Starting phenix.real_space_refine on Mon Oct 14 01:06:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgv_40469/10_2024/8sgv_40469.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgv_40469/10_2024/8sgv_40469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgv_40469/10_2024/8sgv_40469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgv_40469/10_2024/8sgv_40469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgv_40469/10_2024/8sgv_40469.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgv_40469/10_2024/8sgv_40469.cif" } resolution = 2.58 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= 0.002 sd= 0.022 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 12 5.49 5 S 52 5.16 5 C 10415 2.51 5 N 2893 2.21 5 O 3033 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 16409 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4010 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4006 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4006 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4120 Chain: "A" Number of atoms: 4010 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4006 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4006 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4120 Chain: "C" Number of atoms: 4010 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4006 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4006 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4120 Chain: "D" Number of atoms: 4015 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 499, 4011 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 462} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 499, 4011 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 462} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4125 Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLY B 121 " occ=0.82 ... (6 atoms not shown) pdb=" O BGLY B 121 " occ=0.18 residue: pdb=" N AGLY A 121 " occ=0.82 ... (6 atoms not shown) pdb=" O BGLY A 121 " occ=0.18 residue: pdb=" N AGLY C 121 " occ=0.82 ... (6 atoms not shown) pdb=" O BGLY C 121 " occ=0.18 residue: pdb=" N AGLY D 121 " occ=0.82 ... (6 atoms not shown) pdb=" O BGLY D 121 " occ=0.18 Time building chain proxies: 18.11, per 1000 atoms: 1.10 Number of scatterers: 16409 At special positions: 0 Unit cell: (113.093, 83.3755, 108.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 52 16.00 P 12 15.00 O 3033 8.00 N 2893 7.00 C 10415 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.20 Conformation dependent library (CDL) restraints added in 4.2 seconds 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3722 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 40.8% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'B' and resid 7 through 9 No H-bonds generated for 'chain 'B' and resid 7 through 9' Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 54 through 65 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 160 through 169 Processing helix chain 'B' and resid 178 through 189 removed outlier: 3.562A pdb=" N VAL B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 202 through 205 removed outlier: 3.663A pdb=" N ILE B 205 " --> pdb=" O ASP B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 202 through 205' Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.618A pdb=" N HIS B 211 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET B 212 " --> pdb=" O HIS B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 212' Processing helix chain 'B' and resid 246 through 257 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 348 through 366 removed outlier: 3.681A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 440 through 449 Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 471 through 486 Processing helix chain 'B' and resid 486 through 502 Processing helix chain 'A' and resid 7 through 9 No H-bonds generated for 'chain 'A' and resid 7 through 9' Processing helix chain 'A' and resid 10 through 19 Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.561A pdb=" N VAL A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 202 through 205 removed outlier: 3.662A pdb=" N ILE A 205 " --> pdb=" O ASP A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.618A pdb=" N HIS A 211 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET A 212 " --> pdb=" O HIS A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 259 through 272 Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 348 through 366 removed outlier: 3.680A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 440 through 449 Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 471 through 486 Processing helix chain 'A' and resid 486 through 502 Processing helix chain 'C' and resid 7 through 9 No H-bonds generated for 'chain 'C' and resid 7 through 9' Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 54 through 65 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 178 through 189 removed outlier: 3.561A pdb=" N VAL C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 202 through 205 removed outlier: 3.662A pdb=" N ILE C 205 " --> pdb=" O ASP C 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 202 through 205' Processing helix chain 'C' and resid 208 through 212 removed outlier: 3.618A pdb=" N HIS C 211 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET C 212 " --> pdb=" O HIS C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 208 through 212' Processing helix chain 'C' and resid 246 through 257 Processing helix chain 'C' and resid 259 through 272 Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 348 through 366 removed outlier: 3.680A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 440 through 449 Processing helix chain 'C' and resid 452 through 468 Processing helix chain 'C' and resid 471 through 486 Processing helix chain 'C' and resid 486 through 502 Processing helix chain 'D' and resid 7 through 9 No H-bonds generated for 'chain 'D' and resid 7 through 9' Processing helix chain 'D' and resid 10 through 19 Processing helix chain 'D' and resid 54 through 65 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 160 through 169 Processing helix chain 'D' and resid 178 through 189 removed outlier: 3.561A pdb=" N VAL D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 201 Processing helix chain 'D' and resid 202 through 205 removed outlier: 3.662A pdb=" N ILE D 205 " --> pdb=" O ASP D 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 202 through 205' Processing helix chain 'D' and resid 208 through 212 removed outlier: 3.618A pdb=" N HIS D 211 " --> pdb=" O GLY D 208 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET D 212 " --> pdb=" O HIS D 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 208 through 212' Processing helix chain 'D' and resid 246 through 257 Processing helix chain 'D' and resid 259 through 272 Processing helix chain 'D' and resid 285 through 292 Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 348 through 366 removed outlier: 3.680A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) Proline residue: D 359 - end of helix Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 440 through 449 Processing helix chain 'D' and resid 452 through 468 Processing helix chain 'D' and resid 471 through 486 Processing helix chain 'D' and resid 486 through 503 Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 44 removed outlier: 3.522A pdb=" N ARG D 430 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 343 through 344 removed outlier: 3.994A pdb=" N PHE B 234 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N HIS B 218 " --> pdb=" O CYS B 232 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N CYS B 232 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE B 220 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 230 " --> pdb=" O PHE B 220 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B 314 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE B 281 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE B 82 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS B 77 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 15.177A pdb=" N ASN B 142 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 14.216A pdb=" N LYS B 221 " --> pdb=" O ASN B 142 " (cutoff:3.500A) removed outlier: 13.671A pdb=" N ASP B 144 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N THR B 219 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 10.501A pdb=" N VAL B 146 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N SER B 217 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 429 through 431 removed outlier: 3.538A pdb=" N ARG B 430 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.519A pdb=" N ARG C 430 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344 removed outlier: 3.995A pdb=" N PHE A 234 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS A 218 " --> pdb=" O CYS A 232 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N CYS A 232 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE A 220 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 230 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 314 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE A 281 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE A 82 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS A 77 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 15.177A pdb=" N ASN A 142 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 14.215A pdb=" N LYS A 221 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 13.671A pdb=" N ASP A 144 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N THR A 219 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 10.501A pdb=" N VAL A 146 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N SER A 217 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 431 removed outlier: 3.515A pdb=" N ARG A 430 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 344 removed outlier: 3.994A pdb=" N PHE C 234 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N HIS C 218 " --> pdb=" O CYS C 232 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N CYS C 232 " --> pdb=" O HIS C 218 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE C 220 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C 230 " --> pdb=" O PHE C 220 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY C 314 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE C 281 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE C 82 " --> pdb=" O ASN C 319 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS C 77 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 15.178A pdb=" N ASN C 142 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 14.216A pdb=" N LYS C 221 " --> pdb=" O ASN C 142 " (cutoff:3.500A) removed outlier: 13.671A pdb=" N ASP C 144 " --> pdb=" O THR C 219 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N THR C 219 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 10.501A pdb=" N VAL C 146 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N SER C 217 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 343 through 344 removed outlier: 3.995A pdb=" N PHE D 234 " --> pdb=" O GLY D 216 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N HIS D 218 " --> pdb=" O CYS D 232 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N CYS D 232 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE D 220 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL D 230 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY D 314 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE D 281 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE D 82 " --> pdb=" O ASN D 319 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS D 77 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 15.177A pdb=" N ASN D 142 " --> pdb=" O LYS D 221 " (cutoff:3.500A) removed outlier: 14.217A pdb=" N LYS D 221 " --> pdb=" O ASN D 142 " (cutoff:3.500A) removed outlier: 13.672A pdb=" N ASP D 144 " --> pdb=" O THR D 219 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N THR D 219 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 10.501A pdb=" N VAL D 146 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N SER D 217 " --> pdb=" O VAL D 146 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1899 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.38 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 7059 1.38 - 1.55: 9745 1.55 - 1.71: 25 1.71 - 1.88: 88 1.88 - 2.04: 16 Bond restraints: 16933 Sorted by residual: bond pdb=" O2B NDP C1202 " pdb=" P2B NDP C1202 " ideal model delta sigma weight residual 1.833 1.609 0.224 3.80e-02 6.93e+02 3.49e+01 bond pdb=" O2B NDP B1202 " pdb=" P2B NDP B1202 " ideal model delta sigma weight residual 1.833 1.609 0.224 3.80e-02 6.93e+02 3.48e+01 bond pdb=" O2B NDP D1202 " pdb=" P2B NDP D1202 " ideal model delta sigma weight residual 1.833 1.609 0.224 3.80e-02 6.93e+02 3.46e+01 bond pdb=" O2B NDP A1202 " pdb=" P2B NDP A1202 " ideal model delta sigma weight residual 1.833 1.610 0.223 3.80e-02 6.93e+02 3.46e+01 bond pdb=" O5D NDP C1202 " pdb=" PN NDP C1202 " ideal model delta sigma weight residual 1.757 1.607 0.150 3.50e-02 8.16e+02 1.84e+01 ... (remaining 16928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 22821 3.24 - 6.47: 238 6.47 - 9.71: 36 9.71 - 12.95: 2 12.95 - 16.19: 10 Bond angle restraints: 23107 Sorted by residual: angle pdb=" C5B NDP A1202 " pdb=" O5B NDP A1202 " pdb=" PA NDP A1202 " ideal model delta sigma weight residual 103.84 120.03 -16.19 1.91e+00 2.73e-01 7.14e+01 angle pdb=" C5B NDP D1202 " pdb=" O5B NDP D1202 " pdb=" PA NDP D1202 " ideal model delta sigma weight residual 103.84 119.64 -15.80 1.91e+00 2.73e-01 6.81e+01 angle pdb=" C5B NDP C1202 " pdb=" O5B NDP C1202 " pdb=" PA NDP C1202 " ideal model delta sigma weight residual 103.84 119.51 -15.67 1.91e+00 2.73e-01 6.70e+01 angle pdb=" C5B NDP B1202 " pdb=" O5B NDP B1202 " pdb=" PA NDP B1202 " ideal model delta sigma weight residual 103.84 119.46 -15.62 1.91e+00 2.73e-01 6.65e+01 angle pdb=" PA NDP B1202 " pdb=" O3 NDP B1202 " pdb=" PN NDP B1202 " ideal model delta sigma weight residual 107.74 120.86 -13.12 1.95e+00 2.62e-01 4.51e+01 ... (remaining 23102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.09: 9747 25.09 - 50.18: 104 50.18 - 75.27: 28 75.27 - 100.35: 0 100.35 - 125.44: 4 Dihedral angle restraints: 9883 sinusoidal: 4080 harmonic: 5803 Sorted by residual: dihedral pdb=" C5B NDP D1202 " pdb=" O5B NDP D1202 " pdb=" PA NDP D1202 " pdb=" O3 NDP D1202 " ideal model delta sinusoidal sigma weight residual 175.04 49.60 125.44 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C5B NDP C1202 " pdb=" O5B NDP C1202 " pdb=" PA NDP C1202 " pdb=" O3 NDP C1202 " ideal model delta sinusoidal sigma weight residual 175.04 51.56 123.48 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" C5B NDP B1202 " pdb=" O5B NDP B1202 " pdb=" PA NDP B1202 " pdb=" O3 NDP B1202 " ideal model delta sinusoidal sigma weight residual 175.04 51.72 123.32 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 9880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1626 0.041 - 0.083: 491 0.083 - 0.124: 187 0.124 - 0.165: 21 0.165 - 0.207: 8 Chirality restraints: 2333 Sorted by residual: chirality pdb=" C4D NDP A1202 " pdb=" C3D NDP A1202 " pdb=" C5D NDP A1202 " pdb=" O4D NDP A1202 " both_signs ideal model delta sigma weight residual False -2.71 -2.51 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C4D NDP C1202 " pdb=" C3D NDP C1202 " pdb=" C5D NDP C1202 " pdb=" O4D NDP C1202 " both_signs ideal model delta sigma weight residual False -2.71 -2.51 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C4D NDP D1202 " pdb=" C3D NDP D1202 " pdb=" C5D NDP D1202 " pdb=" O4D NDP D1202 " both_signs ideal model delta sigma weight residual False -2.71 -2.51 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2330 not shown) Planarity restraints: 3065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 346 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO B 347 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 347 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 347 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 346 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO D 347 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 347 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 347 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 346 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO A 347 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 347 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 347 " 0.026 5.00e-02 4.00e+02 ... (remaining 3062 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3867 2.79 - 3.32: 15569 3.32 - 3.84: 28803 3.84 - 4.37: 36180 4.37 - 4.90: 59816 Nonbonded interactions: 144235 Sorted by model distance: nonbonded pdb=" O ASP A 128 " pdb=" NH1 ARG A 130 " model vdw 2.260 3.120 nonbonded pdb=" O ASP B 128 " pdb=" NH1 ARG B 130 " model vdw 2.261 3.120 nonbonded pdb=" O ASP C 128 " pdb=" NH1 ARG C 130 " model vdw 2.261 3.120 nonbonded pdb=" O ASP D 128 " pdb=" NH1 ARG D 130 " model vdw 2.262 3.120 nonbonded pdb=" OD1 ASP B 360 " pdb=" NH2 ARG D 66 " model vdw 2.266 3.120 ... (remaining 144230 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' and (resid 5 through 120 or resid 122 through 502 or resid 1201 throu \ gh 1202)) selection = (chain 'B' and (resid 5 through 120 or resid 122 through 502 or resid 1201 throu \ gh 1202)) selection = (chain 'C' and (resid 5 through 120 or resid 122 through 502 or resid 1201 throu \ gh 1202)) selection = (chain 'D' and (resid 5 through 120 or resid 122 through 502 or resid 1201 throu \ gh 1202)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.18 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: 2.030 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: 0.760 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 49.950 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.120 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:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 : 0.007 0.224 16933 Z= 0.470 Angle : 0.803 16.185 23107 Z= 0.385 Chirality : 0.046 0.207 2333 Planarity : 0.004 0.047 3065 Dihedral : 9.843 125.442 6161 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.23 % Allowed : 2.10 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.82 (0.19), residues: 1997 helix: 1.04 (0.19), residues: 697 sheet: 0.70 (0.31), residues: 292 loop : 0.28 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 183 HIS 0.004 0.001 HIS B 235 PHE 0.014 0.001 PHE B 136 TYR 0.018 0.002 TYR A 236 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 2.053 Fit side-chains outliers start: 4 outliers final: 7 residues processed: 188 average time/residue: 2.0038 time to fit residues: 408.7600 Evaluate side-chains 92 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 264 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 HIS B 352 GLN B 372 HIS A 352 GLN C 352 GLN D 352 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16933 Z= 0.241 Angle : 0.571 6.107 23107 Z= 0.278 Chirality : 0.046 0.153 2333 Planarity : 0.005 0.041 3065 Dihedral : 8.810 126.827 2279 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.29 % Allowed : 6.95 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.19), residues: 1997 helix: 1.32 (0.20), residues: 697 sheet: 0.76 (0.31), residues: 296 loop : 0.20 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 183 HIS 0.003 0.001 HIS C 194 PHE 0.015 0.002 PHE B 136 TYR 0.015 0.001 TYR A 236 ARG 0.009 0.001 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 2.568 Fit side-chains REVERT: B 119 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6920 (mt-10) REVERT: C 119 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6891 (mt-10) outliers start: 22 outliers final: 4 residues processed: 97 average time/residue: 1.8042 time to fit residues: 193.3400 Evaluate side-chains 73 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.0770 chunk 55 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 176 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 492 HIS A 18 GLN A 492 HIS C 18 GLN C 492 HIS D 18 GLN D 492 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16933 Z= 0.213 Angle : 0.533 6.131 23107 Z= 0.258 Chirality : 0.044 0.149 2333 Planarity : 0.004 0.044 3065 Dihedral : 8.642 121.171 2273 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.17 % Allowed : 7.13 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.18), residues: 1997 helix: 1.32 (0.19), residues: 697 sheet: 0.90 (0.30), residues: 292 loop : 0.15 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 183 HIS 0.003 0.001 HIS B 372 PHE 0.014 0.001 PHE B 136 TYR 0.015 0.001 TYR A 236 ARG 0.006 0.000 ARG C 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 2.465 Fit side-chains outliers start: 20 outliers final: 4 residues processed: 84 average time/residue: 1.9415 time to fit residues: 178.8949 Evaluate side-chains 71 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN A 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16933 Z= 0.232 Angle : 0.529 6.368 23107 Z= 0.258 Chirality : 0.044 0.149 2333 Planarity : 0.004 0.043 3065 Dihedral : 8.724 119.052 2273 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.05 % Allowed : 6.78 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.85 (0.18), residues: 1997 helix: 1.27 (0.20), residues: 693 sheet: 0.78 (0.30), residues: 292 loop : 0.10 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 183 HIS 0.002 0.001 HIS C 235 PHE 0.014 0.001 PHE B 136 TYR 0.016 0.001 TYR A 236 ARG 0.007 0.000 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 2.016 Fit side-chains REVERT: B 119 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.6908 (mt-10) REVERT: C 119 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6890 (mt-10) outliers start: 18 outliers final: 4 residues processed: 89 average time/residue: 2.0267 time to fit residues: 196.8245 Evaluate side-chains 79 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.8418 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16933 Z= 0.217 Angle : 0.521 7.023 23107 Z= 0.254 Chirality : 0.044 0.149 2333 Planarity : 0.004 0.044 3065 Dihedral : 8.642 117.194 2273 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.47 % Allowed : 7.65 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.88 (0.18), residues: 1997 helix: 1.28 (0.20), residues: 693 sheet: 0.79 (0.31), residues: 288 loop : 0.14 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 183 HIS 0.002 0.001 HIS B 372 PHE 0.014 0.001 PHE C 136 TYR 0.015 0.001 TYR A 236 ARG 0.007 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 2.103 Fit side-chains REVERT: B 119 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6891 (mt-10) REVERT: A 119 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6871 (mt-10) REVERT: C 119 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6868 (mt-10) REVERT: D 119 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6864 (mt-10) outliers start: 8 outliers final: 4 residues processed: 93 average time/residue: 1.9469 time to fit residues: 198.5883 Evaluate side-chains 83 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 chunk 157 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8396 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16933 Z= 0.178 Angle : 0.503 6.104 23107 Z= 0.243 Chirality : 0.043 0.148 2333 Planarity : 0.004 0.043 3065 Dihedral : 8.426 113.265 2273 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.99 % Allowed : 6.95 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.92 (0.18), residues: 1997 helix: 1.28 (0.20), residues: 699 sheet: 0.85 (0.31), residues: 288 loop : 0.17 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 183 HIS 0.002 0.001 HIS C 235 PHE 0.013 0.001 PHE C 136 TYR 0.014 0.001 TYR A 236 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 1.910 Fit side-chains REVERT: B 119 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6806 (mt-10) REVERT: A 119 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6819 (mt-10) REVERT: C 119 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6808 (mt-10) REVERT: D 119 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6790 (mt-10) outliers start: 17 outliers final: 4 residues processed: 96 average time/residue: 1.9849 time to fit residues: 208.7569 Evaluate side-chains 85 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 188 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.8423 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16933 Z= 0.235 Angle : 0.524 6.270 23107 Z= 0.257 Chirality : 0.044 0.148 2333 Planarity : 0.005 0.055 3065 Dihedral : 8.518 113.768 2273 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.47 % Allowed : 7.13 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.18), residues: 1997 helix: 1.22 (0.20), residues: 699 sheet: 0.77 (0.30), residues: 288 loop : 0.16 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 183 HIS 0.003 0.001 HIS B 372 PHE 0.015 0.001 PHE B 136 TYR 0.016 0.001 TYR A 236 ARG 0.014 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 2.527 Fit side-chains REVERT: B 119 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6858 (mt-10) REVERT: A 119 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6863 (mt-10) REVERT: C 119 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6864 (mt-10) REVERT: D 119 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6854 (mt-10) outliers start: 8 outliers final: 4 residues processed: 87 average time/residue: 2.1098 time to fit residues: 199.9527 Evaluate side-chains 84 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 148 optimal weight: 0.0040 overall best weight: 0.9194 ------------------------------------------------------------------------------- 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: 0.8412 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16933 Z= 0.207 Angle : 0.517 6.190 23107 Z= 0.252 Chirality : 0.043 0.147 2333 Planarity : 0.005 0.058 3065 Dihedral : 8.410 112.249 2273 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.47 % Allowed : 7.18 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.89 (0.18), residues: 1997 helix: 1.24 (0.20), residues: 699 sheet: 0.83 (0.30), residues: 288 loop : 0.16 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 183 HIS 0.003 0.001 HIS B 372 PHE 0.013 0.001 PHE C 136 TYR 0.015 0.001 TYR A 236 ARG 0.014 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 2.106 Fit side-chains REVERT: B 119 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6847 (mt-10) REVERT: A 119 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6843 (mt-10) REVERT: C 119 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6839 (mt-10) REVERT: D 119 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6837 (mt-10) outliers start: 8 outliers final: 4 residues processed: 89 average time/residue: 2.1878 time to fit residues: 212.5202 Evaluate side-chains 84 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.9990 chunk 180 optimal weight: 0.0040 chunk 165 optimal weight: 0.7980 chunk 176 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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: 0.8371 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16933 Z= 0.158 Angle : 0.502 6.404 23107 Z= 0.241 Chirality : 0.042 0.147 2333 Planarity : 0.004 0.053 3065 Dihedral : 8.092 108.050 2273 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.47 % Allowed : 7.36 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.98 (0.19), residues: 1997 helix: 1.35 (0.20), residues: 699 sheet: 0.97 (0.31), residues: 288 loop : 0.16 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 183 HIS 0.002 0.000 HIS C 235 PHE 0.012 0.001 PHE C 136 TYR 0.014 0.001 TYR A 236 ARG 0.013 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 2.052 Fit side-chains REVERT: B 119 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6746 (mt-10) REVERT: A 119 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6720 (mt-10) REVERT: C 119 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6738 (mt-10) REVERT: D 119 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6716 (mt-10) outliers start: 8 outliers final: 4 residues processed: 93 average time/residue: 1.9705 time to fit residues: 200.3092 Evaluate side-chains 85 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 88 optimal weight: 0.4980 chunk 129 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.8407 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16933 Z= 0.217 Angle : 0.536 11.644 23107 Z= 0.258 Chirality : 0.043 0.146 2333 Planarity : 0.005 0.051 3065 Dihedral : 8.239 109.327 2273 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.47 % Allowed : 7.65 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.19), residues: 1997 helix: 1.26 (0.20), residues: 699 sheet: 0.88 (0.31), residues: 288 loop : 0.16 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 183 HIS 0.003 0.001 HIS B 235 PHE 0.014 0.001 PHE A 136 TYR 0.016 0.001 TYR A 236 ARG 0.013 0.001 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 2.251 Fit side-chains REVERT: B 119 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6810 (mt-10) REVERT: A 119 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6800 (mt-10) REVERT: C 119 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6802 (mt-10) REVERT: D 119 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6799 (mt-10) outliers start: 8 outliers final: 4 residues processed: 81 average time/residue: 2.1375 time to fit residues: 189.3441 Evaluate side-chains 80 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 159 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.077337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.063753 restraints weight = 77453.985| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.35 r_work: 0.2600 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16933 Z= 0.200 Angle : 0.530 11.025 23107 Z= 0.254 Chirality : 0.043 0.148 2333 Planarity : 0.005 0.053 3065 Dihedral : 8.135 108.596 2273 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.47 % Allowed : 7.89 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.92 (0.19), residues: 1997 helix: 1.24 (0.20), residues: 703 sheet: 0.93 (0.31), residues: 288 loop : 0.17 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 183 HIS 0.002 0.001 HIS B 235 PHE 0.013 0.001 PHE B 136 TYR 0.015 0.001 TYR A 236 ARG 0.013 0.001 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4630.96 seconds wall clock time: 91 minutes 53.04 seconds (5513.04 seconds total)