.154 Angle : 0.784 10.559 21124 Z= 0.367 Chirality : 0.055 0.270 2196 Planarity : 0.004 0.053 2562 Dihedral : 14.140 146.689 2336 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.81 % Allowed : 19.19 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.21), residues: 1654 helix: 1.96 (0.22), residues: 580 sheet: 0.36 (0.25), residues: 416 loop : -0.31 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 93 TYR 0.009 0.001 TYR C 69 PHE 0.012 0.001 PHE F 143 TRP 0.013 0.001 TRP E 70 HIS 0.003 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (15500) covalent geometry : angle 0.78387 / 0.37 (21124) hydrogen bonds : bond 0.03116 / 2.13 ( 684) hydrogen bonds : angle 4.36053 / 3.11 ( 2091) metal coordination : bond 0.00247 / 0.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 TYR cc_start: 0.8303 (m-80) cc_final: 0.7954 (m-80) REVERT: A 321 MET cc_start: 0.8821 (mpp) cc_final: 0.8464 (mmm) REVERT: B 202 TYR cc_start: 0.8308 (m-80) cc_final: 0.7958 (m-80) REVERT: B 321 MET cc_start: 0.8820 (mpp) cc_final: 0.8465 (mmm) REVERT: C 36 LYS cc_start: 0.9549 (OUTLIER) cc_final: 0.9024 (mtmm) REVERT: D 149 ARG cc_start: 0.9224 (mmm160) cc_final: 0.8881 (tpm170) REVERT: E 105 GLN cc_start: 0.9567 (mm110) cc_final: 0.9270 (mm-40) REVERT: F 114 ILE cc_start: 0.9496 (pt) cc_final: 0.9113 (mt) REVERT: F 122 MET cc_start: 0.8531 (tpp) cc_final: 0.8278 (tpp) REVERT: G 36 LYS cc_start: 0.9538 (OUTLIER) cc_final: 0.9016 (mtmm) REVERT: G 88 GLU cc_start: 0.7345 (pp20) cc_final: 0.7073 (pp20) REVERT: H 149 ARG cc_start: 0.9219 (mmm160) cc_final: 0.8890 (tpm170) REVERT: I 14 ASP cc_start: 0.8607 (t0) cc_final: 0.8375 (t0) REVERT: I 105 GLN cc_start: 0.9547 (mm110) cc_final: 0.9265 (mm-40) REVERT: J 122 MET cc_start: 0.8225 (tpp) cc_final: 0.7951 (tpp) outliers start: 27 outliers final: 13 residues processed: 175 average time/residue: 0.5169 time to fit residues: 99.7871 Evaluate side-chains 169 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 108 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.071296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.047857 restraints weight = 57187.215| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.96 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15512 Z= 0.214 Angle : 0.820 12.300 21124 Z= 0.387 Chirality : 0.055 0.300 2196 Planarity : 0.004 0.053 2562 Dihedral : 14.183 146.505 2336 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.95 % Allowed : 19.19 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.21), residues: 1654 helix: 1.91 (0.22), residues: 580 sheet: 0.32 (0.25), residues: 418 loop : -0.31 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 93 TYR 0.020 0.001 TYR J 85 PHE 0.017 0.001 PHE F 143 TRP 0.034 0.001 TRP E 174 HIS 0.005 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (15500) covalent geometry : angle 0.81958 / 0.39 (21124) hydrogen bonds : bond 0.03401 / 2.32 ( 684) hydrogen bonds : angle 4.48559 / 3.20 ( 2091) metal coordination : bond 0.00517 / 0.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.8826 (mpp) cc_final: 0.8476 (mmm) REVERT: B 321 MET cc_start: 0.8828 (mpp) cc_final: 0.8476 (mmm) REVERT: C 36 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9012 (mtmm) REVERT: D 98 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8739 (ttmm) REVERT: D 149 ARG cc_start: 0.9209 (mmm160) cc_final: 0.8870 (tpm170) REVERT: E 101 ASP cc_start: 0.9464 (m-30) cc_final: 0.9260 (m-30) REVERT: E 105 GLN cc_start: 0.9567 (mm110) cc_final: 0.9277 (mm110) REVERT: E 174 TRP cc_start: 0.7978 (t-100) cc_final: 0.7333 (t-100) REVERT: F 114 ILE cc_start: 0.9494 (pt) cc_final: 0.9134 (mt) REVERT: G 36 LYS cc_start: 0.9531 (OUTLIER) cc_final: 0.9004 (mtmm) REVERT: H 98 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8745 (ttmm) REVERT: H 149 ARG cc_start: 0.9208 (mmm160) cc_final: 0.8871 (tpm170) REVERT: I 105 GLN cc_start: 0.9561 (mm110) cc_final: 0.9273 (mm-40) REVERT: I 174 TRP cc_start: 0.7548 (t-100) cc_final: 0.7285 (t-100) REVERT: J 122 MET cc_start: 0.8293 (tpp) cc_final: 0.8087 (tpp) outliers start: 29 outliers final: 14 residues processed: 181 average time/residue: 0.5241 time to fit residues: 104.8659 Evaluate side-chains 171 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 56 optimal weight: 30.0000 chunk 20 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.071335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.047891 restraints weight = 57348.983| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.97 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15512 Z= 0.211 Angle : 0.850 12.215 21124 Z= 0.402 Chirality : 0.055 0.299 2196 Planarity : 0.004 0.054 2562 Dihedral : 14.201 146.456 2336 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.34 % Allowed : 19.87 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.21), residues: 1654 helix: 1.83 (0.22), residues: 582 sheet: 0.31 (0.25), residues: 418 loop : -0.34 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 148 TYR 0.011 0.001 TYR C 69 PHE 0.014 0.001 PHE D 143 TRP 0.025 0.001 TRP E 174 HIS 0.005 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (15500) covalent geometry : angle 0.84955 / 0.40 (21124) hydrogen bonds : bond 0.03455 / 2.37 ( 684) hydrogen bonds : angle 4.49753 / 3.22 ( 2091) metal coordination : bond 0.00458 / 0.30 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.8816 (mpp) cc_final: 0.8510 (mmm) REVERT: B 321 MET cc_start: 0.8810 (mpp) cc_final: 0.8505 (mmm) REVERT: C 36 LYS cc_start: 0.9529 (OUTLIER) cc_final: 0.9006 (mtmm) REVERT: D 98 LYS cc_start: 0.9071 (ttmt) cc_final: 0.8745 (ttmm) REVERT: D 149 ARG cc_start: 0.9203 (mmm160) cc_final: 0.8942 (tpm170) REVERT: E 101 ASP cc_start: 0.9475 (m-30) cc_final: 0.9270 (m-30) REVERT: E 105 GLN cc_start: 0.9571 (mm110) cc_final: 0.9285 (mm110) REVERT: E 174 TRP cc_start: 0.8019 (t-100) cc_final: 0.7377 (t-100) REVERT: F 114 ILE cc_start: 0.9523 (pt) cc_final: 0.9121 (mt) REVERT: G 36 LYS cc_start: 0.9522 (OUTLIER) cc_final: 0.9003 (mtmm) REVERT: H 98 LYS cc_start: 0.9077 (ttmt) cc_final: 0.8756 (ttmm) REVERT: H 149 ARG cc_start: 0.9196 (mmm160) cc_final: 0.8942 (tpm170) REVERT: I 105 GLN cc_start: 0.9560 (mm110) cc_final: 0.9271 (mm-40) REVERT: I 174 TRP cc_start: 0.7562 (t-100) cc_final: 0.7268 (t-100) REVERT: J 122 MET cc_start: 0.8313 (tpp) cc_final: 0.8093 (tpp) outliers start: 20 outliers final: 14 residues processed: 175 average time/residue: 0.5435 time to fit residues: 105.4773 Evaluate side-chains 168 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 85 TYR Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 42 optimal weight: 0.7980 chunk 33 optimal weight: 30.0000 chunk 6 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.071496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.048136 restraints weight = 56804.985| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.95 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15512 Z= 0.180 Angle : 0.838 12.031 21124 Z= 0.397 Chirality : 0.055 0.284 2196 Planarity : 0.004 0.054 2562 Dihedral : 14.181 146.379 2336 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.34 % Allowed : 20.27 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.21), residues: 1654 helix: 1.88 (0.22), residues: 580 sheet: 0.23 (0.25), residues: 428 loop : -0.28 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 148 TYR 0.010 0.001 TYR C 69 PHE 0.012 0.001 PHE D 143 TRP 0.020 0.001 TRP E 174 HIS 0.005 0.001 HIS E 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (15500) covalent geometry : angle 0.83774 / 0.40 (21124) hydrogen bonds : bond 0.03329 / 2.28 ( 684) hydrogen bonds : angle 4.45991 / 3.19 ( 2091) metal coordination : bond 0.00349 / 0.23 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4154.30 seconds wall clock time: 71 minutes 53.92 seconds (4313.92 seconds total)