Starting phenix.real_space_refine on Sun Dec 10 11:23:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/12_2023/8c54_16433_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/12_2023/8c54_16433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/12_2023/8c54_16433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/12_2023/8c54_16433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/12_2023/8c54_16433_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/12_2023/8c54_16433_updated.pdb" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 72 5.16 5 C 8884 2.51 5 N 2404 2.21 5 O 2898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 41": "OD1" <-> "OD2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "C ASP 41": "OD1" <-> "OD2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C GLU 375": "OE1" <-> "OE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "D ASP 41": "OD1" <-> "OD2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 261": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14266 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 Conformer: "B" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 bond proxies already assigned to first conformer: 3464 Chain: "B" Number of atoms: 3440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 Conformer: "B" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 bond proxies already assigned to first conformer: 3464 Chain: "C" Number of atoms: 3440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 Conformer: "B" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 bond proxies already assigned to first conformer: 3464 Chain: "D" Number of atoms: 3440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 Conformer: "B" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 bond proxies already assigned to first conformer: 3464 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAI': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Time building chain proxies: 13.93, per 1000 atoms: 0.98 Number of scatterers: 14266 At special positions: 0 Unit cell: (97.4365, 103.464, 97.4365, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 8 15.00 O 2898 8.00 N 2404 7.00 C 8884 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=0, symmetry=0 Time building additional restraints: 5.52 Conformation dependent library (CDL) restraints added in 5.1 seconds 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3472 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 20 sheets defined 41.1% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 12 through 14 No H-bonds generated for 'chain 'A' and resid 12 through 14' Processing helix chain 'A' and resid 53 through 70 Processing helix chain 'A' and resid 75 through 91 Processing helix chain 'A' and resid 93 through 104 Processing helix chain 'A' and resid 108 through 131 removed outlier: 4.526A pdb=" N TYR A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.855A pdb=" N ARG A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 172 " --> pdb=" O MET A 168 " (cutoff:3.500A) Proline residue: A 175 - end of helix Processing helix chain 'A' and resid 193 through 204 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 276 through 292 removed outlier: 3.674A pdb=" N ARG A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ALA A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.916A pdb=" N GLY A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 356 Processing helix chain 'A' and resid 387 through 390 No H-bonds generated for 'chain 'A' and resid 387 through 390' Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 429 through 438 Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'B' and resid 12 through 14 No H-bonds generated for 'chain 'B' and resid 12 through 14' Processing helix chain 'B' and resid 53 through 70 Processing helix chain 'B' and resid 75 through 91 Processing helix chain 'B' and resid 93 through 104 Processing helix chain 'B' and resid 108 through 131 removed outlier: 4.525A pdb=" N TYR B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.860A pdb=" N ARG B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 172 " --> pdb=" O MET B 168 " (cutoff:3.500A) Proline residue: B 175 - end of helix Processing helix chain 'B' and resid 193 through 204 Processing helix chain 'B' and resid 219 through 228 Processing helix chain 'B' and resid 241 through 250 Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 276 through 292 removed outlier: 3.673A pdb=" N ARG B 289 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASN B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ALA B 291 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.916A pdb=" N GLY B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 356 Processing helix chain 'B' and resid 387 through 390 No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'B' and resid 429 through 438 Processing helix chain 'B' and resid 462 through 464 No H-bonds generated for 'chain 'B' and resid 462 through 464' Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'C' and resid 12 through 14 No H-bonds generated for 'chain 'C' and resid 12 through 14' Processing helix chain 'C' and resid 53 through 70 Processing helix chain 'C' and resid 75 through 91 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 108 through 131 removed outlier: 4.525A pdb=" N TYR C 121 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU C 122 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.859A pdb=" N ARG C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 172 " --> pdb=" O MET C 168 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 193 through 204 Processing helix chain 'C' and resid 219 through 228 Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 252 through 254 No H-bonds generated for 'chain 'C' and resid 252 through 254' Processing helix chain 'C' and resid 276 through 292 removed outlier: 3.678A pdb=" N ARG C 289 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASN C 290 " --> pdb=" O SER C 286 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ALA C 291 " --> pdb=" O LYS C 287 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.916A pdb=" N GLY C 321 " --> pdb=" O ALA C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 356 Processing helix chain 'C' and resid 387 through 390 No H-bonds generated for 'chain 'C' and resid 387 through 390' Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 429 through 438 Processing helix chain 'C' and resid 462 through 464 No H-bonds generated for 'chain 'C' and resid 462 through 464' Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'D' and resid 12 through 14 No H-bonds generated for 'chain 'D' and resid 12 through 14' Processing helix chain 'D' and resid 53 through 70 Processing helix chain 'D' and resid 75 through 91 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 108 through 131 removed outlier: 4.525A pdb=" N TYR D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU D 122 " --> pdb=" O ASN D 118 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.862A pdb=" N ARG D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 172 " --> pdb=" O MET D 168 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 193 through 204 Processing helix chain 'D' and resid 219 through 228 Processing helix chain 'D' and resid 241 through 250 Processing helix chain 'D' and resid 252 through 254 No H-bonds generated for 'chain 'D' and resid 252 through 254' Processing helix chain 'D' and resid 276 through 292 removed outlier: 3.677A pdb=" N ARG D 289 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASN D 290 " --> pdb=" O SER D 286 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ALA D 291 " --> pdb=" O LYS D 287 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.916A pdb=" N GLY D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 356 Processing helix chain 'D' and resid 387 through 390 No H-bonds generated for 'chain 'D' and resid 387 through 390' Processing helix chain 'D' and resid 406 through 413 Processing helix chain 'D' and resid 429 through 438 Processing helix chain 'D' and resid 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 Processing sheet with id= B, first strand: chain 'A' and resid 135 through 137 removed outlier: 3.788A pdb=" N ILE A 146 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 212 through 214 removed outlier: 6.639A pdb=" N MET A 183 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ALA A 157 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE A 235 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE A 159 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE A 237 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG A 257 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N PHE A 237 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER A 259 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 443 through 446 removed outlier: 8.243A pdb=" N TYR A 425 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE A 269 " --> pdb=" O TYR A 425 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE A 268 " --> pdb=" O ASN A 299 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE A 301 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 270 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL A 303 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN A 299 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR A 377 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 400 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL A 379 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N SER A 402 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR A 380 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL A 360 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 33 through 37 removed outlier: 3.700A pdb=" N ALA A 46 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 19 through 21 Processing sheet with id= G, first strand: chain 'B' and resid 135 through 137 removed outlier: 3.789A pdb=" N ILE B 146 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 212 through 214 removed outlier: 6.643A pdb=" N MET B 183 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ALA B 157 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE B 235 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE B 159 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B 237 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG B 257 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE B 237 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER B 259 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 443 through 446 removed outlier: 8.247A pdb=" N TYR B 425 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE B 269 " --> pdb=" O TYR B 425 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE B 268 " --> pdb=" O ASN B 299 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE B 301 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B 270 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL B 303 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASN B 299 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR B 377 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE B 400 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL B 379 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N SER B 402 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR B 380 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL B 360 " --> pdb=" O THR B 380 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 33 through 37 removed outlier: 3.696A pdb=" N ALA B 46 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 19 through 21 Processing sheet with id= L, first strand: chain 'C' and resid 135 through 137 removed outlier: 3.792A pdb=" N ILE C 146 " --> pdb=" O ILE C 137 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 212 through 214 removed outlier: 6.637A pdb=" N MET C 183 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ALA C 157 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE C 235 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE C 159 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE C 237 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG C 257 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE C 237 " --> pdb=" O ARG C 257 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER C 259 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 443 through 446 removed outlier: 8.242A pdb=" N TYR C 425 " --> pdb=" O PRO C 267 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE C 269 " --> pdb=" O TYR C 425 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE C 268 " --> pdb=" O ASN C 299 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE C 301 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C 270 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL C 303 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN C 299 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR C 377 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE C 400 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL C 379 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N SER C 402 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR C 380 " --> pdb=" O VAL C 360 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL C 360 " --> pdb=" O THR C 380 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 33 through 37 removed outlier: 3.699A pdb=" N ALA C 46 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 19 through 21 Processing sheet with id= Q, first strand: chain 'D' and resid 135 through 137 removed outlier: 3.790A pdb=" N ILE D 146 " --> pdb=" O ILE D 137 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 212 through 214 removed outlier: 6.640A pdb=" N MET D 183 " --> pdb=" O SER D 213 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ALA D 157 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE D 235 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE D 159 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE D 237 " --> pdb=" O ILE D 159 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG D 257 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE D 237 " --> pdb=" O ARG D 257 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER D 259 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 443 through 446 removed outlier: 8.244A pdb=" N TYR D 425 " --> pdb=" O PRO D 267 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE D 269 " --> pdb=" O TYR D 425 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N PHE D 268 " --> pdb=" O ASN D 299 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE D 301 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL D 270 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL D 303 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN D 299 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N THR D 377 " --> pdb=" O ALA D 398 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE D 400 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL D 379 " --> pdb=" O ILE D 400 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N SER D 402 " --> pdb=" O VAL D 379 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR D 380 " --> pdb=" O VAL D 360 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL D 360 " --> pdb=" O THR D 380 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 33 through 37 removed outlier: 3.699A pdb=" N ALA D 46 " --> pdb=" O VAL D 36 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1736 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: 5.27 Time building geometry restraints manager: 5.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4600 1.34 - 1.46: 2015 1.46 - 1.57: 7473 1.57 - 1.69: 12 1.69 - 1.81: 124 Bond restraints: 14224 Sorted by residual: bond pdb=" O5B NAI D 501 " pdb=" PA NAI D 501 " ideal model delta sigma weight residual 1.644 1.569 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" O5B NAI B 501 " pdb=" PA NAI B 501 " ideal model delta sigma weight residual 1.644 1.570 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" O5B NAI A 501 " pdb=" PA NAI A 501 " ideal model delta sigma weight residual 1.644 1.570 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" O5B NAI C 501 " pdb=" PA NAI C 501 " ideal model delta sigma weight residual 1.644 1.571 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" O5D NAI C 501 " pdb=" PN NAI C 501 " ideal model delta sigma weight residual 1.650 1.578 0.072 2.00e-02 2.50e+03 1.28e+01 ... (remaining 14219 not shown) Histogram of bond angle deviations from ideal: 100.26 - 107.55: 637 107.55 - 114.84: 8410 114.84 - 122.14: 7655 122.14 - 129.43: 2630 129.43 - 136.72: 80 Bond angle restraints: 19412 Sorted by residual: angle pdb=" O1N NAI D 501 " pdb=" PN NAI D 501 " pdb=" O2N NAI D 501 " ideal model delta sigma weight residual 123.22 114.98 8.24 3.00e+00 1.11e-01 7.54e+00 angle pdb=" O1N NAI C 501 " pdb=" PN NAI C 501 " pdb=" O2N NAI C 501 " ideal model delta sigma weight residual 123.22 114.99 8.23 3.00e+00 1.11e-01 7.53e+00 angle pdb=" O1N NAI B 501 " pdb=" PN NAI B 501 " pdb=" O2N NAI B 501 " ideal model delta sigma weight residual 123.22 115.01 8.21 3.00e+00 1.11e-01 7.49e+00 angle pdb=" O1N NAI A 501 " pdb=" PN NAI A 501 " pdb=" O2N NAI A 501 " ideal model delta sigma weight residual 123.22 115.01 8.21 3.00e+00 1.11e-01 7.48e+00 angle pdb=" PA NAI C 501 " pdb=" O3 NAI C 501 " pdb=" PN NAI C 501 " ideal model delta sigma weight residual 129.27 136.72 -7.45 3.00e+00 1.11e-01 6.17e+00 ... (remaining 19407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 7447 17.86 - 35.73: 761 35.73 - 53.59: 236 53.59 - 71.45: 84 71.45 - 89.32: 56 Dihedral angle restraints: 8584 sinusoidal: 3128 harmonic: 5456 Sorted by residual: dihedral pdb=" CA ASN A 118 " pdb=" C ASN A 118 " pdb=" N ALA A 119 " pdb=" CA ALA A 119 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASN C 118 " pdb=" C ASN C 118 " pdb=" N ALA C 119 " pdb=" CA ALA C 119 " ideal model delta harmonic sigma weight residual 180.00 162.59 17.41 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASN B 118 " pdb=" C ASN B 118 " pdb=" N ALA B 119 " pdb=" CA ALA B 119 " ideal model delta harmonic sigma weight residual 180.00 162.59 17.41 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 8581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1343 0.029 - 0.058: 576 0.058 - 0.087: 177 0.087 - 0.116: 150 0.116 - 0.146: 30 Chirality restraints: 2276 Sorted by residual: chirality pdb=" C2B NAI D 501 " pdb=" C1B NAI D 501 " pdb=" C3B NAI D 501 " pdb=" O2B NAI D 501 " both_signs ideal model delta sigma weight residual False -2.55 -2.69 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" C2B NAI A 501 " pdb=" C1B NAI A 501 " pdb=" C3B NAI A 501 " pdb=" O2B NAI A 501 " both_signs ideal model delta sigma weight residual False -2.55 -2.69 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" C2B NAI B 501 " pdb=" C1B NAI B 501 " pdb=" C3B NAI B 501 " pdb=" O2B NAI B 501 " both_signs ideal model delta sigma weight residual False -2.55 -2.69 0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 2273 not shown) Planarity restraints: 2500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 307 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C VAL A 307 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL A 307 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 308 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 307 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C VAL C 307 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL C 307 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA C 308 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 307 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" C VAL D 307 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL D 307 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA D 308 " -0.008 2.00e-02 2.50e+03 ... (remaining 2497 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2676 2.77 - 3.30: 13763 3.30 - 3.83: 27071 3.83 - 4.37: 32828 4.37 - 4.90: 52866 Nonbonded interactions: 129204 Sorted by model distance: nonbonded pdb=" OH TYR A 473 " pdb=" OD2 ASP C 135 " model vdw 2.233 2.440 nonbonded pdb=" O CYS A 297 " pdb=" O HOH A 601 " model vdw 2.236 2.440 nonbonded pdb=" O CYS B 297 " pdb=" O HOH B 601 " model vdw 2.236 2.440 nonbonded pdb=" O CYS C 297 " pdb=" O HOH C 601 " model vdw 2.237 2.440 nonbonded pdb=" OD2 ASP A 135 " pdb=" OH TYR C 473 " model vdw 2.237 2.440 ... (remaining 129199 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 8 through 52 or resid 54 through 129 or resid 131 through \ 181 or resid 183 through 285 or resid 287 through 489 or resid 501)) selection = (chain 'B' and (resid 8 through 52 or resid 54 through 129 or resid 131 through \ 181 or resid 183 through 285 or resid 287 through 489 or resid 501)) selection = (chain 'C' and (resid 8 through 52 or resid 54 through 129 or resid 131 through \ 181 or resid 183 through 285 or resid 287 through 489 or resid 501)) selection = (chain 'D' and (resid 8 through 52 or resid 54 through 129 or resid 131 through \ 181 or resid 183 through 285 or resid 287 through 489 or resid 501)) } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 4.460 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 50.190 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.090 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:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14224 Z= 0.288 Angle : 0.559 8.240 19412 Z= 0.279 Chirality : 0.043 0.146 2276 Planarity : 0.004 0.024 2500 Dihedral : 18.809 89.318 5112 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.43 % Allowed : 20.48 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 1936 helix: 1.19 (0.19), residues: 792 sheet: -0.22 (0.25), residues: 376 loop : 0.09 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 70 HIS 0.002 0.000 HIS D 349 PHE 0.018 0.002 PHE A 125 TYR 0.008 0.001 TYR C 483 ARG 0.002 0.000 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.552 Fit side-chains outliers start: 36 outliers final: 36 residues processed: 164 average time/residue: 1.1048 time to fit residues: 202.2883 Evaluate side-chains 164 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.504 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 36 residues processed: 0 time to fit residues: 1.9356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.3980 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN C 163 ASN D 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.0424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14224 Z= 0.340 Angle : 0.574 4.412 19412 Z= 0.306 Chirality : 0.045 0.144 2276 Planarity : 0.004 0.030 2500 Dihedral : 7.838 81.707 2300 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.98 % Allowed : 19.24 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.19), residues: 1936 helix: 0.86 (0.19), residues: 796 sheet: -0.31 (0.25), residues: 404 loop : -0.15 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 70 HIS 0.002 0.001 HIS C 349 PHE 0.022 0.003 PHE D 424 TYR 0.008 0.002 TYR C 483 ARG 0.004 0.001 ARG C 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 130 time to evaluate : 1.613 Fit side-chains outliers start: 56 outliers final: 40 residues processed: 178 average time/residue: 1.1960 time to fit residues: 236.7561 Evaluate side-chains 167 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 1.531 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 36 residues processed: 4 average time/residue: 0.1879 time to fit residues: 3.1401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 173 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.8127 moved from start: 0.0456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14224 Z= 0.153 Angle : 0.452 4.468 19412 Z= 0.237 Chirality : 0.041 0.133 2276 Planarity : 0.003 0.025 2500 Dihedral : 7.651 88.312 2300 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.89 % Allowed : 19.94 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 1936 helix: 1.31 (0.19), residues: 792 sheet: -0.02 (0.26), residues: 376 loop : 0.14 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 70 HIS 0.001 0.000 HIS A 349 PHE 0.017 0.002 PHE A 125 TYR 0.004 0.001 TYR B 86 ARG 0.001 0.000 ARG A 431 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 146 time to evaluate : 1.565 Fit side-chains outliers start: 42 outliers final: 40 residues processed: 188 average time/residue: 1.0272 time to fit residues: 217.3118 Evaluate side-chains 181 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 141 time to evaluate : 1.503 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 40 residues processed: 0 time to fit residues: 1.9550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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: 0.8184 moved from start: 0.0533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14224 Z= 0.381 Angle : 0.596 4.752 19412 Z= 0.319 Chirality : 0.046 0.147 2276 Planarity : 0.005 0.032 2500 Dihedral : 7.788 82.338 2300 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.91 % Allowed : 19.08 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 1936 helix: 0.85 (0.19), residues: 796 sheet: -0.26 (0.25), residues: 404 loop : -0.13 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 70 HIS 0.002 0.001 HIS C 349 PHE 0.023 0.003 PHE B 424 TYR 0.008 0.002 TYR A 483 ARG 0.004 0.001 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 127 time to evaluate : 1.676 Fit side-chains outliers start: 55 outliers final: 50 residues processed: 171 average time/residue: 1.0810 time to fit residues: 207.4619 Evaluate side-chains 177 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 127 time to evaluate : 1.664 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 44 residues processed: 6 average time/residue: 0.1648 time to fit residues: 3.9441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.8122 moved from start: 0.0517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14224 Z= 0.142 Angle : 0.446 4.436 19412 Z= 0.235 Chirality : 0.041 0.132 2276 Planarity : 0.003 0.025 2500 Dihedral : 7.489 88.765 2300 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.13 % Allowed : 19.24 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.72 (0.19), residues: 1936 helix: 1.29 (0.19), residues: 800 sheet: -0.14 (0.25), residues: 404 loop : 0.12 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 70 HIS 0.000 0.000 HIS B 349 PHE 0.017 0.002 PHE A 125 TYR 0.004 0.001 TYR B 86 ARG 0.001 0.000 ARG B 431 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 142 time to evaluate : 1.473 Fit side-chains outliers start: 45 outliers final: 38 residues processed: 187 average time/residue: 1.0543 time to fit residues: 221.1888 Evaluate side-chains 183 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 145 time to evaluate : 1.448 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 38 residues processed: 0 time to fit residues: 1.8761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.7980 chunk 167 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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: 0.8168 moved from start: 0.0399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14224 Z= 0.284 Angle : 0.532 4.452 19412 Z= 0.284 Chirality : 0.043 0.140 2276 Planarity : 0.004 0.026 2500 Dihedral : 7.565 86.206 2300 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.36 % Allowed : 19.78 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.48 (0.19), residues: 1936 helix: 1.06 (0.19), residues: 796 sheet: -0.21 (0.25), residues: 404 loop : -0.01 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 70 HIS 0.001 0.000 HIS A 349 PHE 0.020 0.002 PHE A 424 TYR 0.008 0.002 TYR C 483 ARG 0.003 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 130 time to evaluate : 1.747 Fit side-chains outliers start: 48 outliers final: 43 residues processed: 170 average time/residue: 1.0999 time to fit residues: 209.3326 Evaluate side-chains 173 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 130 time to evaluate : 1.573 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 39 residues processed: 4 average time/residue: 0.1899 time to fit residues: 3.1915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 chunk 103 optimal weight: 8.9990 chunk 185 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8115 moved from start: 0.0602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14224 Z= 0.138 Angle : 0.439 4.446 19412 Z= 0.231 Chirality : 0.041 0.132 2276 Planarity : 0.003 0.025 2500 Dihedral : 7.202 84.054 2300 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.58 % Allowed : 20.17 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 1936 helix: 1.36 (0.19), residues: 800 sheet: -0.01 (0.26), residues: 376 loop : 0.22 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 70 HIS 0.000 0.000 HIS C 349 PHE 0.016 0.002 PHE B 125 TYR 0.004 0.001 TYR C 86 ARG 0.001 0.000 ARG D 431 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 1.615 Fit side-chains outliers start: 38 outliers final: 36 residues processed: 188 average time/residue: 1.1188 time to fit residues: 235.0655 Evaluate side-chains 184 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 148 time to evaluate : 1.650 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 36 residues processed: 0 time to fit residues: 2.0957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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: 0.8159 moved from start: 0.0390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14224 Z= 0.248 Angle : 0.508 4.479 19412 Z= 0.271 Chirality : 0.043 0.139 2276 Planarity : 0.004 0.024 2500 Dihedral : 7.494 89.980 2300 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.74 % Allowed : 20.40 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.63 (0.19), residues: 1936 helix: 1.16 (0.19), residues: 796 sheet: -0.10 (0.26), residues: 376 loop : 0.08 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 70 HIS 0.001 0.000 HIS D 349 PHE 0.020 0.002 PHE D 424 TYR 0.007 0.002 TYR C 483 ARG 0.003 0.000 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 135 time to evaluate : 1.628 Fit side-chains outliers start: 40 outliers final: 36 residues processed: 171 average time/residue: 1.1076 time to fit residues: 212.3882 Evaluate side-chains 170 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 1.398 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 36 residues processed: 0 time to fit residues: 1.8710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.8160 moved from start: 0.0422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14224 Z= 0.268 Angle : 0.533 4.458 19412 Z= 0.282 Chirality : 0.043 0.138 2276 Planarity : 0.004 0.026 2500 Dihedral : 7.873 88.995 2300 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.43 % Allowed : 20.40 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.19), residues: 1936 helix: 1.05 (0.19), residues: 796 sheet: -0.13 (0.26), residues: 376 loop : 0.07 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 70 HIS 0.001 0.000 HIS A 349 PHE 0.020 0.002 PHE D 424 TYR 0.008 0.002 TYR C 483 ARG 0.003 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 131 time to evaluate : 1.642 Fit side-chains outliers start: 36 outliers final: 32 residues processed: 167 average time/residue: 1.1331 time to fit residues: 211.8383 Evaluate side-chains 163 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 131 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 32 residues processed: 0 time to fit residues: 2.2226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 191 optimal weight: 0.0970 chunk 176 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- 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: 0.8185 moved from start: 0.0579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14224 Z= 0.382 Angle : 0.605 5.078 19412 Z= 0.324 Chirality : 0.046 0.147 2276 Planarity : 0.005 0.032 2500 Dihedral : 7.884 88.395 2300 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.43 % Allowed : 20.72 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.21 (0.19), residues: 1936 helix: 0.82 (0.19), residues: 796 sheet: -0.34 (0.25), residues: 404 loop : -0.14 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 70 HIS 0.003 0.001 HIS A 349 PHE 0.022 0.003 PHE A 424 TYR 0.010 0.002 TYR C 483 ARG 0.004 0.001 ARG A 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 133 time to evaluate : 1.625 Fit side-chains outliers start: 36 outliers final: 32 residues processed: 165 average time/residue: 1.1159 time to fit residues: 206.2409 Evaluate side-chains 163 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 131 time to evaluate : 1.399 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 32 residues processed: 0 time to fit residues: 1.8186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 133 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.146370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.126194 restraints weight = 47268.478| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.26 r_work: 0.3162 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.0519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14224 Z= 0.142 Angle : 0.457 4.498 19412 Z= 0.240 Chirality : 0.041 0.134 2276 Planarity : 0.003 0.024 2500 Dihedral : 7.347 84.030 2300 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.12 % Allowed : 20.72 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 1936 helix: 1.24 (0.19), residues: 796 sheet: -0.28 (0.25), residues: 404 loop : 0.09 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 70 HIS 0.000 0.000 HIS C 405 PHE 0.017 0.002 PHE A 125 TYR 0.005 0.001 TYR C 483 ARG 0.001 0.000 ARG C 431 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4240.17 seconds wall clock time: 76 minutes 45.06 seconds (4605.06 seconds total)