Starting phenix.real_space_refine on Sat Mar 16 09:40:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/03_2024/8c54_16433_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/03_2024/8c54_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_16433/03_2024/8c54_16433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/03_2024/8c54_16433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/03_2024/8c54_16433_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/03_2024/8c54_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-dev-5265/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: 14.29, per 1000 atoms: 1.00 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: 6.30 Conformation dependent library (CDL) restraints added in 4.8 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: 3.30 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: 5.21 Time building geometry restraints manager: 6.72 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.510 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 51.670 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.930 ------------------------------------------------------------------------------- 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 : 1.664 Fit side-chains outliers start: 36 outliers final: 36 residues processed: 164 average time/residue: 1.0897 time to fit residues: 199.7093 Evaluate side-chains 164 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 ASP 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: 6.9990 chunk 91 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 349 HIS B 349 HIS C 349 HIS D 163 ASN D 349 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14224 Z= 0.323 Angle : 0.563 4.433 19412 Z= 0.300 Chirality : 0.044 0.142 2276 Planarity : 0.004 0.029 2500 Dihedral : 8.871 81.606 2352 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.05 % Allowed : 19.39 % Favored : 76.56 % 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: 0.29 (0.19), residues: 1936 helix: 0.90 (0.19), residues: 796 sheet: -0.29 (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 A 70 HIS 0.001 0.001 HIS C 349 PHE 0.023 0.003 PHE B 424 TYR 0.008 0.002 TYR C 483 ARG 0.003 0.001 ARG B 204 *********************** 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 172 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 128 time to evaluate : 1.527 Fit side-chains REVERT: A 394 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.6529 (m-80) REVERT: B 394 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.6518 (m-80) REVERT: C 394 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.6521 (m-80) REVERT: D 394 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.6521 (m-80) outliers start: 44 outliers final: 28 residues processed: 164 average time/residue: 1.2414 time to fit residues: 225.3939 Evaluate side-chains 158 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 408 ASP 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: 1.9990 chunk 48 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 173 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 140 optimal weight: 0.1980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS B 349 HIS C 349 HIS D 349 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.0401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14224 Z= 0.164 Angle : 0.451 4.482 19412 Z= 0.240 Chirality : 0.041 0.134 2276 Planarity : 0.003 0.025 2500 Dihedral : 7.860 82.285 2336 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.57 % Allowed : 20.48 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.19), residues: 1936 helix: 1.29 (0.19), residues: 792 sheet: -0.02 (0.26), residues: 376 loop : 0.13 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 70 HIS 0.000 0.000 HIS D 349 PHE 0.017 0.002 PHE D 125 TYR 0.004 0.001 TYR D 86 ARG 0.001 0.000 ARG C 231 *********************** 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 162 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 1.683 Fit side-chains REVERT: A 394 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.6459 (m-80) REVERT: B 394 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.6436 (m-80) REVERT: C 394 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.6439 (m-80) REVERT: D 394 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.6433 (m-80) outliers start: 25 outliers final: 16 residues processed: 156 average time/residue: 1.1840 time to fit residues: 204.4847 Evaluate side-chains 155 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 408 ASP 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: 10.0000 chunk 90 optimal weight: 0.6980 chunk 19 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 chunk 185 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS D 349 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14224 Z= 0.327 Angle : 0.559 4.401 19412 Z= 0.299 Chirality : 0.044 0.141 2276 Planarity : 0.004 0.027 2500 Dihedral : 8.224 79.287 2328 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.57 % Allowed : 21.03 % Favored : 76.40 % 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: 0.37 (0.19), residues: 1936 helix: 0.94 (0.19), residues: 796 sheet: -0.20 (0.25), residues: 404 loop : -0.09 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 70 HIS 0.002 0.001 HIS C 349 PHE 0.021 0.003 PHE C 424 TYR 0.007 0.002 TYR A 483 ARG 0.004 0.001 ARG A 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 153 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 1.627 Fit side-chains REVERT: A 394 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.6523 (m-80) REVERT: B 394 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.6510 (m-80) REVERT: C 394 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.6513 (m-80) REVERT: D 394 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.6511 (m-80) outliers start: 25 outliers final: 21 residues processed: 148 average time/residue: 1.2577 time to fit residues: 205.7324 Evaluate side-chains 151 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 408 ASP 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: 3.9990 chunk 2 optimal weight: 0.0370 chunk 138 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 158 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS B 349 HIS C 349 HIS D 349 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14224 Z= 0.122 Angle : 0.418 4.477 19412 Z= 0.222 Chirality : 0.040 0.130 2276 Planarity : 0.003 0.025 2500 Dihedral : 7.563 83.952 2328 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.49 % Allowed : 20.72 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.19), residues: 1936 helix: 1.39 (0.19), residues: 800 sheet: 0.02 (0.26), residues: 376 loop : 0.19 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 70 HIS 0.000 0.000 HIS A 228 PHE 0.015 0.001 PHE D 125 TYR 0.004 0.001 TYR B 86 ARG 0.001 0.000 ARG A 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 173 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 1.545 Fit side-chains REVERT: A 394 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.6430 (m-80) REVERT: B 394 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.6407 (m-80) REVERT: C 394 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.6409 (m-80) REVERT: D 394 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.6415 (m-80) outliers start: 24 outliers final: 12 residues processed: 169 average time/residue: 1.2003 time to fit residues: 225.2164 Evaluate side-chains 164 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 408 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.9980 chunk 167 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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: 0.0392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14224 Z= 0.252 Angle : 0.506 4.488 19412 Z= 0.272 Chirality : 0.042 0.139 2276 Planarity : 0.004 0.025 2500 Dihedral : 7.557 81.615 2312 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.41 % Allowed : 20.95 % 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: 0.68 (0.19), residues: 1936 helix: 1.16 (0.19), residues: 796 sheet: -0.02 (0.26), residues: 376 loop : 0.10 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 70 HIS 0.001 0.000 HIS A 349 PHE 0.019 0.002 PHE D 424 TYR 0.007 0.002 TYR D 483 ARG 0.002 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 157 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 1.717 Fit side-chains REVERT: A 394 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.6499 (m-80) REVERT: B 394 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.6492 (m-80) REVERT: C 394 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.6496 (m-80) REVERT: D 394 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.6484 (m-80) outliers start: 23 outliers final: 15 residues processed: 146 average time/residue: 1.2066 time to fit residues: 194.7899 Evaluate side-chains 153 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 408 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 185 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS B 349 HIS C 349 HIS D 349 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14224 Z= 0.170 Angle : 0.453 4.495 19412 Z= 0.242 Chirality : 0.041 0.135 2276 Planarity : 0.003 0.024 2500 Dihedral : 7.389 82.683 2312 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.41 % Allowed : 20.95 % 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: 0.84 (0.19), residues: 1936 helix: 1.32 (0.19), residues: 792 sheet: -0.04 (0.26), residues: 376 loop : 0.24 (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 C 349 PHE 0.017 0.002 PHE D 125 TYR 0.005 0.001 TYR A 483 ARG 0.003 0.000 ARG D 257 *********************** 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 163 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.385 Fit side-chains REVERT: A 257 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7458 (mpt-90) REVERT: A 394 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.6487 (m-80) REVERT: B 394 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.6471 (m-80) REVERT: C 394 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.6477 (m-80) REVERT: D 394 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.6469 (m-80) outliers start: 23 outliers final: 12 residues processed: 155 average time/residue: 1.2269 time to fit residues: 210.2283 Evaluate side-chains 155 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 408 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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: 0.8173 moved from start: 0.0476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14224 Z= 0.318 Angle : 0.553 4.428 19412 Z= 0.297 Chirality : 0.044 0.141 2276 Planarity : 0.004 0.027 2500 Dihedral : 7.746 79.553 2312 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.41 % Allowed : 21.18 % Favored : 76.40 % 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: 0.39 (0.19), residues: 1936 helix: 0.97 (0.19), residues: 796 sheet: -0.25 (0.25), residues: 404 loop : -0.05 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 70 HIS 0.002 0.001 HIS C 349 PHE 0.020 0.003 PHE A 424 TYR 0.009 0.002 TYR D 483 ARG 0.004 0.001 ARG C 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 157 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 1.660 Fit side-chains REVERT: A 394 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.6532 (m-80) REVERT: B 394 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.6502 (m-80) REVERT: C 394 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.6501 (m-80) REVERT: D 394 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.6521 (m-80) outliers start: 23 outliers final: 15 residues processed: 148 average time/residue: 1.2243 time to fit residues: 200.5377 Evaluate side-chains 149 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 408 ASP 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: 5.9990 chunk 172 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.8153 moved from start: 0.0361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14224 Z= 0.219 Angle : 0.490 4.496 19412 Z= 0.263 Chirality : 0.042 0.136 2276 Planarity : 0.004 0.023 2500 Dihedral : 7.549 80.475 2312 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.95 % Allowed : 21.65 % Favored : 76.40 % 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: 0.57 (0.19), residues: 1936 helix: 1.12 (0.19), residues: 792 sheet: -0.25 (0.25), residues: 404 loop : 0.11 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 70 HIS 0.001 0.000 HIS B 349 PHE 0.019 0.002 PHE A 424 TYR 0.006 0.001 TYR C 483 ARG 0.003 0.000 ARG D 257 *********************** 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 151 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.558 Fit side-chains REVERT: A 394 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.6506 (m-80) REVERT: B 394 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.6486 (m-80) REVERT: C 394 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.6488 (m-80) REVERT: D 394 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.6492 (m-80) outliers start: 17 outliers final: 12 residues processed: 147 average time/residue: 1.2188 time to fit residues: 198.1977 Evaluate side-chains 149 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 408 ASP 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: 1.9990 chunk 191 optimal weight: 0.7980 chunk 176 optimal weight: 10.0000 chunk 152 optimal weight: 0.4980 chunk 15 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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: 0.8158 moved from start: 0.0373 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= 0.237 Angle : 0.502 4.469 19412 Z= 0.269 Chirality : 0.042 0.137 2276 Planarity : 0.004 0.024 2500 Dihedral : 7.580 80.112 2312 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.87 % Allowed : 21.73 % Favored : 76.40 % 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: 0.52 (0.19), residues: 1936 helix: 1.09 (0.19), residues: 792 sheet: -0.27 (0.25), residues: 404 loop : 0.08 (0.22), residues: 740 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 0.019 0.002 PHE D 424 TYR 0.007 0.002 TYR D 483 ARG 0.003 0.000 ARG D 257 ********************** 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 149 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.607 Fit side-chains REVERT: A 394 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.6501 (m-80) REVERT: B 394 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.6484 (m-80) REVERT: C 394 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.6507 (m-80) REVERT: D 394 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.6488 (m-80) outliers start: 16 outliers final: 12 residues processed: 145 average time/residue: 1.2073 time to fit residues: 193.7535 Evaluate side-chains 149 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 408 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 chunk 63 optimal weight: 0.0770 chunk 156 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS B 349 HIS C 349 HIS D 349 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.148165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.127759 restraints weight = 47033.112| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.23 r_work: 0.3210 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14224 Z= 0.122 Angle : 0.419 4.500 19412 Z= 0.223 Chirality : 0.040 0.131 2276 Planarity : 0.003 0.025 2500 Dihedral : 7.210 83.878 2312 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.87 % Allowed : 21.42 % Favored : 76.71 % 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: 1.37 (0.19), residues: 800 sheet: -0.07 (0.26), residues: 376 loop : 0.24 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 25 HIS 0.000 0.000 HIS D 228 PHE 0.015 0.001 PHE B 125 TYR 0.004 0.001 TYR B 86 ARG 0.004 0.000 ARG D 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4395.78 seconds wall clock time: 78 minutes 44.18 seconds (4724.18 seconds total)