Starting phenix.real_space_refine on Fri Jun 13 13:37:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h0i_34412/06_2025/8h0i_34412.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h0i_34412/06_2025/8h0i_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h0i_34412/06_2025/8h0i_34412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h0i_34412/06_2025/8h0i_34412.map" model { file = "/net/cci-nas-00/data/ceres_data/8h0i_34412/06_2025/8h0i_34412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h0i_34412/06_2025/8h0i_34412.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} 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: "Y" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 14, 'rna3p': 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 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: X, I, B, H, G, J Time building chain proxies: 9.95, per 1000 atoms: 0.66 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: 3.55 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 4.87 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: 4.63 Time building geometry restraints manager: 4.22 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: 20774 2.05 - 4.09: 312 4.09 - 6.14: 25 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 - 30.88: 8838 30.88 - 61.76: 254 61.76 - 92.64: 42 92.64 - 123.52: 0 123.52 - 154.40: 2 Dihedral angle restraints: 9136 sinusoidal: 4138 harmonic: 4998 Sorted by residual: dihedral pdb=" O4' C X 1 " pdb=" C1' C X 1 " pdb=" N1 C X 1 " pdb=" C2 C X 1 " ideal model delta sinusoidal sigma weight residual 200.00 45.60 154.40 1 1.50e+01 4.44e-03 8.11e+01 dihedral pdb=" O4' C Y 1 " pdb=" C1' C Y 1 " pdb=" N1 C Y 1 " pdb=" C2 C Y 1 " ideal model delta sinusoidal sigma weight residual 200.00 45.60 154.40 1 1.50e+01 4.44e-03 8.11e+01 dihedral pdb=" CA TYR I 69 " pdb=" C TYR I 69 " pdb=" N TRP I 70 " pdb=" CA TRP I 70 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 9133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2152 0.110 - 0.220: 40 0.220 - 0.329: 2 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=" CA ILE G 51 " pdb=" N ILE G 51 " pdb=" C ILE G 51 " pdb=" CB ILE G 51 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.59e+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: 0.07 Found NCS groups: ncs_group { reference = chain 'Y' selection = chain 'X' } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'J' } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.560 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 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 : 0.004 0.275 15512 Z= 0.213 Angle : 0.605 10.233 21124 Z= 0.339 Chirality : 0.047 0.549 2196 Planarity : 0.004 0.039 2562 Dihedral : 14.234 154.398 5888 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.061 0.001 TRP I 70 HIS 0.002 0.001 HIS E 28 PHE 0.013 0.001 PHE A 245 TYR 0.011 0.001 TYR B 118 ARG 0.003 0.000 ARG B 222 Details of bonding type rmsd hydrogen bonds : bond 0.14274 ( 684) hydrogen bonds : angle 6.46546 ( 2091) metal coordination : bond 0.11430 ( 12) covalent geometry : bond 0.00310 (15500) covalent geometry : angle 0.60498 (21124) *********************** 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 : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 281 average time/residue: 1.2110 time to fit residues: 374.8112 Evaluate side-chains 168 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 67 optimal weight: 30.0000 chunk 130 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 96 optimal weight: 0.0470 chunk 150 optimal weight: 2.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS B 199 HIS C 97 GLN F 37 HIS F 77 GLN F 117 GLN G 97 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.074272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.050737 restraints weight = 55887.623| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.97 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15512 Z= 0.170 Angle : 0.665 9.322 21124 Z= 0.337 Chirality : 0.044 0.146 2196 Planarity : 0.005 0.054 2562 Dihedral : 12.974 152.527 2456 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.68 % Allowed : 12.21 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1654 helix: 1.90 (0.22), residues: 578 sheet: 0.16 (0.26), residues: 410 loop : -0.75 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 70 HIS 0.005 0.001 HIS E 28 PHE 0.020 0.002 PHE H 127 TYR 0.016 0.001 TYR F 85 ARG 0.007 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 684) hydrogen bonds : angle 4.89294 ( 2091) metal coordination : bond 0.00441 ( 12) covalent geometry : bond 0.00379 (15500) covalent geometry : angle 0.66500 (21124) *********************** 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 209 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.565 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: 0.8258 (m-80) cc_final: 0.7951 (m-80) REVERT: B 202 TYR cc_start: 0.8261 (m-80) cc_final: 0.7956 (m-80) REVERT: B 210 MET cc_start: 0.8498 (tpp) cc_final: 0.8298 (tpp) REVERT: C 36 LYS cc_start: 0.9537 (OUTLIER) cc_final: 0.9036 (mtmm) REVERT: D 98 LYS cc_start: 0.8992 (ttmt) cc_final: 0.8721 (ttmm) REVERT: D 149 ARG cc_start: 0.8523 (tpm170) cc_final: 0.8315 (tpp-160) REVERT: E 14 ASP cc_start: 0.8818 (t0) cc_final: 0.8366 (t0) REVERT: E 105 GLN cc_start: 0.9523 (mm110) cc_final: 0.9262 (mm-40) REVERT: E 171 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7977 (pm20) REVERT: F 114 ILE cc_start: 0.9424 (pt) cc_final: 0.9063 (mt) REVERT: G 36 LYS cc_start: 0.9540 (OUTLIER) cc_final: 0.9039 (mtmm) REVERT: H 98 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8719 (ttmm) REVERT: H 149 ARG cc_start: 0.8524 (tpm170) cc_final: 0.8317 (tpp-160) REVERT: I 14 ASP cc_start: 0.8785 (t0) cc_final: 0.8384 (t0) REVERT: I 37 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8040 (p0) REVERT: I 105 GLN cc_start: 0.9515 (mm110) cc_final: 0.9253 (mm-40) REVERT: I 171 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7954 (pm20) outliers start: 25 outliers final: 9 residues processed: 196 average time/residue: 1.2710 time to fit residues: 274.6541 Evaluate side-chains 178 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 171 GLU 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 37 ASP 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 22 optimal weight: 30.0000 chunk 67 optimal weight: 30.0000 chunk 84 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN B 166 GLN E 6 GLN F 45 GLN F 77 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 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 = 0.3791 r_free = 0.3791 target = 0.071027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.047501 restraints weight = 56841.660| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.95 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 15512 Z= 0.327 Angle : 0.697 8.025 21124 Z= 0.363 Chirality : 0.046 0.148 2196 Planarity : 0.005 0.054 2562 Dihedral : 13.219 156.861 2456 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.75 % Allowed : 13.02 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1654 helix: 1.75 (0.22), residues: 580 sheet: 0.36 (0.26), residues: 404 loop : -0.68 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 70 HIS 0.026 0.002 HIS A 199 PHE 0.022 0.002 PHE J 143 TYR 0.017 0.002 TYR C 69 ARG 0.009 0.001 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 684) hydrogen bonds : angle 4.90718 ( 2091) metal coordination : bond 0.01073 ( 12) covalent geometry : bond 0.00740 (15500) covalent geometry : angle 0.69747 (21124) *********************** 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 211 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 1.528 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 56 MET cc_start: 0.9062 (mmt) cc_final: 0.8827 (mmp) REVERT: A 202 TYR cc_start: 0.8275 (m-80) cc_final: 0.7951 (m-80) REVERT: B 56 MET cc_start: 0.9068 (mmt) cc_final: 0.8832 (mmp) REVERT: B 202 TYR cc_start: 0.8273 (m-80) cc_final: 0.7951 (m-80) REVERT: C 2 GLU cc_start: 0.8531 (pm20) cc_final: 0.8288 (pm20) REVERT: C 36 LYS cc_start: 0.9560 (OUTLIER) cc_final: 0.9034 (mtmm) REVERT: D 8 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7643 (pp30) REVERT: D 98 LYS cc_start: 0.9050 (ttmt) cc_final: 0.8717 (ttmm) REVERT: E 105 GLN cc_start: 0.9559 (mm110) cc_final: 0.9342 (mm-40) REVERT: F 114 ILE cc_start: 0.9460 (pt) cc_final: 0.9011 (mt) REVERT: G 2 GLU cc_start: 0.8528 (pm20) cc_final: 0.8285 (pm20) REVERT: G 36 LYS cc_start: 0.9554 (OUTLIER) cc_final: 0.9027 (mtmm) REVERT: H 8 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7648 (pp30) REVERT: I 105 GLN cc_start: 0.9548 (mm110) cc_final: 0.9328 (mm-40) outliers start: 41 outliers final: 17 residues processed: 194 average time/residue: 1.2189 time to fit residues: 261.7059 Evaluate side-chains 175 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 46 SER 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 8 GLN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 74 GLN 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 G residue 67 THR Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain H residue 86 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 119 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 117 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.072260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.048580 restraints weight = 55605.392| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.96 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15512 Z= 0.184 Angle : 0.644 8.392 21124 Z= 0.327 Chirality : 0.043 0.147 2196 Planarity : 0.004 0.056 2562 Dihedral : 13.115 158.197 2456 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.35 % Allowed : 14.97 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1654 helix: 1.89 (0.22), residues: 580 sheet: 0.25 (0.26), residues: 418 loop : -0.54 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 70 HIS 0.003 0.001 HIS B 42 PHE 0.015 0.001 PHE J 143 TYR 0.011 0.001 TYR G 69 ARG 0.003 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 684) hydrogen bonds : angle 4.66308 ( 2091) metal coordination : bond 0.00485 ( 12) covalent geometry : bond 0.00420 (15500) covalent geometry : angle 0.64373 (21124) *********************** 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 205 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 1.754 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 56 MET cc_start: 0.9003 (mmt) cc_final: 0.8762 (mmp) REVERT: A 202 TYR cc_start: 0.8251 (m-80) cc_final: 0.7868 (m-80) REVERT: A 321 MET cc_start: 0.8795 (mpp) cc_final: 0.8387 (mmm) REVERT: B 56 MET cc_start: 0.9008 (mmt) cc_final: 0.8766 (mmp) REVERT: B 202 TYR cc_start: 0.8249 (m-80) cc_final: 0.7908 (m-80) REVERT: B 321 MET cc_start: 0.8792 (mpp) cc_final: 0.8328 (mmm) REVERT: C 2 GLU cc_start: 0.8549 (pm20) cc_final: 0.8297 (pm20) REVERT: C 36 LYS cc_start: 0.9577 (OUTLIER) cc_final: 0.9024 (mtmm) REVERT: D 98 LYS cc_start: 0.9006 (ttmt) cc_final: 0.8693 (ttmm) REVERT: D 148 ARG cc_start: 0.9229 (tpm170) cc_final: 0.8419 (tpm170) REVERT: E 14 ASP cc_start: 0.8608 (t0) cc_final: 0.8236 (t0) REVERT: E 91 LYS cc_start: 0.8928 (tptp) cc_final: 0.8695 (tptp) REVERT: E 105 GLN cc_start: 0.9567 (mm110) cc_final: 0.9302 (mm-40) REVERT: G 2 GLU cc_start: 0.8541 (pm20) cc_final: 0.8290 (pm20) REVERT: G 36 LYS cc_start: 0.9573 (OUTLIER) cc_final: 0.9020 (mtmm) REVERT: H 148 ARG cc_start: 0.9228 (tpm170) cc_final: 0.8411 (tpm170) REVERT: I 14 ASP cc_start: 0.8702 (t0) cc_final: 0.8315 (t0) REVERT: I 91 LYS cc_start: 0.8898 (tptp) cc_final: 0.8662 (tptp) REVERT: I 105 GLN cc_start: 0.9557 (mm110) cc_final: 0.9286 (mm-40) REVERT: J 122 MET cc_start: 0.8399 (tpp) cc_final: 0.8192 (tpp) outliers start: 35 outliers final: 12 residues processed: 185 average time/residue: 1.1957 time to fit residues: 245.6106 Evaluate side-chains 167 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 1.749 ------------------------------------------------------------------------------- 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 60 THR Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 86 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 67 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 111 optimal weight: 0.0970 overall best weight: 2.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN H 8 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.072352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.048663 restraints weight = 55821.730| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.98 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15512 Z= 0.156 Angle : 0.628 8.779 21124 Z= 0.317 Chirality : 0.043 0.151 2196 Planarity : 0.004 0.055 2562 Dihedral : 13.050 157.961 2456 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.55 % Allowed : 15.10 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.21), residues: 1654 helix: 1.98 (0.22), residues: 580 sheet: 0.30 (0.25), residues: 418 loop : -0.47 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 174 HIS 0.003 0.001 HIS B 42 PHE 0.011 0.001 PHE D 143 TYR 0.013 0.001 TYR I 94 ARG 0.005 0.000 ARG H 149 Details of bonding type rmsd hydrogen bonds : bond 0.03206 ( 684) hydrogen bonds : angle 4.52437 ( 2091) metal coordination : bond 0.00366 ( 12) covalent geometry : bond 0.00357 (15500) covalent geometry : angle 0.62783 (21124) *********************** 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 201 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.9005 (mmt) cc_final: 0.8760 (mmp) REVERT: A 202 TYR cc_start: 0.8250 (m-80) cc_final: 0.7901 (m-80) REVERT: A 321 MET cc_start: 0.8808 (mpp) cc_final: 0.8399 (mmm) REVERT: B 56 MET cc_start: 0.9011 (mmt) cc_final: 0.8765 (mmp) REVERT: B 202 TYR cc_start: 0.8247 (m-80) cc_final: 0.7900 (m-80) REVERT: B 321 MET cc_start: 0.8808 (mpp) cc_final: 0.8399 (mmm) REVERT: C 2 GLU cc_start: 0.8568 (pm20) cc_final: 0.8306 (pm20) REVERT: C 36 LYS cc_start: 0.9563 (OUTLIER) cc_final: 0.9019 (mtmm) REVERT: D 98 LYS cc_start: 0.9028 (ttmt) cc_final: 0.8714 (ttmm) REVERT: E 14 ASP cc_start: 0.8582 (t0) cc_final: 0.8352 (t0) REVERT: E 91 LYS cc_start: 0.8904 (tptp) cc_final: 0.8691 (tptp) REVERT: E 105 GLN cc_start: 0.9573 (mm110) cc_final: 0.9274 (mm-40) REVERT: G 2 GLU cc_start: 0.8564 (pm20) cc_final: 0.8303 (pm20) REVERT: G 36 LYS cc_start: 0.9558 (OUTLIER) cc_final: 0.9014 (mtmm) REVERT: I 14 ASP cc_start: 0.8606 (t0) cc_final: 0.8347 (t0) REVERT: I 91 LYS cc_start: 0.8893 (tptp) cc_final: 0.8684 (tptp) REVERT: I 105 GLN cc_start: 0.9570 (mm110) cc_final: 0.9258 (mm-40) outliers start: 38 outliers final: 15 residues processed: 187 average time/residue: 1.2075 time to fit residues: 250.0050 Evaluate side-chains 171 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 65 VAL 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 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 65 VAL 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 29 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 131 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN F 117 GLN H 8 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.071025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.047249 restraints weight = 55968.454| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 4.02 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3410 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= 0.254 Angle : 0.678 8.620 21124 Z= 0.344 Chirality : 0.044 0.141 2196 Planarity : 0.004 0.053 2562 Dihedral : 13.161 159.872 2456 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.55 % Allowed : 16.11 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.21), residues: 1654 helix: 1.92 (0.22), residues: 578 sheet: 0.27 (0.25), residues: 418 loop : -0.42 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 70 HIS 0.004 0.001 HIS A 42 PHE 0.017 0.002 PHE H 143 TYR 0.021 0.001 TYR J 85 ARG 0.006 0.000 ARG C 93 Details of bonding type rmsd hydrogen bonds : bond 0.03631 ( 684) hydrogen bonds : angle 4.64376 ( 2091) metal coordination : bond 0.00686 ( 12) covalent geometry : bond 0.00575 (15500) covalent geometry : angle 0.67807 (21124) *********************** 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 195 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.9010 (mmt) cc_final: 0.8755 (mmp) REVERT: A 202 TYR cc_start: 0.8285 (m-80) cc_final: 0.7907 (m-80) REVERT: A 321 MET cc_start: 0.8884 (mpp) cc_final: 0.8492 (mmm) REVERT: B 56 MET cc_start: 0.9016 (mmt) cc_final: 0.8760 (mmp) REVERT: B 202 TYR cc_start: 0.8279 (m-80) cc_final: 0.7943 (m-80) REVERT: B 321 MET cc_start: 0.8879 (mpp) cc_final: 0.8490 (mmm) REVERT: C 2 GLU cc_start: 0.8612 (pm20) cc_final: 0.8406 (pm20) REVERT: C 36 LYS cc_start: 0.9565 (OUTLIER) cc_final: 0.8996 (mtmm) REVERT: C 88 GLU cc_start: 0.7287 (pp20) cc_final: 0.6931 (pp20) REVERT: C 176 LYS cc_start: 0.9057 (pttp) cc_final: 0.8747 (pttm) REVERT: D 149 ARG cc_start: 0.9179 (mmm160) cc_final: 0.8841 (tpm170) REVERT: E 14 ASP cc_start: 0.8656 (t0) cc_final: 0.8359 (t0) REVERT: E 101 ASP cc_start: 0.9447 (m-30) cc_final: 0.9239 (m-30) REVERT: E 105 GLN cc_start: 0.9567 (mm110) cc_final: 0.9266 (mm110) REVERT: G 2 GLU cc_start: 0.8602 (pm20) cc_final: 0.8398 (pm20) REVERT: G 36 LYS cc_start: 0.9563 (OUTLIER) cc_final: 0.8994 (mtmm) REVERT: G 88 GLU cc_start: 0.7279 (pp20) cc_final: 0.6921 (pp20) REVERT: H 98 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8703 (ttmm) REVERT: H 149 ARG cc_start: 0.9189 (mmm160) cc_final: 0.8829 (tpm170) REVERT: I 88 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6609 (tm-30) REVERT: I 105 GLN cc_start: 0.9554 (mm110) cc_final: 0.9249 (mm110) REVERT: J 122 MET cc_start: 0.8388 (tpp) cc_final: 0.8127 (tpp) outliers start: 38 outliers final: 21 residues processed: 183 average time/residue: 1.2050 time to fit residues: 244.2424 Evaluate side-chains 173 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 13 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 65 VAL 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 I residue 88 GLU 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 87 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 66 optimal weight: 40.0000 chunk 119 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN H 8 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.071438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.047982 restraints weight = 56885.740| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.97 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3432 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= 0.153 Angle : 0.662 9.286 21124 Z= 0.330 Chirality : 0.043 0.149 2196 Planarity : 0.004 0.054 2562 Dihedral : 13.034 158.797 2456 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.95 % Allowed : 17.99 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.21), residues: 1654 helix: 1.96 (0.22), residues: 580 sheet: 0.34 (0.25), residues: 418 loop : -0.33 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 70 HIS 0.003 0.001 HIS A 42 PHE 0.012 0.001 PHE D 143 TYR 0.010 0.001 TYR C 69 ARG 0.012 0.000 ARG E 93 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 684) hydrogen bonds : angle 4.47798 ( 2091) metal coordination : bond 0.00298 ( 12) covalent geometry : bond 0.00351 (15500) covalent geometry : angle 0.66183 (21124) *********************** 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 189 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 1.695 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 56 MET cc_start: 0.8988 (mmt) cc_final: 0.8734 (mmp) REVERT: A 202 TYR cc_start: 0.8260 (m-80) cc_final: 0.7887 (m-80) REVERT: A 321 MET cc_start: 0.8818 (mpp) cc_final: 0.8449 (mmm) REVERT: B 56 MET cc_start: 0.8994 (mmt) cc_final: 0.8740 (mmp) REVERT: B 202 TYR cc_start: 0.8255 (m-80) cc_final: 0.7881 (m-80) REVERT: B 321 MET cc_start: 0.8820 (mpp) cc_final: 0.8450 (mmm) REVERT: C 2 GLU cc_start: 0.8665 (pm20) cc_final: 0.8426 (pm20) REVERT: C 36 LYS cc_start: 0.9541 (OUTLIER) cc_final: 0.9000 (mtmm) REVERT: C 88 GLU cc_start: 0.7304 (pp20) cc_final: 0.6985 (pp20) REVERT: C 176 LYS cc_start: 0.9090 (pttp) cc_final: 0.8809 (pttm) REVERT: D 149 ARG cc_start: 0.9199 (mmm160) cc_final: 0.8737 (tpm170) REVERT: E 14 ASP cc_start: 0.8598 (t0) cc_final: 0.8357 (t0) REVERT: E 91 LYS cc_start: 0.8771 (tptp) cc_final: 0.8521 (tptp) REVERT: E 101 ASP cc_start: 0.9462 (m-30) cc_final: 0.9240 (m-30) REVERT: E 105 GLN cc_start: 0.9545 (mm110) cc_final: 0.9233 (mm110) REVERT: G 2 GLU cc_start: 0.8649 (pm20) cc_final: 0.8411 (pm20) REVERT: G 36 LYS cc_start: 0.9534 (OUTLIER) cc_final: 0.8995 (mtmm) REVERT: G 88 GLU cc_start: 0.7304 (pp20) cc_final: 0.6980 (pp20) REVERT: H 149 ARG cc_start: 0.9199 (mmm160) cc_final: 0.8727 (tpm170) REVERT: I 14 ASP cc_start: 0.8609 (t0) cc_final: 0.8327 (t0) REVERT: I 101 ASP cc_start: 0.9464 (m-30) cc_final: 0.9248 (m-30) REVERT: I 105 GLN cc_start: 0.9536 (mm110) cc_final: 0.9219 (mm110) REVERT: J 122 MET cc_start: 0.8360 (tpp) cc_final: 0.8143 (tpp) outliers start: 29 outliers final: 17 residues processed: 181 average time/residue: 1.2584 time to fit residues: 251.7184 Evaluate side-chains 172 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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 E residue 13 VAL 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 65 VAL 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 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 58 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 66 optimal weight: 40.0000 chunk 13 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.069737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.046263 restraints weight = 57546.660| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.95 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 15512 Z= 0.325 Angle : 0.750 10.603 21124 Z= 0.376 Chirality : 0.046 0.157 2196 Planarity : 0.004 0.052 2562 Dihedral : 13.214 161.159 2456 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.35 % Allowed : 18.19 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.21), residues: 1654 helix: 1.83 (0.22), residues: 580 sheet: 0.25 (0.25), residues: 418 loop : -0.39 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 70 HIS 0.005 0.001 HIS B 42 PHE 0.021 0.002 PHE D 143 TYR 0.015 0.001 TYR G 69 ARG 0.015 0.001 ARG I 93 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 684) hydrogen bonds : angle 4.73739 ( 2091) metal coordination : bond 0.00845 ( 12) covalent geometry : bond 0.00734 (15500) covalent geometry : angle 0.74968 (21124) *********************** 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 192 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.9041 (mmt) cc_final: 0.8768 (mmp) REVERT: A 202 TYR cc_start: 0.8311 (m-80) cc_final: 0.7941 (m-80) REVERT: A 321 MET cc_start: 0.8870 (mpp) cc_final: 0.8522 (mmm) REVERT: B 56 MET cc_start: 0.9045 (mmt) cc_final: 0.8771 (mmp) REVERT: B 202 TYR cc_start: 0.8312 (m-80) cc_final: 0.7945 (m-80) REVERT: B 321 MET cc_start: 0.8872 (mpp) cc_final: 0.8114 (mpp) REVERT: C 2 GLU cc_start: 0.8644 (pm20) cc_final: 0.8369 (pm20) REVERT: C 36 LYS cc_start: 0.9534 (OUTLIER) cc_final: 0.9020 (mtmm) REVERT: D 98 LYS cc_start: 0.9098 (ttmt) cc_final: 0.8775 (ttmm) REVERT: D 149 ARG cc_start: 0.9278 (mmm160) cc_final: 0.8877 (tpm170) REVERT: E 101 ASP cc_start: 0.9478 (m-30) cc_final: 0.9253 (m-30) REVERT: E 105 GLN cc_start: 0.9552 (mm110) cc_final: 0.9236 (mm110) REVERT: F 114 ILE cc_start: 0.9499 (pt) cc_final: 0.9066 (mt) REVERT: F 122 MET cc_start: 0.8592 (tpp) cc_final: 0.8302 (tpp) REVERT: F 145 GLU cc_start: 0.9657 (tp30) cc_final: 0.9369 (tp30) REVERT: G 2 GLU cc_start: 0.8630 (pm20) cc_final: 0.8356 (pm20) REVERT: G 36 LYS cc_start: 0.9525 (OUTLIER) cc_final: 0.9011 (mtmm) REVERT: H 98 LYS cc_start: 0.9091 (ttmt) cc_final: 0.8767 (ttmm) REVERT: H 149 ARG cc_start: 0.9273 (mmm160) cc_final: 0.8875 (tpm170) REVERT: I 14 ASP cc_start: 0.8558 (t0) cc_final: 0.8327 (t0) REVERT: I 88 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6699 (tm-30) REVERT: I 101 ASP cc_start: 0.9476 (m-30) cc_final: 0.9260 (m-30) REVERT: I 105 GLN cc_start: 0.9535 (mm110) cc_final: 0.9224 (mm110) outliers start: 35 outliers final: 18 residues processed: 180 average time/residue: 1.1887 time to fit residues: 237.6901 Evaluate side-chains 172 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.590 ------------------------------------------------------------------------------- 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 13 VAL Chi-restraints excluded: chain E residue 46 SER 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 65 VAL 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 I residue 88 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 101 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.071109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.047862 restraints weight = 56655.959| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.95 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15512 Z= 0.158 Angle : 0.720 12.231 21124 Z= 0.355 Chirality : 0.043 0.146 2196 Planarity : 0.004 0.054 2562 Dihedral : 13.013 159.243 2456 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.28 % Allowed : 19.66 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.21), residues: 1654 helix: 1.94 (0.22), residues: 580 sheet: 0.33 (0.25), residues: 418 loop : -0.31 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 174 HIS 0.004 0.001 HIS B 42 PHE 0.010 0.001 PHE D 143 TYR 0.009 0.001 TYR C 69 ARG 0.011 0.000 ARG I 93 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 684) hydrogen bonds : angle 4.49678 ( 2091) metal coordination : bond 0.00262 ( 12) covalent geometry : bond 0.00367 (15500) covalent geometry : angle 0.72009 (21124) *********************** 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 178 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8962 (mmt) cc_final: 0.8699 (mmp) REVERT: A 202 TYR cc_start: 0.8308 (m-80) cc_final: 0.7926 (m-80) REVERT: A 321 MET cc_start: 0.8817 (mpp) cc_final: 0.8473 (mmm) REVERT: B 56 MET cc_start: 0.8969 (mmt) cc_final: 0.8705 (mmp) REVERT: B 321 MET cc_start: 0.8821 (mpp) cc_final: 0.8475 (mmm) REVERT: C 1 MET cc_start: 0.9072 (tpp) cc_final: 0.8628 (tpp) REVERT: C 2 GLU cc_start: 0.8663 (pm20) cc_final: 0.8208 (pm20) REVERT: C 36 LYS cc_start: 0.9531 (OUTLIER) cc_final: 0.9021 (mtmm) REVERT: D 98 LYS cc_start: 0.9068 (ttmt) cc_final: 0.8745 (ttmm) REVERT: D 149 ARG cc_start: 0.9279 (mmm160) cc_final: 0.8890 (tpm170) REVERT: E 14 ASP cc_start: 0.8675 (t0) cc_final: 0.8436 (t0) REVERT: E 101 ASP cc_start: 0.9462 (m-30) cc_final: 0.9235 (m-30) REVERT: E 105 GLN cc_start: 0.9545 (mm110) cc_final: 0.9232 (mm110) REVERT: F 114 ILE cc_start: 0.9530 (pt) cc_final: 0.9151 (mt) REVERT: G 1 MET cc_start: 0.9082 (tpp) cc_final: 0.8638 (tpp) REVERT: G 2 GLU cc_start: 0.8650 (pm20) cc_final: 0.8196 (pm20) REVERT: G 36 LYS cc_start: 0.9520 (OUTLIER) cc_final: 0.9007 (mtmm) REVERT: H 98 LYS cc_start: 0.9056 (ttmt) cc_final: 0.8749 (ttmm) REVERT: H 149 ARG cc_start: 0.9271 (mmm160) cc_final: 0.8885 (tpm170) REVERT: I 101 ASP cc_start: 0.9464 (m-30) cc_final: 0.9240 (m-30) REVERT: I 105 GLN cc_start: 0.9530 (mm110) cc_final: 0.9233 (mm110) REVERT: J 122 MET cc_start: 0.8286 (tpp) cc_final: 0.7865 (tpp) outliers start: 19 outliers final: 14 residues processed: 175 average time/residue: 1.1846 time to fit residues: 230.4550 Evaluate side-chains 167 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.784 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 114 optimal weight: 0.0970 chunk 32 optimal weight: 40.0000 chunk 110 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 134 optimal weight: 0.4980 chunk 18 optimal weight: 8.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.071109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.047645 restraints weight = 57192.786| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.99 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15512 Z= 0.165 Angle : 0.750 12.192 21124 Z= 0.368 Chirality : 0.043 0.150 2196 Planarity : 0.004 0.054 2562 Dihedral : 12.949 158.731 2456 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.21 % Allowed : 20.13 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.21), residues: 1654 helix: 1.89 (0.22), residues: 580 sheet: 0.36 (0.25), residues: 418 loop : -0.25 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 174 HIS 0.005 0.001 HIS E 80 PHE 0.011 0.001 PHE H 143 TYR 0.024 0.001 TYR F 85 ARG 0.010 0.000 ARG I 93 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 684) hydrogen bonds : angle 4.46781 ( 2091) metal coordination : bond 0.00314 ( 12) covalent geometry : bond 0.00382 (15500) covalent geometry : angle 0.74960 (21124) ********************** 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 174 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8978 (mmt) cc_final: 0.8727 (mmp) REVERT: A 321 MET cc_start: 0.8808 (mpp) cc_final: 0.8501 (mmm) REVERT: B 56 MET cc_start: 0.8985 (mmt) cc_final: 0.8733 (mmp) REVERT: B 321 MET cc_start: 0.8808 (mpp) cc_final: 0.8501 (mmm) REVERT: C 36 LYS cc_start: 0.9535 (OUTLIER) cc_final: 0.9027 (mtmm) REVERT: C 61 ASP cc_start: 0.9216 (p0) cc_final: 0.9005 (p0) REVERT: D 98 LYS cc_start: 0.9050 (ttmt) cc_final: 0.8740 (ttmm) REVERT: D 149 ARG cc_start: 0.9228 (mmm160) cc_final: 0.8869 (tpm170) REVERT: E 101 ASP cc_start: 0.9470 (m-30) cc_final: 0.9246 (m-30) REVERT: E 105 GLN cc_start: 0.9554 (mm110) cc_final: 0.9242 (mm-40) REVERT: E 174 TRP cc_start: 0.7889 (t-100) cc_final: 0.7492 (t-100) REVERT: F 114 ILE cc_start: 0.9561 (pt) cc_final: 0.9145 (mt) REVERT: F 122 MET cc_start: 0.8463 (tpp) cc_final: 0.8172 (tpp) REVERT: G 36 LYS cc_start: 0.9524 (OUTLIER) cc_final: 0.9014 (mtmm) REVERT: H 98 LYS cc_start: 0.9072 (ttmt) cc_final: 0.8767 (ttmm) REVERT: H 149 ARG cc_start: 0.9222 (mmm160) cc_final: 0.8860 (tpm170) REVERT: I 14 ASP cc_start: 0.8405 (t0) cc_final: 0.8190 (t0) REVERT: I 101 ASP cc_start: 0.9471 (m-30) cc_final: 0.9252 (m-30) REVERT: I 105 GLN cc_start: 0.9546 (mm110) cc_final: 0.9257 (mm110) REVERT: J 122 MET cc_start: 0.8271 (tpp) cc_final: 0.7939 (tpp) outliers start: 18 outliers final: 13 residues processed: 171 average time/residue: 1.2720 time to fit residues: 242.1995 Evaluate side-chains 167 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 1.589 ------------------------------------------------------------------------------- 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 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 46 SER 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 0 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 chunk 139 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 53 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.071190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.047727 restraints weight = 56999.706| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.99 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3803 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= 0.165 Angle : 0.756 12.148 21124 Z= 0.373 Chirality : 0.044 0.176 2196 Planarity : 0.004 0.054 2562 Dihedral : 12.897 158.004 2456 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.94 % Allowed : 20.87 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.21), residues: 1654 helix: 1.87 (0.22), residues: 580 sheet: 0.39 (0.25), residues: 416 loop : -0.28 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP E 174 HIS 0.006 0.001 HIS I 80 PHE 0.015 0.001 PHE F 143 TYR 0.009 0.001 TYR C 69 ARG 0.010 0.000 ARG I 93 Details of bonding type rmsd hydrogen bonds : bond 0.03257 ( 684) hydrogen bonds : angle 4.46717 ( 2091) metal coordination : bond 0.00313 ( 12) covalent geometry : bond 0.00382 (15500) covalent geometry : angle 0.75573 (21124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8537.49 seconds wall clock time: 146 minutes 38.58 seconds (8798.58 seconds total)