Starting phenix.real_space_refine on Tue Dec 31 06:48:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h0i_34412/12_2024/8h0i_34412.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h0i_34412/12_2024/8h0i_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_34412/12_2024/8h0i_34412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h0i_34412/12_2024/8h0i_34412.map" model { file = "/net/cci-nas-00/data/ceres_data/8h0i_34412/12_2024/8h0i_34412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h0i_34412/12_2024/8h0i_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 9.17, per 1000 atoms: 0.61 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: 3.39 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: 4.68 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: 4.54 Time building geometry restraints manager: 3.94 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 112 or resid 161 through 176)) selection = chain 'E' selection = (chain 'G' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 112 or resid 161 through 176)) selection = chain 'I' } ncs_group { reference = (chain 'D' and (resid 15 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 151)) selection = (chain 'F' and (resid 15 through 77 or resid 83 through 128 or resid 139 through \ 151)) selection = (chain 'H' and (resid 15 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 151)) selection = (chain 'J' and (resid 15 through 77 or resid 83 through 128 or resid 139 through \ 151)) } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 39.590 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.840 ------------------------------------------------------------------------------- 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 : 0.003 0.063 15500 Z= 0.201 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 *********************** 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 : 1.614 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: 1.2839 time to fit residues: 396.9204 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 : 1.500 ------------------------------------------------------------------------------- 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: 9.9990 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: 3.4086 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN G 97 GLN J 37 HIS ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15500 Z= 0.270 Angle : 0.670 9.138 21124 Z= 0.340 Chirality : 0.044 0.147 2196 Planarity : 0.005 0.053 2562 Dihedral : 12.992 152.901 2456 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.61 % Allowed : 12.01 % Favored : 86.38 % 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: 1.91 (0.22), residues: 578 sheet: 0.12 (0.26), residues: 412 loop : -0.72 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 70 HIS 0.005 0.001 HIS E 28 PHE 0.019 0.002 PHE H 127 TYR 0.015 0.001 TYR F 85 ARG 0.007 0.001 ARG H 19 *********************** 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 208 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 1.920 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: I 171 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8119 (pm20) outliers start: 24 outliers final: 9 residues processed: 195 average time/residue: 1.3448 time to fit residues: 288.8266 Evaluate side-chains 168 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 1.977 ------------------------------------------------------------------------------- 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 46 SER Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 171 GLU Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN J 74 GLN J 117 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15500 Z= 0.274 Angle : 0.631 8.298 21124 Z= 0.322 Chirality : 0.043 0.160 2196 Planarity : 0.004 0.055 2562 Dihedral : 12.989 154.034 2456 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.88 % Allowed : 13.83 % Favored : 84.30 % 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: 0.74 (0.21), residues: 1654 helix: 1.89 (0.22), residues: 580 sheet: 0.32 (0.26), residues: 410 loop : -0.63 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 70 HIS 0.015 0.001 HIS B 199 PHE 0.018 0.001 PHE J 143 TYR 0.012 0.001 TYR C 69 ARG 0.008 0.000 ARG A 198 *********************** 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 198 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 185 average time/residue: 1.2516 time to fit residues: 256.7823 Evaluate side-chains 163 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 THR 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 148 ARG Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 31 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 77 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15500 Z= 0.365 Angle : 0.665 8.433 21124 Z= 0.341 Chirality : 0.044 0.176 2196 Planarity : 0.004 0.055 2562 Dihedral : 13.100 156.816 2456 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.01 % Allowed : 14.77 % Favored : 83.22 % 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: 0.78 (0.21), residues: 1654 helix: 1.87 (0.22), residues: 580 sheet: 0.27 (0.26), residues: 418 loop : -0.50 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 70 HIS 0.004 0.001 HIS A 42 PHE 0.020 0.002 PHE J 143 TYR 0.014 0.001 TYR G 69 ARG 0.004 0.000 ARG I 93 *********************** 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 191 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 19 residues processed: 179 average time/residue: 1.2474 time to fit residues: 247.8197 Evaluate side-chains 167 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 86 VAL Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 46 SER 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 66 ILE Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 144 optimal weight: 0.0470 chunk 40 optimal weight: 1.9990 overall best weight: 3.2084 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15500 Z= 0.249 Angle : 0.648 8.580 21124 Z= 0.326 Chirality : 0.043 0.158 2196 Planarity : 0.004 0.055 2562 Dihedral : 13.042 157.631 2456 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.68 % Allowed : 14.70 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.91 (0.21), residues: 1654 helix: 1.99 (0.22), residues: 580 sheet: 0.44 (0.26), residues: 408 loop : -0.49 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 70 HIS 0.004 0.001 HIS A 42 PHE 0.012 0.001 PHE H 143 TYR 0.011 0.001 TYR E 94 ARG 0.003 0.000 ARG I 93 *********************** 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 195 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 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: symmetry clash REVERT: A 321 MET cc_start: 0.8046 (mmm) cc_final: 0.7508 (mmt) REVERT: B 321 MET cc_start: 0.8047 (mmm) cc_final: 0.7512 (mmt) REVERT: D 148 ARG cc_start: 0.7950 (tpm170) cc_final: 0.7535 (tpm170) REVERT: H 148 ARG cc_start: 0.7953 (tpm170) cc_final: 0.7533 (tpm170) outliers start: 40 outliers final: 17 residues processed: 178 average time/residue: 1.2278 time to fit residues: 242.5754 Evaluate side-chains 164 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 29 MET 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 67 THR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 29 MET Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15500 Z= 0.260 Angle : 0.659 8.866 21124 Z= 0.330 Chirality : 0.043 0.153 2196 Planarity : 0.004 0.054 2562 Dihedral : 13.025 157.704 2456 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.15 % Allowed : 16.78 % Favored : 81.07 % 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: 0.95 (0.21), residues: 1654 helix: 1.96 (0.22), residues: 582 sheet: 0.47 (0.25), residues: 408 loop : -0.43 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 70 HIS 0.003 0.001 HIS B 42 PHE 0.012 0.001 PHE D 143 TYR 0.021 0.001 TYR J 85 ARG 0.006 0.000 ARG G 93 *********************** 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 188 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8270 (ttm) cc_final: 0.8069 (ttp) REVERT: B 1 MET cc_start: 0.8266 (ttm) cc_final: 0.8062 (ttp) outliers start: 32 outliers final: 21 residues processed: 175 average time/residue: 1.2304 time to fit residues: 240.1263 Evaluate side-chains 171 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 14 ASP Chi-restraints excluded: chain E residue 29 MET 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 67 THR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 29 MET Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 159 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15500 Z= 0.319 Angle : 0.702 9.174 21124 Z= 0.350 Chirality : 0.043 0.151 2196 Planarity : 0.004 0.053 2562 Dihedral : 13.043 158.274 2456 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.01 % Allowed : 18.26 % Favored : 79.73 % 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: 1.93 (0.22), residues: 582 sheet: 0.49 (0.25), residues: 408 loop : -0.40 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 174 HIS 0.004 0.001 HIS A 42 PHE 0.014 0.001 PHE H 143 TYR 0.011 0.001 TYR C 69 ARG 0.004 0.000 ARG G 93 *********************** 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 184 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 2.020 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: A 321 MET cc_start: 0.8067 (mmm) cc_final: 0.7484 (mmt) REVERT: B 321 MET cc_start: 0.8066 (mmm) cc_final: 0.7486 (mmt) outliers start: 30 outliers final: 22 residues processed: 176 average time/residue: 1.2891 time to fit residues: 252.1036 Evaluate side-chains 172 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 29 MET 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 46 SER Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 29 MET Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 101 optimal weight: 0.6980 chunk 109 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 145 optimal weight: 0.3980 overall best weight: 2.2182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15500 Z= 0.215 Angle : 0.713 10.707 21124 Z= 0.349 Chirality : 0.043 0.151 2196 Planarity : 0.004 0.054 2562 Dihedral : 12.910 156.605 2456 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.21 % Allowed : 18.99 % Favored : 79.80 % 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: 1.05 (0.21), residues: 1654 helix: 1.97 (0.22), residues: 582 sheet: 0.61 (0.25), residues: 406 loop : -0.33 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 70 HIS 0.003 0.000 HIS I 80 PHE 0.009 0.001 PHE D 143 TYR 0.008 0.001 TYR G 69 ARG 0.004 0.000 ARG F 83 *********************** 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 177 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 1.852 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: A 321 MET cc_start: 0.8091 (mmm) cc_final: 0.7504 (mmt) REVERT: B 321 MET cc_start: 0.8095 (mmm) cc_final: 0.7510 (mmt) outliers start: 18 outliers final: 12 residues processed: 167 average time/residue: 1.3446 time to fit residues: 248.9042 Evaluate side-chains 158 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL 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 153 optimal weight: 10.0000 chunk 139 optimal weight: 30.0000 chunk 149 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 97 optimal weight: 0.0970 overall best weight: 1.7182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15500 Z= 0.200 Angle : 0.731 12.191 21124 Z= 0.357 Chirality : 0.043 0.152 2196 Planarity : 0.004 0.055 2562 Dihedral : 12.806 154.863 2456 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.94 % Allowed : 20.00 % 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: 1.06 (0.21), residues: 1654 helix: 1.95 (0.22), residues: 582 sheet: 0.64 (0.25), residues: 408 loop : -0.32 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 70 HIS 0.003 0.000 HIS A 42 PHE 0.008 0.001 PHE H 143 TYR 0.020 0.001 TYR J 85 ARG 0.003 0.000 ARG D 149 *********************** 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 172 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.8127 (mmm) cc_final: 0.7535 (mmt) REVERT: B 321 MET cc_start: 0.8130 (mmm) cc_final: 0.7539 (mmt) REVERT: D 148 ARG cc_start: 0.8151 (tpm170) cc_final: 0.7481 (tpm170) REVERT: H 148 ARG cc_start: 0.8172 (tpm170) cc_final: 0.7494 (tpm170) outliers start: 14 outliers final: 13 residues processed: 167 average time/residue: 1.2642 time to fit residues: 234.3494 Evaluate side-chains 166 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 15500 Z= 0.550 Angle : 0.844 12.406 21124 Z= 0.422 Chirality : 0.048 0.169 2196 Planarity : 0.005 0.053 2562 Dihedral : 13.139 158.911 2456 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.14 % Allowed : 20.07 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.77 (0.21), residues: 1654 helix: 1.67 (0.22), residues: 582 sheet: 0.23 (0.24), residues: 434 loop : -0.27 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 70 HIS 0.006 0.001 HIS B 42 PHE 0.023 0.002 PHE H 143 TYR 0.025 0.002 TYR F 85 ARG 0.021 0.001 ARG D 149 ********************** 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 160 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 1.908 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: D 148 ARG cc_start: 0.8093 (tpm170) cc_final: 0.7760 (tpm170) REVERT: D 149 ARG cc_start: 0.8201 (mmm160) cc_final: 0.7891 (mmm160) REVERT: H 148 ARG cc_start: 0.8100 (tpm170) cc_final: 0.7759 (tpm170) REVERT: H 149 ARG cc_start: 0.8215 (mmm160) cc_final: 0.7893 (mmm160) outliers start: 17 outliers final: 13 residues processed: 157 average time/residue: 1.2185 time to fit residues: 213.2745 Evaluate side-chains 158 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G residue 67 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 148 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.071039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.047651 restraints weight = 57098.697| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.99 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15500 Z= 0.275 Angle : 0.768 12.135 21124 Z= 0.378 Chirality : 0.044 0.149 2196 Planarity : 0.004 0.054 2562 Dihedral : 12.977 157.517 2456 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.01 % Allowed : 20.27 % Favored : 78.72 % 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: 0.93 (0.21), residues: 1654 helix: 1.79 (0.22), residues: 582 sheet: 0.48 (0.25), residues: 418 loop : -0.29 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 89 HIS 0.005 0.001 HIS A 42 PHE 0.012 0.001 PHE D 143 TYR 0.010 0.001 TYR G 69 ARG 0.006 0.000 ARG D 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4561.31 seconds wall clock time: 83 minutes 1.14 seconds (4981.14 seconds total)