Starting phenix.real_space_refine on Mon Jul 22 10:26:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8o_31491/07_2024/7f8o_31491.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8o_31491/07_2024/7f8o_31491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8o_31491/07_2024/7f8o_31491.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8o_31491/07_2024/7f8o_31491.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8o_31491/07_2024/7f8o_31491.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8o_31491/07_2024/7f8o_31491.cif" } resolution = 3.6 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= 0.003 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 21 5.49 5 S 77 5.16 5 C 12012 2.51 5 N 2681 2.21 5 O 3241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 18032 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2498 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 297} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2498 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 297} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2498 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 297} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2498 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 297} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2498 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 297} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2498 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 297} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "G" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2498 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 297} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {'LBN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'LBN:plan-2': 1, 'LBN:plan-3': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {'LBN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'LBN:plan-2': 1, 'LBN:plan-3': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {'LBN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'LBN:plan-2': 1, 'LBN:plan-3': 3} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {'LBN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'LBN:plan-2': 1, 'LBN:plan-3': 3} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {'LBN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'LBN:plan-2': 1, 'LBN:plan-3': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {'LBN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'LBN:plan-2': 1, 'LBN:plan-3': 3} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {'LBN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'LBN:plan-2': 1, 'LBN:plan-3': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 9.87, per 1000 atoms: 0.55 Number of scatterers: 18032 At special positions: 0 Unit cell: (109.35, 108.54, 116.64, 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 21 15.00 O 3241 8.00 N 2681 7.00 C 12012 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=2.03 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: 7.72 Conformation dependent library (CDL) restraints added in 3.3 seconds 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4256 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 7 sheets defined 73.1% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 4.007A pdb=" N TYR A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.565A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.547A pdb=" N TRP A 104 " --> pdb=" O ASN A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 120 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'A' and resid 131 through 155 Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.704A pdb=" N SER A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 237 Processing helix chain 'A' and resid 238 through 242 removed outlier: 4.083A pdb=" N ASP A 242 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 270 through 296 Proline residue: A 289 - end of helix removed outlier: 3.560A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 302 through 312 removed outlier: 4.150A pdb=" N LEU A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL A 308 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.640A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 removed outlier: 3.799A pdb=" N LYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 removed outlier: 4.007A pdb=" N TYR B 10 " --> pdb=" O LEU B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.564A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.547A pdb=" N TRP B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 120 Processing helix chain 'B' and resid 121 through 131 Processing helix chain 'B' and resid 131 through 155 Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.704A pdb=" N SER B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 237 Processing helix chain 'B' and resid 238 through 242 removed outlier: 4.084A pdb=" N ASP B 242 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 270 through 296 Proline residue: B 289 - end of helix removed outlier: 3.560A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 302 through 312 removed outlier: 4.150A pdb=" N LEU B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B 308 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.641A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 353 removed outlier: 3.799A pdb=" N LYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 351 " --> pdb=" O CYS B 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 removed outlier: 4.007A pdb=" N TYR C 10 " --> pdb=" O LEU C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.565A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 100 through 108 removed outlier: 3.547A pdb=" N TRP C 104 " --> pdb=" O ASN C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 120 Processing helix chain 'C' and resid 121 through 131 Processing helix chain 'C' and resid 131 through 155 Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.704A pdb=" N SER C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 237 Processing helix chain 'C' and resid 238 through 242 removed outlier: 4.083A pdb=" N ASP C 242 " --> pdb=" O SER C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 270 through 296 Proline residue: C 289 - end of helix removed outlier: 3.560A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 302 through 312 removed outlier: 4.151A pdb=" N LEU C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL C 308 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 3.640A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 353 removed outlier: 3.799A pdb=" N LYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 351 " --> pdb=" O CYS C 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 removed outlier: 4.007A pdb=" N TYR D 10 " --> pdb=" O LEU D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.564A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 100 through 108 removed outlier: 3.547A pdb=" N TRP D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 120 Processing helix chain 'D' and resid 121 through 131 Processing helix chain 'D' and resid 131 through 155 Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.704A pdb=" N SER D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 237 Processing helix chain 'D' and resid 238 through 242 removed outlier: 4.083A pdb=" N ASP D 242 " --> pdb=" O SER D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 270 through 296 Proline residue: D 289 - end of helix removed outlier: 3.559A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 302 through 312 removed outlier: 4.150A pdb=" N LEU D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL D 308 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 3.640A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 353 removed outlier: 3.799A pdb=" N LYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 351 " --> pdb=" O CYS D 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 removed outlier: 4.007A pdb=" N TYR E 10 " --> pdb=" O LEU E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.564A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 87 Processing helix chain 'E' and resid 100 through 108 removed outlier: 3.547A pdb=" N TRP E 104 " --> pdb=" O ASN E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 120 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 131 through 155 Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.704A pdb=" N SER E 206 " --> pdb=" O THR E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 237 Processing helix chain 'E' and resid 238 through 242 removed outlier: 4.084A pdb=" N ASP E 242 " --> pdb=" O SER E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 256 Processing helix chain 'E' and resid 270 through 296 Proline residue: E 289 - end of helix removed outlier: 3.560A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 302 through 312 removed outlier: 4.150A pdb=" N LEU E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL E 308 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 339 removed outlier: 3.641A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 353 removed outlier: 3.799A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU E 351 " --> pdb=" O CYS E 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 removed outlier: 4.007A pdb=" N TYR F 10 " --> pdb=" O LEU F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.564A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 87 Processing helix chain 'F' and resid 100 through 108 removed outlier: 3.548A pdb=" N TRP F 104 " --> pdb=" O ASN F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 120 Processing helix chain 'F' and resid 121 through 131 Processing helix chain 'F' and resid 131 through 155 Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.704A pdb=" N SER F 206 " --> pdb=" O THR F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 237 Processing helix chain 'F' and resid 238 through 242 removed outlier: 4.083A pdb=" N ASP F 242 " --> pdb=" O SER F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 270 through 296 Proline residue: F 289 - end of helix removed outlier: 3.559A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 302 through 312 removed outlier: 4.149A pdb=" N LEU F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL F 308 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.640A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 353 removed outlier: 3.799A pdb=" N LYS F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU F 351 " --> pdb=" O CYS F 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 removed outlier: 4.006A pdb=" N TYR G 10 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.564A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 87 Processing helix chain 'G' and resid 100 through 108 removed outlier: 3.547A pdb=" N TRP G 104 " --> pdb=" O ASN G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 120 Processing helix chain 'G' and resid 121 through 131 Processing helix chain 'G' and resid 131 through 155 Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.705A pdb=" N SER G 206 " --> pdb=" O THR G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 237 Processing helix chain 'G' and resid 238 through 242 removed outlier: 4.084A pdb=" N ASP G 242 " --> pdb=" O SER G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 256 Processing helix chain 'G' and resid 270 through 296 Proline residue: G 289 - end of helix removed outlier: 3.560A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 302 through 312 removed outlier: 4.150A pdb=" N LEU G 306 " --> pdb=" O THR G 303 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL G 308 " --> pdb=" O VAL G 305 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 3.641A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 353 removed outlier: 3.800A pdb=" N LYS G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU G 351 " --> pdb=" O CYS G 347 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 4.514A pdb=" N GLN A 264 " --> pdb=" O PHE A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 67 removed outlier: 4.514A pdb=" N GLN B 264 " --> pdb=" O PHE B 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 67 removed outlier: 4.514A pdb=" N GLN C 264 " --> pdb=" O PHE C 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 67 removed outlier: 4.514A pdb=" N GLN D 264 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 67 removed outlier: 4.513A pdb=" N GLN E 264 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 67 removed outlier: 4.514A pdb=" N GLN F 264 " --> pdb=" O PHE F 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 67 removed outlier: 4.514A pdb=" N GLN G 264 " --> pdb=" O PHE G 67 " (cutoff:3.500A) 1079 hydrogen bonds defined for protein. 3048 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: 4.96 Time building geometry restraints manager: 8.05 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: 5213 1.34 - 1.46: 3162 1.46 - 1.57: 9881 1.57 - 1.69: 21 1.69 - 1.81: 133 Bond restraints: 18410 Sorted by residual: bond pdb=" O2 LBN C 501 " pdb=" P1 LBN C 501 " ideal model delta sigma weight residual 1.650 1.785 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" O2 LBN G 502 " pdb=" P1 LBN G 502 " ideal model delta sigma weight residual 1.650 1.785 -0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" O2 LBN E 501 " pdb=" P1 LBN E 501 " ideal model delta sigma weight residual 1.650 1.785 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" O2 LBN G 501 " pdb=" P1 LBN G 501 " ideal model delta sigma weight residual 1.650 1.785 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" O2 LBN F 502 " pdb=" P1 LBN F 502 " ideal model delta sigma weight residual 1.650 1.785 -0.135 2.00e-02 2.50e+03 4.55e+01 ... (remaining 18405 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.45: 595 107.45 - 114.10: 10556 114.10 - 120.74: 8337 120.74 - 127.39: 5292 127.39 - 134.03: 154 Bond angle restraints: 24934 Sorted by residual: angle pdb=" N ILE C 58 " pdb=" CA ILE C 58 " pdb=" C ILE C 58 " ideal model delta sigma weight residual 113.71 108.73 4.98 9.50e-01 1.11e+00 2.75e+01 angle pdb=" N ILE B 58 " pdb=" CA ILE B 58 " pdb=" C ILE B 58 " ideal model delta sigma weight residual 113.71 108.75 4.96 9.50e-01 1.11e+00 2.72e+01 angle pdb=" N ILE E 58 " pdb=" CA ILE E 58 " pdb=" C ILE E 58 " ideal model delta sigma weight residual 113.71 108.76 4.95 9.50e-01 1.11e+00 2.72e+01 angle pdb=" N ILE A 58 " pdb=" CA ILE A 58 " pdb=" C ILE A 58 " ideal model delta sigma weight residual 113.71 108.76 4.95 9.50e-01 1.11e+00 2.71e+01 angle pdb=" N ILE F 58 " pdb=" CA ILE F 58 " pdb=" C ILE F 58 " ideal model delta sigma weight residual 113.71 108.77 4.94 9.50e-01 1.11e+00 2.70e+01 ... (remaining 24929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 10906 35.91 - 71.81: 196 71.81 - 107.72: 7 107.72 - 143.62: 7 143.62 - 179.53: 21 Dihedral angle restraints: 11137 sinusoidal: 4613 harmonic: 6524 Sorted by residual: dihedral pdb=" O5 LBN D 501 " pdb=" C2 LBN D 501 " pdb=" C3 LBN D 501 " pdb=" O7 LBN D 501 " ideal model delta sinusoidal sigma weight residual 62.67 -116.86 179.53 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN F 501 " pdb=" C2 LBN F 501 " pdb=" C3 LBN F 501 " pdb=" O7 LBN F 501 " ideal model delta sinusoidal sigma weight residual 62.67 -116.80 179.47 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN G 501 " pdb=" C2 LBN G 501 " pdb=" C3 LBN G 501 " pdb=" O7 LBN G 501 " ideal model delta sinusoidal sigma weight residual 62.67 -116.78 179.45 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 11134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2204 0.043 - 0.087: 617 0.087 - 0.130: 91 0.130 - 0.174: 0 0.174 - 0.217: 21 Chirality restraints: 2933 Sorted by residual: chirality pdb=" C2 LBN D 501 " pdb=" C1 LBN D 501 " pdb=" C3 LBN D 501 " pdb=" O7 LBN D 501 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C2 LBN F 501 " pdb=" C1 LBN F 501 " pdb=" C3 LBN F 501 " pdb=" O7 LBN F 501 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C2 LBN E 501 " pdb=" C1 LBN E 501 " pdb=" C3 LBN E 501 " pdb=" O7 LBN E 501 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2930 not shown) Planarity restraints: 2982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 123 " 0.026 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO D 124 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 124 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 124 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 123 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO G 124 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO G 124 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 124 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 123 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO C 124 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 124 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 124 " 0.022 5.00e-02 4.00e+02 ... (remaining 2979 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 168 2.66 - 3.22: 18003 3.22 - 3.78: 27862 3.78 - 4.34: 37999 4.34 - 4.90: 64176 Nonbonded interactions: 148208 Sorted by model distance: nonbonded pdb=" OH TYR A 111 " pdb=" O LEU B 52 " model vdw 2.106 2.440 nonbonded pdb=" OH TYR B 111 " pdb=" O LEU C 52 " model vdw 2.200 2.440 nonbonded pdb=" NE2 GLN F 76 " pdb=" O SER G 68 " model vdw 2.251 2.520 nonbonded pdb=" O GLY A 27 " pdb=" NZ LYS G 24 " model vdw 2.264 2.520 nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 52 " model vdw 2.266 2.440 ... (remaining 148203 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 47.120 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.008 0.135 18410 Z= 0.533 Angle : 0.875 9.093 24934 Z= 0.363 Chirality : 0.040 0.217 2933 Planarity : 0.003 0.038 2982 Dihedral : 15.885 179.528 6839 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.71 % Allowed : 5.69 % Favored : 93.59 % 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: 0.47 (0.19), residues: 2128 helix: 1.48 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -2.50 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 104 HIS 0.001 0.000 HIS E 106 PHE 0.008 0.001 PHE A 244 TYR 0.005 0.001 TYR C 10 ARG 0.003 0.000 ARG E 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 528 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 120 LEU cc_start: 0.8943 (mt) cc_final: 0.8690 (mt) REVERT: B 237 LEU cc_start: 0.8457 (mt) cc_final: 0.8175 (mt) REVERT: D 82 SER cc_start: 0.8984 (p) cc_final: 0.8717 (m) REVERT: E 204 LYS cc_start: 0.8465 (ttpt) cc_final: 0.8257 (ttpt) REVERT: E 352 GLU cc_start: 0.6317 (tm-30) cc_final: 0.5822 (tm-30) REVERT: F 325 TYR cc_start: 0.7708 (m-10) cc_final: 0.7371 (m-80) outliers start: 14 outliers final: 0 residues processed: 537 average time/residue: 0.2744 time to fit residues: 225.9956 Evaluate side-chains 443 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 443 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 10.0000 chunk 164 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 126 optimal weight: 0.0040 chunk 197 optimal weight: 0.7980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 134 HIS ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN C 100 ASN C 262 GLN D 89 GLN D 100 ASN E 89 GLN E 100 ASN E 301 GLN E 332 ASN F 89 GLN F 100 ASN G 89 GLN G 100 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18410 Z= 0.179 Angle : 0.597 8.041 24934 Z= 0.294 Chirality : 0.038 0.125 2933 Planarity : 0.004 0.044 2982 Dihedral : 18.136 169.802 2737 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.93 % Allowed : 11.29 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.19), residues: 2128 helix: 1.28 (0.14), residues: 1463 sheet: None (None), residues: 0 loop : -2.33 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 104 HIS 0.004 0.001 HIS C 134 PHE 0.031 0.002 PHE C 235 TYR 0.026 0.001 TYR E 345 ARG 0.007 0.000 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 414 time to evaluate : 1.984 Fit side-chains REVERT: B 120 LEU cc_start: 0.9061 (mt) cc_final: 0.8852 (mt) REVERT: B 239 SER cc_start: 0.8057 (m) cc_final: 0.7818 (p) REVERT: E 40 CYS cc_start: 0.9001 (t) cc_final: 0.8773 (t) REVERT: E 204 LYS cc_start: 0.8706 (ttpt) cc_final: 0.8478 (ttpt) REVERT: F 213 TYR cc_start: 0.8681 (t80) cc_final: 0.8459 (t80) REVERT: F 325 TYR cc_start: 0.7821 (m-10) cc_final: 0.7340 (m-80) REVERT: G 54 PHE cc_start: 0.6691 (m-80) cc_final: 0.6163 (m-80) outliers start: 38 outliers final: 23 residues processed: 434 average time/residue: 0.2726 time to fit residues: 182.0340 Evaluate side-chains 407 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 384 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 197 optimal weight: 0.5980 chunk 213 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 195 optimal weight: 0.0270 chunk 67 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 301 GLN A 332 ASN B 301 GLN B 332 ASN C 100 ASN C 262 GLN D 89 GLN D 301 GLN D 332 ASN E 90 GLN E 100 ASN E 332 ASN F 100 ASN F 301 GLN F 332 ASN G 100 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18410 Z= 0.193 Angle : 0.590 7.917 24934 Z= 0.283 Chirality : 0.038 0.201 2933 Planarity : 0.004 0.039 2982 Dihedral : 17.158 167.630 2737 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.49 % Allowed : 12.96 % Favored : 84.54 % 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: 0.30 (0.19), residues: 2128 helix: 1.27 (0.14), residues: 1463 sheet: None (None), residues: 0 loop : -2.33 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 104 HIS 0.004 0.001 HIS A 134 PHE 0.027 0.001 PHE D 235 TYR 0.018 0.001 TYR E 230 ARG 0.006 0.000 ARG D 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 426 time to evaluate : 1.958 Fit side-chains revert: symmetry clash REVERT: B 30 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6709 (pt) REVERT: B 120 LEU cc_start: 0.9087 (mt) cc_final: 0.8872 (mt) REVERT: B 239 SER cc_start: 0.8177 (m) cc_final: 0.7940 (p) REVERT: E 204 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8453 (ttpt) REVERT: F 213 TYR cc_start: 0.8692 (t80) cc_final: 0.8414 (t80) REVERT: F 325 TYR cc_start: 0.7866 (m-10) cc_final: 0.7420 (m-80) REVERT: G 54 PHE cc_start: 0.6815 (m-80) cc_final: 0.6301 (m-80) outliers start: 49 outliers final: 33 residues processed: 453 average time/residue: 0.2708 time to fit residues: 190.8243 Evaluate side-chains 439 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 405 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 6.9990 chunk 148 optimal weight: 0.5980 chunk 102 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 132 optimal weight: 0.6980 chunk 198 optimal weight: 0.8980 chunk 209 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 187 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN D 100 ASN ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN E 90 GLN E 100 ASN F 100 ASN ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN G 301 GLN G 332 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18410 Z= 0.182 Angle : 0.583 8.324 24934 Z= 0.279 Chirality : 0.037 0.118 2933 Planarity : 0.004 0.038 2982 Dihedral : 16.677 166.447 2737 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.24 % Allowed : 16.17 % Favored : 81.60 % 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: 2128 helix: 1.09 (0.14), residues: 1498 sheet: None (None), residues: 0 loop : -2.33 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 104 HIS 0.002 0.001 HIS F 134 PHE 0.024 0.001 PHE C 235 TYR 0.019 0.001 TYR E 230 ARG 0.003 0.000 ARG F 254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 431 time to evaluate : 1.936 Fit side-chains REVERT: A 338 ASN cc_start: 0.8333 (p0) cc_final: 0.7957 (p0) REVERT: A 352 GLU cc_start: 0.6234 (tm-30) cc_final: 0.5765 (tm-30) REVERT: B 120 LEU cc_start: 0.9052 (mt) cc_final: 0.8847 (mt) REVERT: B 239 SER cc_start: 0.8275 (m) cc_final: 0.8063 (p) REVERT: D 252 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7440 (mp) REVERT: E 204 LYS cc_start: 0.8642 (ttpt) cc_final: 0.8380 (ttpt) REVERT: F 82 SER cc_start: 0.9096 (p) cc_final: 0.8819 (m) REVERT: F 325 TYR cc_start: 0.7925 (m-10) cc_final: 0.7467 (m-80) REVERT: G 54 PHE cc_start: 0.6994 (m-80) cc_final: 0.6549 (m-80) outliers start: 44 outliers final: 35 residues processed: 457 average time/residue: 0.2720 time to fit residues: 192.4530 Evaluate side-chains 445 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 409 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 305 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 144 optimal weight: 0.0970 chunk 0 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 188 optimal weight: 0.0980 chunk 52 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN C 100 ASN C 262 GLN D 100 ASN D 332 ASN E 90 GLN E 100 ASN F 100 ASN G 100 ASN G 332 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18410 Z= 0.191 Angle : 0.592 8.106 24934 Z= 0.281 Chirality : 0.038 0.128 2933 Planarity : 0.004 0.039 2982 Dihedral : 16.343 164.325 2737 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.59 % Allowed : 17.08 % Favored : 80.33 % 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: 0.18 (0.19), residues: 2128 helix: 1.09 (0.14), residues: 1498 sheet: None (None), residues: 0 loop : -2.30 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 104 HIS 0.003 0.001 HIS A 134 PHE 0.023 0.001 PHE G 12 TYR 0.021 0.001 TYR E 345 ARG 0.004 0.000 ARG D 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 431 time to evaluate : 1.874 Fit side-chains REVERT: A 338 ASN cc_start: 0.8375 (p0) cc_final: 0.8038 (p0) REVERT: A 352 GLU cc_start: 0.6281 (tm-30) cc_final: 0.5751 (tm-30) REVERT: B 120 LEU cc_start: 0.9086 (mt) cc_final: 0.8877 (mt) REVERT: F 82 SER cc_start: 0.9117 (p) cc_final: 0.8851 (m) REVERT: F 325 TYR cc_start: 0.7987 (m-10) cc_final: 0.7533 (m-80) REVERT: G 54 PHE cc_start: 0.7072 (m-80) cc_final: 0.6608 (m-80) outliers start: 51 outliers final: 40 residues processed: 460 average time/residue: 0.2799 time to fit residues: 199.3086 Evaluate side-chains 455 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 415 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 chunk 41 optimal weight: 0.4980 chunk 123 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 332 ASN B 89 GLN B 100 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 262 GLN D 100 ASN E 100 ASN E 264 GLN F 100 ASN ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18410 Z= 0.191 Angle : 0.595 8.314 24934 Z= 0.281 Chirality : 0.038 0.152 2933 Planarity : 0.004 0.039 2982 Dihedral : 16.066 162.611 2737 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.95 % Allowed : 17.74 % Favored : 79.31 % 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: 0.23 (0.19), residues: 2128 helix: 1.11 (0.14), residues: 1498 sheet: None (None), residues: 0 loop : -2.24 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 104 HIS 0.002 0.001 HIS A 134 PHE 0.019 0.001 PHE A 235 TYR 0.026 0.001 TYR E 345 ARG 0.004 0.000 ARG B 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 432 time to evaluate : 1.994 Fit side-chains REVERT: A 338 ASN cc_start: 0.8410 (p0) cc_final: 0.8102 (p0) REVERT: A 352 GLU cc_start: 0.6286 (tm-30) cc_final: 0.5741 (tm-30) REVERT: C 252 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7238 (mp) REVERT: F 82 SER cc_start: 0.9136 (p) cc_final: 0.8865 (m) REVERT: F 325 TYR cc_start: 0.7986 (m-10) cc_final: 0.7560 (m-80) REVERT: G 54 PHE cc_start: 0.7164 (m-80) cc_final: 0.6738 (m-80) outliers start: 58 outliers final: 46 residues processed: 468 average time/residue: 0.2750 time to fit residues: 200.0097 Evaluate side-chains 472 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 425 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN B 100 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 262 GLN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN E 100 ASN ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18410 Z= 0.254 Angle : 0.624 8.356 24934 Z= 0.296 Chirality : 0.039 0.140 2933 Planarity : 0.004 0.039 2982 Dihedral : 15.907 161.625 2737 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.64 % Allowed : 18.40 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 2128 helix: 1.08 (0.14), residues: 1498 sheet: None (None), residues: 0 loop : -2.25 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 104 HIS 0.002 0.001 HIS A 134 PHE 0.021 0.001 PHE B 299 TYR 0.022 0.001 TYR E 230 ARG 0.003 0.000 ARG D 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 445 time to evaluate : 2.112 Fit side-chains revert: symmetry clash REVERT: A 120 LEU cc_start: 0.8591 (mt) cc_final: 0.8254 (mt) REVERT: A 338 ASN cc_start: 0.8453 (p0) cc_final: 0.8194 (p0) REVERT: A 345 TYR cc_start: 0.8758 (t80) cc_final: 0.8515 (t80) REVERT: B 213 TYR cc_start: 0.8778 (t80) cc_final: 0.8568 (t80) REVERT: B 349 LYS cc_start: 0.8405 (mtpp) cc_final: 0.7981 (mtpt) REVERT: C 333 LEU cc_start: 0.8434 (mt) cc_final: 0.8153 (mt) REVERT: D 120 LEU cc_start: 0.8755 (mt) cc_final: 0.8528 (mt) REVERT: E 338 ASN cc_start: 0.7892 (p0) cc_final: 0.7556 (p0) REVERT: F 82 SER cc_start: 0.9151 (p) cc_final: 0.8889 (m) REVERT: F 325 TYR cc_start: 0.8090 (m-10) cc_final: 0.7689 (m-80) REVERT: G 54 PHE cc_start: 0.7415 (m-80) cc_final: 0.6953 (m-80) outliers start: 52 outliers final: 45 residues processed: 481 average time/residue: 0.2613 time to fit residues: 196.6945 Evaluate side-chains 488 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 443 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 90 GLN A 100 ASN B 100 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 262 GLN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN E 100 ASN F 100 ASN ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18410 Z= 0.191 Angle : 0.606 8.509 24934 Z= 0.286 Chirality : 0.039 0.136 2933 Planarity : 0.004 0.039 2982 Dihedral : 15.461 159.079 2737 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.95 % Allowed : 18.40 % Favored : 78.65 % 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: 0.12 (0.19), residues: 2128 helix: 1.06 (0.14), residues: 1498 sheet: None (None), residues: 0 loop : -2.36 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 104 HIS 0.002 0.001 HIS A 134 PHE 0.035 0.001 PHE B 235 TYR 0.023 0.001 TYR E 230 ARG 0.004 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 437 time to evaluate : 2.149 Fit side-chains revert: symmetry clash REVERT: A 338 ASN cc_start: 0.8466 (p0) cc_final: 0.8240 (p0) REVERT: C 333 LEU cc_start: 0.8434 (mt) cc_final: 0.8134 (mt) REVERT: E 338 ASN cc_start: 0.8014 (p0) cc_final: 0.7566 (p0) REVERT: F 82 SER cc_start: 0.9137 (p) cc_final: 0.8889 (m) REVERT: F 325 TYR cc_start: 0.8019 (m-10) cc_final: 0.7439 (m-80) REVERT: G 54 PHE cc_start: 0.7350 (m-80) cc_final: 0.6915 (m-80) REVERT: G 252 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7195 (mp) outliers start: 58 outliers final: 48 residues processed: 478 average time/residue: 0.2645 time to fit residues: 197.4837 Evaluate side-chains 481 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 432 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 1.9990 chunk 200 optimal weight: 9.9990 chunk 182 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 176 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 262 GLN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN E 89 GLN E 100 ASN ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18410 Z= 0.341 Angle : 0.686 10.336 24934 Z= 0.326 Chirality : 0.042 0.190 2933 Planarity : 0.004 0.040 2982 Dihedral : 15.510 160.404 2737 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.80 % Allowed : 19.12 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.19), residues: 2128 helix: 1.00 (0.14), residues: 1491 sheet: None (None), residues: 0 loop : -2.35 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 74 HIS 0.002 0.001 HIS D 106 PHE 0.034 0.002 PHE B 235 TYR 0.028 0.002 TYR E 230 ARG 0.003 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 450 time to evaluate : 2.043 Fit side-chains revert: symmetry clash REVERT: A 338 ASN cc_start: 0.8471 (p0) cc_final: 0.8265 (p0) REVERT: C 333 LEU cc_start: 0.8512 (mt) cc_final: 0.8146 (mt) REVERT: D 120 LEU cc_start: 0.8692 (mt) cc_final: 0.8367 (mt) REVERT: E 204 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8321 (ttpt) REVERT: E 338 ASN cc_start: 0.8015 (p0) cc_final: 0.7546 (p0) REVERT: F 82 SER cc_start: 0.9184 (p) cc_final: 0.8865 (m) REVERT: F 325 TYR cc_start: 0.8131 (m-10) cc_final: 0.7589 (m-80) REVERT: G 90 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7672 (mp10) outliers start: 55 outliers final: 47 residues processed: 491 average time/residue: 0.2718 time to fit residues: 212.7724 Evaluate side-chains 497 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 449 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 0.1980 chunk 125 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 216 optimal weight: 7.9990 chunk 198 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 100 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN F 100 ASN ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18410 Z= 0.182 Angle : 0.627 10.704 24934 Z= 0.298 Chirality : 0.039 0.143 2933 Planarity : 0.004 0.040 2982 Dihedral : 14.968 161.094 2737 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.44 % Allowed : 19.83 % Favored : 77.73 % 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: -0.01 (0.19), residues: 2128 helix: 0.96 (0.14), residues: 1491 sheet: None (None), residues: 0 loop : -2.37 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 104 HIS 0.002 0.001 HIS A 134 PHE 0.028 0.001 PHE B 235 TYR 0.059 0.001 TYR G 345 ARG 0.004 0.000 ARG C 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 430 time to evaluate : 1.775 Fit side-chains revert: symmetry clash REVERT: E 204 LYS cc_start: 0.8533 (ttpt) cc_final: 0.8293 (ttpt) REVERT: E 338 ASN cc_start: 0.8044 (p0) cc_final: 0.7602 (p0) REVERT: F 82 SER cc_start: 0.9195 (p) cc_final: 0.8619 (m) REVERT: F 325 TYR cc_start: 0.8006 (m-10) cc_final: 0.7382 (m-80) outliers start: 48 outliers final: 43 residues processed: 464 average time/residue: 0.2607 time to fit residues: 190.2475 Evaluate side-chains 458 residues out of total 1981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 415 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 305 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 177 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 151 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 262 GLN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.168348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.131217 restraints weight = 20875.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.132665 restraints weight = 18589.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.134199 restraints weight = 15260.605| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18410 Z= 0.204 Angle : 0.650 15.594 24934 Z= 0.305 Chirality : 0.040 0.184 2933 Planarity : 0.004 0.040 2982 Dihedral : 14.712 161.781 2737 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.44 % Allowed : 19.98 % Favored : 77.58 % 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: -0.02 (0.19), residues: 2128 helix: 0.94 (0.14), residues: 1491 sheet: None (None), residues: 0 loop : -2.34 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 104 HIS 0.002 0.001 HIS A 134 PHE 0.028 0.001 PHE B 235 TYR 0.047 0.001 TYR G 345 ARG 0.004 0.000 ARG C 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4001.66 seconds wall clock time: 72 minutes 38.45 seconds (4358.45 seconds total)