Starting phenix.real_space_refine on Tue Apr 9 12:47:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgv_40469/04_2024/8sgv_40469_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgv_40469/04_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_40469/04_2024/8sgv_40469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgv_40469/04_2024/8sgv_40469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgv_40469/04_2024/8sgv_40469_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgv_40469/04_2024/8sgv_40469_updated.pdb" } 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 Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 15.98, per 1000 atoms: 0.97 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 - 3.50 Amino acid : False - 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: 6.87 Conformation dependent library (CDL) restraints added in 6.0 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... running ksdssp... Secondary structure from input PDB file: 76 helices and 4 sheets defined 35.0% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'B' and resid 8 through 18 removed outlier: 5.088A pdb=" N MET B 12 " --> pdb=" O SER B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 66 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 158 through 168 Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 179 through 188 Processing helix chain 'B' and resid 190 through 200 removed outlier: 4.173A pdb=" N HIS B 194 " --> pdb=" O GLU B 191 " (cutoff:3.500A) 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 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 325 through 328 No H-bonds generated for 'chain 'B' and resid 325 through 328' Processing helix chain 'B' and resid 349 through 365 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 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 441 through 448 Processing helix chain 'B' and resid 453 through 469 removed outlier: 4.876A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 485 Processing helix chain 'B' and resid 487 through 501 Processing helix chain 'A' and resid 8 through 18 removed outlier: 5.088A pdb=" N MET A 12 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 158 through 168 Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 179 through 188 Processing helix chain 'A' and resid 190 through 200 removed outlier: 4.173A pdb=" N HIS A 194 " --> pdb=" O GLU A 191 " (cutoff:3.500A) 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 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 247 through 256 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 325 through 328 No H-bonds generated for 'chain 'A' and resid 325 through 328' Processing helix chain 'A' and resid 349 through 365 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 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 441 through 448 Processing helix chain 'A' and resid 453 through 469 removed outlier: 4.877A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 487 through 501 Processing helix chain 'C' and resid 8 through 18 removed outlier: 5.089A pdb=" N MET C 12 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 66 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 158 through 168 Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 179 through 188 Processing helix chain 'C' and resid 190 through 200 removed outlier: 4.173A pdb=" N HIS C 194 " --> pdb=" O GLU C 191 " (cutoff:3.500A) 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 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 260 through 271 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 325 through 328 No H-bonds generated for 'chain 'C' and resid 325 through 328' Processing helix chain 'C' and resid 349 through 365 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 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 441 through 448 Processing helix chain 'C' and resid 453 through 469 removed outlier: 4.877A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 487 through 501 Processing helix chain 'D' and resid 8 through 18 removed outlier: 5.089A pdb=" N MET D 12 " --> pdb=" O SER D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 158 through 168 Proline residue: D 162 - end of helix Processing helix chain 'D' and resid 179 through 188 Processing helix chain 'D' and resid 190 through 200 removed outlier: 4.173A pdb=" N HIS D 194 " --> pdb=" O GLU D 191 " (cutoff:3.500A) 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 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 247 through 256 Processing helix chain 'D' and resid 260 through 271 Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 325 through 328 No H-bonds generated for 'chain 'D' and resid 325 through 328' Processing helix chain 'D' and resid 349 through 365 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 370 through 372 No H-bonds generated for 'chain 'D' and resid 370 through 372' Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 441 through 448 Processing helix chain 'D' and resid 453 through 469 removed outlier: 4.876A pdb=" N ASP D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 487 through 502 Processing sheet with id= A, first strand: chain 'B' and resid 141 through 148 removed outlier: 4.478A pdb=" N LYS B 77 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TYR B 84 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU B 318 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU B 86 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU B 316 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE B 279 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS B 315 " --> pdb=" O TRP B 277 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP B 277 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE B 234 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HIS B 218 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N TYR B 236 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLY B 216 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR B 238 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N GLY B 214 " --> pdb=" O THR B 238 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 141 through 148 removed outlier: 4.477A pdb=" N LYS A 77 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TYR A 84 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU A 318 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLU A 86 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU A 316 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE A 279 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS A 315 " --> pdb=" O TRP A 277 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP A 277 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE A 234 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N HIS A 218 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N TYR A 236 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY A 216 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR A 238 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N GLY A 214 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 141 through 148 removed outlier: 4.478A pdb=" N LYS C 77 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR C 84 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU C 318 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLU C 86 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU C 316 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE C 279 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS C 315 " --> pdb=" O TRP C 277 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP C 277 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE C 234 " --> pdb=" O HIS C 218 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N HIS C 218 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N TYR C 236 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY C 216 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR C 238 " --> pdb=" O GLY C 214 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N GLY C 214 " --> pdb=" O THR C 238 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 141 through 148 removed outlier: 4.479A pdb=" N LYS D 77 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR D 84 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU D 318 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLU D 86 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU D 316 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE D 279 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LYS D 315 " --> pdb=" O TRP D 277 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP D 277 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE D 234 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HIS D 218 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N TYR D 236 " --> pdb=" O GLY D 216 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY D 216 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR D 238 " --> pdb=" O GLY D 214 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N GLY D 214 " --> pdb=" O THR D 238 " (cutoff:3.500A) 545 hydrogen bonds defined for protein. 1383 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: 5.09 Time building geometry restraints manager: 7.34 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: 88.09 - 106.34: 754 106.34 - 124.59: 21758 124.59 - 142.85: 587 142.85 - 161.10: 0 161.10 - 179.36: 8 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: 3931 2.79 - 3.32: 15633 3.32 - 3.84: 28834 3.84 - 4.37: 36480 4.37 - 4.90: 59837 Nonbonded interactions: 144715 Sorted by model distance: nonbonded pdb=" O ASP A 128 " pdb=" NH1 ARG A 130 " model vdw 2.260 2.520 nonbonded pdb=" O ASP B 128 " pdb=" NH1 ARG B 130 " model vdw 2.261 2.520 nonbonded pdb=" O ASP C 128 " pdb=" NH1 ARG C 130 " model vdw 2.261 2.520 nonbonded pdb=" O ASP D 128 " pdb=" NH1 ARG D 130 " model vdw 2.262 2.520 nonbonded pdb=" OD1 ASP B 360 " pdb=" NH2 ARG D 66 " model vdw 2.266 2.520 ... (remaining 144710 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.770 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: 0.010 Extract box with map and model: 9.990 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 57.020 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.360 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:15.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.190 ------------------------------------------------------------------------------- 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= 0.482 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 : 2.001 Fit side-chains outliers start: 4 outliers final: 7 residues processed: 188 average time/residue: 1.8291 time to fit residues: 374.8607 Evaluate side-chains 92 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 1.999 ------------------------------------------------------------------------------- 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: 0.9980 chunk 148 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 A 352 GLN C 352 GLN D 352 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1441 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= 0.207 Angle : 0.544 6.816 23107 Z= 0.261 Chirality : 0.044 0.152 2333 Planarity : 0.004 0.042 3065 Dihedral : 8.598 123.941 2279 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.93 % Allowed : 7.54 % Favored : 91.53 % 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: 0.75 (0.19), residues: 1997 helix: 0.86 (0.20), residues: 693 sheet: 0.88 (0.31), residues: 292 loop : 0.26 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 183 HIS 0.003 0.001 HIS B 235 PHE 0.014 0.001 PHE A 136 TYR 0.015 0.001 TYR D 236 ARG 0.009 0.000 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 86 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 1.822 Fit side-chains REVERT: B 119 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6779 (mt-10) REVERT: C 119 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6767 (mt-10) outliers start: 16 outliers final: 4 residues processed: 80 average time/residue: 1.6124 time to fit residues: 142.9491 Evaluate side-chains 67 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 1.781 ------------------------------------------------------------------------------- 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: 1.9990 chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 372 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 16933 Z= 0.415 Angle : 0.606 6.611 23107 Z= 0.301 Chirality : 0.049 0.154 2333 Planarity : 0.005 0.045 3065 Dihedral : 9.115 130.475 2273 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.05 % Allowed : 7.18 % 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: 0.23 (0.18), residues: 1997 helix: 0.28 (0.19), residues: 693 sheet: 0.69 (0.30), residues: 296 loop : 0.04 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 183 HIS 0.005 0.001 HIS A 63 PHE 0.017 0.002 PHE C 136 TYR 0.018 0.002 TYR B 236 ARG 0.005 0.001 ARG B 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 81 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 1.937 Fit side-chains REVERT: B 119 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7202 (mt-10) REVERT: A 119 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7216 (mt-10) REVERT: C 119 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7187 (mt-10) REVERT: D 119 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7218 (mt-10) outliers start: 18 outliers final: 8 residues processed: 80 average time/residue: 1.8737 time to fit residues: 164.6838 Evaluate side-chains 72 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 122 SER 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: 0.7980 chunk 134 optimal weight: 0.7980 chunk 92 optimal weight: 0.1980 chunk 19 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 51 optimal weight: 0.0070 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16933 Z= 0.160 Angle : 0.507 5.694 23107 Z= 0.244 Chirality : 0.042 0.150 2333 Planarity : 0.004 0.040 3065 Dihedral : 8.432 120.281 2273 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.70 % Allowed : 7.30 % Favored : 92.00 % 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: 0.52 (0.19), residues: 1997 helix: 0.48 (0.19), residues: 695 sheet: 1.09 (0.31), residues: 292 loop : 0.15 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 183 HIS 0.003 0.000 HIS C 235 PHE 0.013 0.001 PHE B 136 TYR 0.016 0.001 TYR C 236 ARG 0.010 0.000 ARG B 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 82 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 2.072 Fit side-chains REVERT: B 119 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6971 (mt-10) REVERT: A 119 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6953 (mt-10) REVERT: C 119 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6969 (mt-10) REVERT: D 119 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6949 (mt-10) outliers start: 12 outliers final: 4 residues processed: 81 average time/residue: 1.7779 time to fit residues: 158.3895 Evaluate side-chains 74 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 2.069 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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: 0.8467 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16933 Z= 0.316 Angle : 0.549 6.166 23107 Z= 0.272 Chirality : 0.046 0.151 2333 Planarity : 0.004 0.043 3065 Dihedral : 8.801 121.802 2273 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.70 % Allowed : 7.94 % Favored : 91.36 % 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: 0.23 (0.18), residues: 1997 helix: 0.10 (0.19), residues: 717 sheet: 0.86 (0.31), residues: 292 loop : 0.14 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 183 HIS 0.003 0.001 HIS D 63 PHE 0.015 0.002 PHE D 136 TYR 0.018 0.001 TYR A 236 ARG 0.006 0.001 ARG B 382 *********************** 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 73 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 2.042 Fit side-chains REVERT: B 119 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7105 (mt-10) REVERT: A 119 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7118 (mt-10) REVERT: C 119 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: D 119 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7134 (mt-10) outliers start: 12 outliers final: 4 residues processed: 73 average time/residue: 1.9557 time to fit residues: 156.1082 Evaluate side-chains 68 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 1.891 ------------------------------------------------------------------------------- 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: 5.9990 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.8427 moved from start: 0.2314 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 : 0.504 5.594 23107 Z= 0.246 Chirality : 0.043 0.149 2333 Planarity : 0.004 0.041 3065 Dihedral : 8.404 116.685 2273 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.05 % Allowed : 7.42 % Favored : 91.53 % 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: 0.32 (0.18), residues: 1997 helix: 0.22 (0.19), residues: 717 sheet: 0.97 (0.31), residues: 292 loop : 0.13 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 183 HIS 0.003 0.001 HIS B 235 PHE 0.014 0.001 PHE B 136 TYR 0.017 0.001 TYR A 236 ARG 0.010 0.000 ARG B 382 *********************** 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 83 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 2.202 Fit side-chains REVERT: B 119 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7005 (mt-10) REVERT: A 119 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7006 (mt-10) REVERT: C 119 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6998 (mt-10) REVERT: D 119 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6995 (mt-10) outliers start: 18 outliers final: 4 residues processed: 80 average time/residue: 1.7909 time to fit residues: 158.9316 Evaluate side-chains 75 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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: 3.9990 chunk 21 optimal weight: 4.9990 chunk 108 optimal weight: 0.1980 chunk 138 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 188 optimal weight: 0.1980 chunk 118 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.8421 moved from start: 0.2321 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= 0.196 Angle : 0.498 5.497 23107 Z= 0.243 Chirality : 0.043 0.148 2333 Planarity : 0.004 0.041 3065 Dihedral : 8.254 112.470 2273 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.53 % Allowed : 7.71 % 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: 0.45 (0.19), residues: 1997 helix: 0.41 (0.19), residues: 699 sheet: 1.03 (0.31), residues: 292 loop : 0.14 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 183 HIS 0.003 0.001 HIS C 235 PHE 0.013 0.001 PHE B 136 TYR 0.016 0.001 TYR A 236 ARG 0.007 0.000 ARG B 382 *********************** 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 80 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 1.734 Fit side-chains REVERT: B 119 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6967 (mt-10) REVERT: A 119 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6971 (mt-10) REVERT: C 119 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6962 (mt-10) REVERT: D 119 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6973 (mt-10) outliers start: 9 outliers final: 4 residues processed: 80 average time/residue: 1.7520 time to fit residues: 154.4259 Evaluate side-chains 78 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 1.998 ------------------------------------------------------------------------------- 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: 2.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 148 optimal weight: 0.0030 overall best weight: 1.1794 ------------------------------------------------------------------------------- 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: 0.8440 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16933 Z= 0.238 Angle : 0.515 5.654 23107 Z= 0.253 Chirality : 0.044 0.150 2333 Planarity : 0.004 0.042 3065 Dihedral : 8.245 112.078 2273 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.53 % Allowed : 7.65 % Favored : 91.82 % 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: 0.38 (0.19), residues: 1997 helix: 0.33 (0.19), residues: 699 sheet: 0.98 (0.31), residues: 292 loop : 0.10 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 183 HIS 0.003 0.001 HIS C 235 PHE 0.014 0.001 PHE D 136 TYR 0.017 0.001 TYR A 236 ARG 0.010 0.000 ARG C 382 *********************** 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 79 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 1.840 Fit side-chains REVERT: B 119 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6994 (mt-10) REVERT: A 119 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7036 (mt-10) REVERT: C 119 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6986 (mt-10) REVERT: D 119 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7035 (mt-10) outliers start: 9 outliers final: 4 residues processed: 79 average time/residue: 1.7327 time to fit residues: 150.6541 Evaluate side-chains 73 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 2.199 ------------------------------------------------------------------------------- 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: 0.9980 chunk 180 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 chunk 176 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.2364 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= 0.194 Angle : 0.499 8.027 23107 Z= 0.243 Chirality : 0.043 0.148 2333 Planarity : 0.004 0.041 3065 Dihedral : 7.923 108.591 2273 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.47 % Allowed : 8.24 % Favored : 91.30 % 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: 0.46 (0.19), residues: 1997 helix: 0.41 (0.19), residues: 699 sheet: 1.08 (0.31), residues: 292 loop : 0.13 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 183 HIS 0.003 0.001 HIS B 235 PHE 0.013 0.001 PHE B 136 TYR 0.017 0.001 TYR A 236 ARG 0.007 0.000 ARG B 382 *********************** 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 77 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 1.615 Fit side-chains REVERT: B 119 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6959 (mt-10) REVERT: A 119 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6970 (mt-10) REVERT: C 119 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6950 (mt-10) REVERT: D 119 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6969 (mt-10) outliers start: 8 outliers final: 4 residues processed: 77 average time/residue: 1.7748 time to fit residues: 150.3454 Evaluate side-chains 76 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 2.048 ------------------------------------------------------------------------------- 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: 1.9990 chunk 186 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 88 optimal weight: 0.0270 chunk 129 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 120 optimal weight: 0.1980 chunk 95 optimal weight: 0.4980 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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: 0.8377 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16933 Z= 0.143 Angle : 0.486 7.326 23107 Z= 0.233 Chirality : 0.041 0.147 2333 Planarity : 0.004 0.040 3065 Dihedral : 7.480 101.957 2273 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.53 % Allowed : 8.24 % Favored : 91.24 % 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: 0.61 (0.19), residues: 1997 helix: 0.55 (0.19), residues: 699 sheet: 1.28 (0.31), residues: 292 loop : 0.15 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 183 HIS 0.003 0.000 HIS A 235 PHE 0.011 0.001 PHE C 136 TYR 0.015 0.001 TYR C 236 ARG 0.007 0.000 ARG D 382 ********************** 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 79 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 1.909 Fit side-chains REVERT: B 119 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6894 (mt-10) REVERT: A 119 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6882 (mt-10) REVERT: C 119 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6884 (mt-10) REVERT: D 119 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6889 (mt-10) outliers start: 9 outliers final: 4 residues processed: 79 average time/residue: 1.6894 time to fit residues: 147.1389 Evaluate side-chains 74 residues out of total 1713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 1.811 ------------------------------------------------------------------------------- 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: 3.9990 chunk 165 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.074234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.060739 restraints weight = 78000.334| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 3.31 r_work: 0.2497 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16933 Z= 0.379 Angle : 0.566 8.381 23107 Z= 0.281 Chirality : 0.047 0.150 2333 Planarity : 0.005 0.043 3065 Dihedral : 7.990 106.381 2273 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.53 % Allowed : 8.53 % Favored : 90.95 % 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: 0.31 (0.19), residues: 1997 helix: 0.29 (0.19), residues: 699 sheet: 0.93 (0.31), residues: 292 loop : 0.06 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 183 HIS 0.004 0.001 HIS B 372 PHE 0.015 0.002 PHE D 136 TYR 0.018 0.002 TYR A 236 ARG 0.010 0.001 ARG C 382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4438.07 seconds wall clock time: 81 minutes 15.04 seconds (4875.04 seconds total)