Starting phenix.real_space_refine on Sat Feb 17 11:19:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8n_31490/02_2024/7f8n_31490_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8n_31490/02_2024/7f8n_31490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8n_31490/02_2024/7f8n_31490.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8n_31490/02_2024/7f8n_31490.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8n_31490/02_2024/7f8n_31490_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8n_31490/02_2024/7f8n_31490_updated.pdb" } resolution = 3.4 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= 0.004 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 28 5.49 5 S 77 5.16 5 C 12474 2.51 5 N 2716 2.21 5 O 3227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18522 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2467 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2467 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2467 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2467 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2467 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2467 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2467 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 139 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'LBN:plan-2': 3, 'LBN:plan-3': 4, 'LBN:plan-1': 3} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {'LBN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'LBN:plan-2': 3, 'LBN:plan-3': 4, 'LBN:plan-1': 3} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'LBN:plan-2': 2, 'LBN:plan-3': 3, 'LBN:plan-1': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 151 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'LBN:plan-2': 3, 'LBN:plan-3': 4, 'LBN:plan-1': 2} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 218 Unusual residues: {'LBN': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LBN:plan-2': 4, 'LBN:plan-3': 5, 'LBN:plan-1': 5} Unresolved non-hydrogen planarities: 49 Chain: "F" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {'LBN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'LBN:plan-2': 3, 'LBN:plan-3': 4, 'LBN:plan-1': 3} Unresolved non-hydrogen planarities: 36 Chain: "G" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 219 Unusual residues: {'LBN': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'LBN:plan-2': 3, 'LBN:plan-3': 4, 'LBN:plan-1': 3} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 9.48, per 1000 atoms: 0.51 Number of scatterers: 18522 At special positions: 0 Unit cell: (101.25, 102.06, 119.07, 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 77 16.00 P 28 15.00 O 3227 8.00 N 2716 7.00 C 12474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.02 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 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: 7.46 Conformation dependent library (CDL) restraints added in 3.3 seconds 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4214 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 7 sheets defined 64.1% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 33 through 59 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 101 through 130 Proline residue: A 110 - end of helix removed outlier: 3.608A pdb=" N TYR A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 132 through 159 Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 208 through 236 Processing helix chain 'A' and resid 239 through 242 removed outlier: 3.658A pdb=" N ASP A 242 " --> pdb=" O SER A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 270 through 295 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.725A pdb=" N GLU A 310 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 311' Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.629A pdb=" N CYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 59 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 101 through 130 Proline residue: B 110 - end of helix removed outlier: 3.609A pdb=" N TYR B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 132 through 159 Processing helix chain 'B' and resid 195 through 204 Processing helix chain 'B' and resid 208 through 236 Processing helix chain 'B' and resid 239 through 242 removed outlier: 3.657A pdb=" N ASP B 242 " --> pdb=" O SER B 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 239 through 242' Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 270 through 295 Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.726A pdb=" N GLU B 310 " --> pdb=" O LYS B 307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 307 through 311' Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 343 through 353 removed outlier: 3.630A pdb=" N CYS B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 59 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 74 through 87 Processing helix chain 'C' and resid 101 through 130 Proline residue: C 110 - end of helix removed outlier: 3.608A pdb=" N TYR C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 132 through 159 Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 208 through 236 Processing helix chain 'C' and resid 239 through 242 removed outlier: 3.658A pdb=" N ASP C 242 " --> pdb=" O SER C 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 239 through 242' Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 270 through 295 Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 307 through 311 removed outlier: 3.725A pdb=" N GLU C 310 " --> pdb=" O LYS C 307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 307 through 311' Processing helix chain 'C' and resid 327 through 337 Processing helix chain 'C' and resid 343 through 353 removed outlier: 3.629A pdb=" N CYS C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 59 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 74 through 87 Processing helix chain 'D' and resid 101 through 130 Proline residue: D 110 - end of helix removed outlier: 3.608A pdb=" N TYR D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 132 through 159 Processing helix chain 'D' and resid 195 through 204 Processing helix chain 'D' and resid 208 through 236 Processing helix chain 'D' and resid 239 through 242 removed outlier: 3.656A pdb=" N ASP D 242 " --> pdb=" O SER D 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 239 through 242' Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 270 through 295 Proline residue: D 289 - end of helix Processing helix chain 'D' and resid 307 through 311 removed outlier: 3.725A pdb=" N GLU D 310 " --> pdb=" O LYS D 307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 307 through 311' Processing helix chain 'D' and resid 327 through 337 Processing helix chain 'D' and resid 343 through 353 removed outlier: 3.630A pdb=" N CYS D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 350 " --> pdb=" O LYS D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 59 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 74 through 87 Processing helix chain 'E' and resid 101 through 130 Proline residue: E 110 - end of helix removed outlier: 3.608A pdb=" N TYR E 121 " --> pdb=" O ALA E 117 " (cutoff:3.500A) Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 132 through 159 Processing helix chain 'E' and resid 195 through 204 Processing helix chain 'E' and resid 208 through 236 Processing helix chain 'E' and resid 239 through 242 removed outlier: 3.657A pdb=" N ASP E 242 " --> pdb=" O SER E 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 239 through 242' Processing helix chain 'E' and resid 251 through 253 No H-bonds generated for 'chain 'E' and resid 251 through 253' Processing helix chain 'E' and resid 270 through 295 Proline residue: E 289 - end of helix Processing helix chain 'E' and resid 307 through 311 removed outlier: 3.725A pdb=" N GLU E 310 " --> pdb=" O LYS E 307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 307 through 311' Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 343 through 353 removed outlier: 3.630A pdb=" N CYS E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 350 " --> pdb=" O LYS E 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 59 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 74 through 87 Processing helix chain 'F' and resid 101 through 130 Proline residue: F 110 - end of helix removed outlier: 3.609A pdb=" N TYR F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 132 through 159 Processing helix chain 'F' and resid 195 through 204 Processing helix chain 'F' and resid 208 through 236 Processing helix chain 'F' and resid 239 through 242 removed outlier: 3.658A pdb=" N ASP F 242 " --> pdb=" O SER F 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 239 through 242' Processing helix chain 'F' and resid 251 through 253 No H-bonds generated for 'chain 'F' and resid 251 through 253' Processing helix chain 'F' and resid 270 through 295 Proline residue: F 289 - end of helix Processing helix chain 'F' and resid 307 through 311 removed outlier: 3.726A pdb=" N GLU F 310 " --> pdb=" O LYS F 307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 307 through 311' Processing helix chain 'F' and resid 327 through 337 Processing helix chain 'F' and resid 343 through 353 removed outlier: 3.629A pdb=" N CYS F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL F 350 " --> pdb=" O LYS F 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 59 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 74 through 87 Processing helix chain 'G' and resid 101 through 130 Proline residue: G 110 - end of helix removed outlier: 3.609A pdb=" N TYR G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 132 through 159 Processing helix chain 'G' and resid 195 through 204 Processing helix chain 'G' and resid 208 through 236 Processing helix chain 'G' and resid 239 through 242 removed outlier: 3.657A pdb=" N ASP G 242 " --> pdb=" O SER G 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 239 through 242' Processing helix chain 'G' and resid 251 through 253 No H-bonds generated for 'chain 'G' and resid 251 through 253' Processing helix chain 'G' and resid 270 through 295 Proline residue: G 289 - end of helix Processing helix chain 'G' and resid 307 through 311 removed outlier: 3.726A pdb=" N GLU G 310 " --> pdb=" O LYS G 307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 307 through 311' Processing helix chain 'G' and resid 327 through 337 Processing helix chain 'G' and resid 343 through 353 removed outlier: 3.628A pdb=" N CYS G 347 " --> pdb=" O LYS G 343 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL G 350 " --> pdb=" O LYS G 346 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 64 through 67 removed outlier: 4.380A pdb=" N GLN A 264 " --> pdb=" O PHE A 67 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 64 through 67 removed outlier: 4.381A pdb=" N GLN B 264 " --> pdb=" O PHE B 67 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 64 through 67 removed outlier: 4.380A pdb=" N GLN C 264 " --> pdb=" O PHE C 67 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 64 through 67 removed outlier: 4.381A pdb=" N GLN D 264 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 64 through 67 removed outlier: 4.381A pdb=" N GLN E 264 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 64 through 67 removed outlier: 4.380A pdb=" N GLN F 264 " --> pdb=" O PHE F 67 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 64 through 67 removed outlier: 4.380A pdb=" N GLN G 264 " --> pdb=" O PHE G 67 " (cutoff:3.500A) 966 hydrogen bonds defined for protein. 2898 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: 5.06 Time building geometry restraints manager: 8.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5131 1.34 - 1.46: 2861 1.46 - 1.57: 10698 1.57 - 1.69: 28 1.69 - 1.81: 147 Bond restraints: 18865 Sorted by residual: bond pdb=" C42 LBN E 507 " pdb=" C5 LBN E 507 " ideal model delta sigma weight residual 1.333 1.558 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C42 LBN D 505 " pdb=" C5 LBN D 505 " ideal model delta sigma weight residual 1.333 1.557 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C42 LBN G 506 " pdb=" C5 LBN G 506 " ideal model delta sigma weight residual 1.333 1.557 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C42 LBN F 505 " pdb=" C5 LBN F 505 " ideal model delta sigma weight residual 1.333 1.557 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C42 LBN A 503 " pdb=" C5 LBN A 503 " ideal model delta sigma weight residual 1.333 1.557 -0.224 2.00e-02 2.50e+03 1.25e+02 ... (remaining 18860 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.27: 563 107.27 - 113.97: 10565 113.97 - 120.68: 8591 120.68 - 127.39: 5495 127.39 - 134.09: 147 Bond angle restraints: 25361 Sorted by residual: angle pdb=" N PRO C 23 " pdb=" CA PRO C 23 " pdb=" CB PRO C 23 " ideal model delta sigma weight residual 103.25 110.72 -7.47 1.05e+00 9.07e-01 5.06e+01 angle pdb=" N PRO F 23 " pdb=" CA PRO F 23 " pdb=" CB PRO F 23 " ideal model delta sigma weight residual 103.25 110.72 -7.47 1.05e+00 9.07e-01 5.06e+01 angle pdb=" N PRO D 23 " pdb=" CA PRO D 23 " pdb=" CB PRO D 23 " ideal model delta sigma weight residual 103.25 110.71 -7.46 1.05e+00 9.07e-01 5.05e+01 angle pdb=" N PRO E 23 " pdb=" CA PRO E 23 " pdb=" CB PRO E 23 " ideal model delta sigma weight residual 103.25 110.71 -7.46 1.05e+00 9.07e-01 5.04e+01 angle pdb=" N PRO B 23 " pdb=" CA PRO B 23 " pdb=" CB PRO B 23 " ideal model delta sigma weight residual 103.25 110.69 -7.44 1.05e+00 9.07e-01 5.02e+01 ... (remaining 25356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.55: 11067 32.55 - 65.10: 455 65.10 - 97.65: 63 97.65 - 130.20: 21 130.20 - 162.74: 21 Dihedral angle restraints: 11627 sinusoidal: 5166 harmonic: 6461 Sorted by residual: dihedral pdb=" C1 LBN G 502 " pdb=" O1 LBN G 502 " pdb=" P1 LBN G 502 " pdb=" O3 LBN G 502 " ideal model delta sinusoidal sigma weight residual -84.60 78.14 -162.74 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C1 LBN E 503 " pdb=" O1 LBN E 503 " pdb=" P1 LBN E 503 " pdb=" O3 LBN E 503 " ideal model delta sinusoidal sigma weight residual -84.60 78.11 -162.71 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C1 LBN A 506 " pdb=" O1 LBN A 506 " pdb=" P1 LBN A 506 " pdb=" O3 LBN A 506 " ideal model delta sinusoidal sigma weight residual -84.60 78.11 -162.71 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 11624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2200 0.042 - 0.083: 510 0.083 - 0.125: 119 0.125 - 0.166: 6 0.166 - 0.208: 35 Chirality restraints: 2870 Sorted by residual: chirality pdb=" C2 LBN E 506 " pdb=" C1 LBN E 506 " pdb=" C3 LBN E 506 " pdb=" O7 LBN E 506 " both_signs ideal model delta sigma weight residual False -2.36 -2.57 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C2 LBN C 504 " pdb=" C1 LBN C 504 " pdb=" C3 LBN C 504 " pdb=" O7 LBN C 504 " both_signs ideal model delta sigma weight residual False -2.36 -2.57 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C2 LBN G 502 " pdb=" C1 LBN G 502 " pdb=" C3 LBN G 502 " pdb=" O7 LBN G 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.57 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2867 not shown) Planarity restraints: 2968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN F 505 " -0.111 2.00e-02 2.50e+03 1.12e-01 1.25e+02 pdb=" C42 LBN F 505 " 0.110 2.00e-02 2.50e+03 pdb=" C5 LBN F 505 " 0.114 2.00e-02 2.50e+03 pdb=" C8 LBN F 505 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN A 503 " 0.112 2.00e-02 2.50e+03 1.12e-01 1.25e+02 pdb=" C42 LBN A 503 " -0.110 2.00e-02 2.50e+03 pdb=" C5 LBN A 503 " -0.114 2.00e-02 2.50e+03 pdb=" C8 LBN A 503 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 505 " 0.111 2.00e-02 2.50e+03 1.12e-01 1.25e+02 pdb=" C42 LBN C 505 " -0.110 2.00e-02 2.50e+03 pdb=" C5 LBN C 505 " -0.114 2.00e-02 2.50e+03 pdb=" C8 LBN C 505 " 0.112 2.00e-02 2.50e+03 ... (remaining 2965 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2669 2.75 - 3.29: 18422 3.29 - 3.83: 31360 3.83 - 4.36: 39918 4.36 - 4.90: 65659 Nonbonded interactions: 158028 Sorted by model distance: nonbonded pdb=" OD2 ASP E 138 " pdb=" OH TYR E 331 " model vdw 2.219 2.440 nonbonded pdb=" OD2 ASP A 138 " pdb=" OH TYR A 331 " model vdw 2.219 2.440 nonbonded pdb=" OD2 ASP F 138 " pdb=" OH TYR F 331 " model vdw 2.219 2.440 nonbonded pdb=" OD2 ASP C 138 " pdb=" OH TYR C 331 " model vdw 2.219 2.440 nonbonded pdb=" OD2 ASP D 138 " pdb=" OH TYR D 331 " model vdw 2.219 2.440 ... (remaining 158023 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 13 through 356 or (resid 501 and (name C1 or name C12 or n \ ame C15 or name C18 or name C2 or name C6 or name C9 or name N1 or name O1 or na \ me O2 or name O3 or name O4 or name O5 or name O7 or name O8 or name P1 )) or (r \ esid 502 and (name C1 or name C12 or name C15 or name C18 or name C2 or name C3 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C6 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 \ or name O7 or name O8 or name P1 )))) selection = (chain 'B' and (resid 13 through 356 or (resid 501 and (name C1 or name C12 or n \ ame C15 or name C18 or name C2 or name C6 or name C9 or name N1 or name O1 or na \ me O2 or name O3 or name O4 or name O5 or name O7 or name O8 or name P1 )) or (r \ esid 502 and (name C1 or name C12 or name C15 or name C18 or name C2 or name C3 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C6 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 \ or name O7 or name O8 or name P1 )))) selection = (chain 'C' and (resid 13 through 356 or (resid 501 and (name C1 or name C12 or n \ ame C15 or name C18 or name C2 or name C6 or name C9 or name N1 or name O1 or na \ me O2 or name O3 or name O4 or name O5 or name O7 or name O8 or name P1 )) or (r \ esid 502 and (name C1 or name C12 or name C15 or name C18 or name C2 or name C3 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C6 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 \ or name O7 or name O8 or name P1 )))) selection = (chain 'D' and (resid 13 through 356 or (resid 501 and (name C1 or name C12 or n \ ame C15 or name C18 or name C2 or name C6 or name C9 or name N1 or name O1 or na \ me O2 or name O3 or name O4 or name O5 or name O7 or name O8 or name P1 )) or (r \ esid 502 and (name C1 or name C12 or name C15 or name C18 or name C2 or name C3 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C6 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 \ or name O7 or name O8 or name P1 )))) selection = (chain 'E' and (resid 13 through 356 or (resid 501 and (name C1 or name C12 or n \ ame C15 or name C18 or name C2 or name C6 or name C9 or name N1 or name O1 or na \ me O2 or name O3 or name O4 or name O5 or name O7 or name O8 or name P1 )) or (r \ esid 502 and (name C1 or name C12 or name C15 or name C18 or name C2 or name C3 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C6 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 \ or name O7 or name O8 or name P1 )))) selection = (chain 'F' and (resid 13 through 356 or (resid 501 and (name C1 or name C12 or n \ ame C15 or name C18 or name C2 or name C6 or name C9 or name N1 or name O1 or na \ me O2 or name O3 or name O4 or name O5 or name O7 or name O8 or name P1 )) or (r \ esid 502 and (name C1 or name C12 or name C15 or name C18 or name C2 or name C3 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C6 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 \ or name O7 or name O8 or name P1 )))) selection = (chain 'G' and (resid 13 through 356 or (resid 501 and (name C1 or name C12 or n \ ame C15 or name C18 or name C2 or name C6 or name C9 or name N1 or name O1 or na \ me O2 or name O3 or name O4 or name O5 or name O7 or name O8 or name P1 )) or (r \ esid 502 and (name C1 or name C12 or name C15 or name C18 or name C2 or name C3 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ C6 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 \ or name O7 or name O8 or name P1 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 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: 5.690 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 50.410 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.140 Set refine NCS operators: 0.010 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.012 0.225 18865 Z= 0.729 Angle : 1.084 12.119 25361 Z= 0.433 Chirality : 0.043 0.208 2870 Planarity : 0.006 0.112 2968 Dihedral : 18.972 162.744 7371 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.55 % Allowed : 3.69 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.19), residues: 2107 helix: 0.43 (0.14), residues: 1463 sheet: None (None), residues: 0 loop : -3.06 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 104 HIS 0.001 0.000 HIS B 106 PHE 0.012 0.001 PHE A 116 TYR 0.006 0.001 TYR E 331 ARG 0.002 0.000 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 134 time to evaluate : 2.070 Fit side-chains REVERT: C 209 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8504 (tp) outliers start: 49 outliers final: 18 residues processed: 176 average time/residue: 0.3025 time to fit residues: 82.3762 Evaluate side-chains 128 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 9.9990 chunk 159 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 85 optimal weight: 0.0870 chunk 164 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 190 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 92 ASN A 100 ASN A 353 ASN B 56 GLN B 92 ASN B 100 ASN B 353 ASN C 56 GLN C 92 ASN C 100 ASN C 353 ASN D 92 ASN D 100 ASN D 353 ASN E 56 GLN E 92 ASN E 100 ASN E 353 ASN F 56 GLN F 92 ASN F 100 ASN F 353 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN G 100 ASN G 353 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18865 Z= 0.184 Angle : 0.578 9.033 25361 Z= 0.285 Chirality : 0.041 0.154 2870 Planarity : 0.004 0.037 2968 Dihedral : 22.035 176.557 3330 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.81 % Allowed : 7.17 % Favored : 90.03 % 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: -0.54 (0.19), residues: 2107 helix: 0.71 (0.14), residues: 1456 sheet: None (None), residues: 0 loop : -2.90 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 74 HIS 0.001 0.000 HIS B 106 PHE 0.021 0.001 PHE A 116 TYR 0.009 0.001 TYR D 331 ARG 0.005 0.000 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 93 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 28 residues processed: 147 average time/residue: 0.2867 time to fit residues: 67.3067 Evaluate side-chains 116 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 158 optimal weight: 0.0870 chunk 129 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 191 optimal weight: 0.2980 chunk 206 optimal weight: 0.2980 chunk 170 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18865 Z= 0.159 Angle : 0.551 10.731 25361 Z= 0.265 Chirality : 0.040 0.157 2870 Planarity : 0.004 0.035 2968 Dihedral : 20.203 178.297 3328 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.65 % Allowed : 8.21 % Favored : 89.14 % 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: 2107 helix: 0.95 (0.14), residues: 1456 sheet: None (None), residues: 0 loop : -2.80 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 104 HIS 0.001 0.000 HIS G 106 PHE 0.028 0.001 PHE E 299 TYR 0.008 0.001 TYR E 331 ARG 0.004 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 94 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7722 (mp) REVERT: E 211 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7476 (mm) outliers start: 51 outliers final: 28 residues processed: 144 average time/residue: 0.2865 time to fit residues: 66.0253 Evaluate side-chains 116 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 86 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 21 optimal weight: 0.0060 chunk 91 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 202 optimal weight: 0.0770 chunk 100 optimal weight: 0.7980 chunk 181 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN B 100 ASN C 100 ASN D 100 ASN E 100 ASN F 100 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18865 Z= 0.153 Angle : 0.518 7.775 25361 Z= 0.253 Chirality : 0.039 0.168 2870 Planarity : 0.004 0.034 2968 Dihedral : 19.250 179.847 3324 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.01 % Allowed : 8.73 % Favored : 88.26 % 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: 0.06 (0.19), residues: 2107 helix: 1.19 (0.14), residues: 1456 sheet: None (None), residues: 0 loop : -2.73 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 104 HIS 0.003 0.000 HIS E 106 PHE 0.024 0.001 PHE E 116 TYR 0.009 0.001 TYR E 331 ARG 0.003 0.000 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 94 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 311 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7902 (mp) REVERT: G 254 ARG cc_start: 0.8389 (tpp80) cc_final: 0.7847 (tpp-160) outliers start: 58 outliers final: 31 residues processed: 150 average time/residue: 0.2829 time to fit residues: 68.4430 Evaluate side-chains 119 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 87 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 4.9990 chunk 115 optimal weight: 0.0670 chunk 2 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 182 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN D 56 GLN D 100 ASN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18865 Z= 0.193 Angle : 0.537 8.047 25361 Z= 0.262 Chirality : 0.040 0.170 2870 Planarity : 0.004 0.035 2968 Dihedral : 18.756 178.881 3324 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.70 % Allowed : 9.82 % Favored : 87.48 % 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: 0.15 (0.19), residues: 2107 helix: 1.18 (0.14), residues: 1477 sheet: None (None), residues: 0 loop : -2.60 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 104 HIS 0.004 0.001 HIS D 106 PHE 0.023 0.001 PHE G 116 TYR 0.009 0.001 TYR E 331 ARG 0.002 0.000 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 91 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7781 (mp) REVERT: E 311 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7919 (mp) outliers start: 52 outliers final: 34 residues processed: 139 average time/residue: 0.2707 time to fit residues: 61.4279 Evaluate side-chains 123 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 87 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 336 GLU Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 0.2980 chunk 182 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN C 100 ASN D 100 ASN E 100 ASN ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18865 Z= 0.163 Angle : 0.518 9.896 25361 Z= 0.253 Chirality : 0.039 0.164 2870 Planarity : 0.004 0.036 2968 Dihedral : 18.404 179.471 3324 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.55 % Allowed : 10.44 % Favored : 87.01 % 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: 0.25 (0.19), residues: 2107 helix: 1.24 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -2.56 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 104 HIS 0.003 0.000 HIS D 106 PHE 0.027 0.001 PHE F 299 TYR 0.008 0.001 TYR D 331 ARG 0.002 0.000 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 87 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 311 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7746 (mp) REVERT: C 343 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8209 (mtpt) REVERT: E 311 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7876 (mp) outliers start: 49 outliers final: 36 residues processed: 134 average time/residue: 0.2694 time to fit residues: 59.1943 Evaluate side-chains 122 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 84 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18865 Z= 0.225 Angle : 0.549 8.175 25361 Z= 0.271 Chirality : 0.041 0.176 2870 Planarity : 0.004 0.036 2968 Dihedral : 18.090 178.282 3324 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.55 % Allowed : 11.06 % Favored : 86.39 % 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: 0.16 (0.19), residues: 2107 helix: 1.18 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -2.61 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 74 HIS 0.004 0.001 HIS D 106 PHE 0.023 0.001 PHE E 116 TYR 0.009 0.001 TYR B 331 ARG 0.002 0.000 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 93 time to evaluate : 1.907 Fit side-chains revert: symmetry clash REVERT: B 311 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7829 (mp) REVERT: C 343 LYS cc_start: 0.8429 (mtmt) cc_final: 0.8229 (mtpt) REVERT: D 143 MET cc_start: 0.8346 (mtm) cc_final: 0.8143 (mtm) REVERT: E 311 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7915 (mp) outliers start: 49 outliers final: 29 residues processed: 139 average time/residue: 0.2612 time to fit residues: 59.7212 Evaluate side-chains 118 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 87 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18865 Z= 0.233 Angle : 0.548 8.248 25361 Z= 0.270 Chirality : 0.041 0.174 2870 Planarity : 0.004 0.036 2968 Dihedral : 17.867 178.384 3324 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.39 % Allowed : 11.38 % Favored : 86.23 % 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: 0.11 (0.19), residues: 2107 helix: 1.17 (0.14), residues: 1477 sheet: None (None), residues: 0 loop : -2.68 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 74 HIS 0.010 0.001 HIS C 106 PHE 0.022 0.001 PHE E 116 TYR 0.006 0.001 TYR E 111 ARG 0.002 0.000 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 87 time to evaluate : 1.907 Fit side-chains REVERT: A 343 LYS cc_start: 0.8400 (mtmt) cc_final: 0.7936 (mtpp) REVERT: C 343 LYS cc_start: 0.8454 (mtmt) cc_final: 0.8056 (mtpp) REVERT: E 311 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7890 (mp) outliers start: 46 outliers final: 37 residues processed: 129 average time/residue: 0.2892 time to fit residues: 60.8439 Evaluate side-chains 123 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 85 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 188 optimal weight: 0.3980 chunk 113 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 178 optimal weight: 0.2980 chunk 187 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18865 Z= 0.162 Angle : 0.516 7.424 25361 Z= 0.253 Chirality : 0.039 0.164 2870 Planarity : 0.004 0.036 2968 Dihedral : 17.477 179.844 3324 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.23 % Allowed : 11.58 % Favored : 86.18 % 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: 0.25 (0.19), residues: 2107 helix: 1.25 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -2.59 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 74 HIS 0.005 0.000 HIS C 106 PHE 0.023 0.001 PHE E 116 TYR 0.006 0.001 TYR E 111 ARG 0.002 0.000 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 89 time to evaluate : 2.084 Fit side-chains REVERT: A 343 LYS cc_start: 0.8347 (mtmt) cc_final: 0.7880 (mtpp) REVERT: C 343 LYS cc_start: 0.8422 (mtmt) cc_final: 0.8024 (mtpp) REVERT: F 343 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8089 (mtpp) outliers start: 43 outliers final: 37 residues processed: 128 average time/residue: 0.2696 time to fit residues: 56.6473 Evaluate side-chains 122 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 85 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 349 LYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 138 optimal weight: 0.4980 chunk 209 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18865 Z= 0.206 Angle : 0.531 7.734 25361 Z= 0.262 Chirality : 0.040 0.170 2870 Planarity : 0.004 0.036 2968 Dihedral : 17.333 179.969 3324 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.23 % Allowed : 11.64 % Favored : 86.13 % 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: 0.22 (0.19), residues: 2107 helix: 1.21 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -2.56 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 74 HIS 0.006 0.001 HIS C 106 PHE 0.022 0.001 PHE E 116 TYR 0.006 0.001 TYR A 331 ARG 0.002 0.000 ARG G 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4214 Ramachandran restraints generated. 2107 Oldfield, 0 Emsley, 2107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 87 time to evaluate : 1.808 Fit side-chains REVERT: A 343 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7902 (mtpp) REVERT: C 343 LYS cc_start: 0.8430 (mtmt) cc_final: 0.8031 (mtpp) REVERT: F 343 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8080 (mtpp) outliers start: 43 outliers final: 38 residues processed: 126 average time/residue: 0.2686 time to fit residues: 55.4310 Evaluate side-chains 124 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 86 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 153 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 171 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.168565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.140639 restraints weight = 17509.047| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.34 r_work: 0.3296 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18865 Z= 0.168 Angle : 0.513 7.343 25361 Z= 0.253 Chirality : 0.039 0.164 2870 Planarity : 0.004 0.036 2968 Dihedral : 17.118 179.985 3324 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.13 % Allowed : 11.58 % Favored : 86.29 % 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: 0.28 (0.19), residues: 2107 helix: 1.27 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -2.55 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 74 HIS 0.006 0.001 HIS G 106 PHE 0.023 0.001 PHE E 116 TYR 0.006 0.001 TYR E 111 ARG 0.002 0.000 ARG G 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2980.57 seconds wall clock time: 56 minutes 26.08 seconds (3386.08 seconds total)