Starting phenix.real_space_refine on Sun Mar 17 21:17:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8j_31489/03_2024/7f8j_31489_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8j_31489/03_2024/7f8j_31489.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/7f8j_31489/03_2024/7f8j_31489.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8j_31489/03_2024/7f8j_31489.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8j_31489/03_2024/7f8j_31489_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f8j_31489/03_2024/7f8j_31489_updated.pdb" } 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 77 5.16 5 C 12824 2.51 5 N 2765 2.21 5 O 3304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 9": "OE1" <-> "OE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "B GLU 9": "OE1" <-> "OE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "C GLU 9": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "E GLU 9": "OE1" <-> "OE2" Residue "E GLU 243": "OE1" <-> "OE2" Residue "F GLU 9": "OE1" <-> "OE2" Residue "F GLU 243": "OE1" <-> "OE2" Residue "G GLU 9": "OE1" <-> "OE2" Residue "G GLU 243": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18984 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2566 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2566 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2566 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2566 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2566 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2566 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2566 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 146 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LBN:plan-2': 3, 'LBN:plan-3': 3, 'LBN:plan-1': 3} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 146 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LBN:plan-2': 3, 'LBN:plan-3': 2, 'LBN:plan-1': 3} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 146 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LBN:plan-2': 3, 'LBN:plan-3': 2, 'LBN:plan-1': 3} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 146 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LBN:plan-2': 3, 'LBN:plan-3': 2, 'LBN:plan-1': 3} Unresolved non-hydrogen planarities: 28 Chain: "E" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 146 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LBN:plan-2': 3, 'LBN:plan-3': 2, 'LBN:plan-1': 3} Unresolved non-hydrogen planarities: 28 Chain: "F" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 146 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LBN:plan-2': 3, 'LBN:plan-3': 2, 'LBN:plan-1': 3} Unresolved non-hydrogen planarities: 28 Chain: "G" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 146 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LBN:plan-2': 3, 'LBN:plan-3': 2, 'LBN:plan-1': 3} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 10.11, per 1000 atoms: 0.53 Number of scatterers: 18984 At special positions: 0 Unit cell: (109.35, 110.16, 115.83, 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 14 15.00 O 3304 8.00 N 2765 7.00 C 12824 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: 7.15 Conformation dependent library (CDL) restraints added in 3.4 seconds 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 7 sheets defined 61.3% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 33 through 54 Proline residue: A 46 - end of helix removed outlier: 3.682A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 101 through 107 Processing helix chain 'A' and resid 109 through 130 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.626A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 4.172A pdb=" N ASN A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 236 Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 271 through 295 removed outlier: 3.905A pdb=" N VAL A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 297 through 300 No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.988A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.516A pdb=" N CYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 Processing helix chain 'B' and resid 33 through 54 Proline residue: B 46 - end of helix removed outlier: 3.682A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 109 through 130 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 132 through 157 removed outlier: 3.626A pdb=" N PHE B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 removed outlier: 4.172A pdb=" N ASN B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 236 Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 271 through 295 removed outlier: 3.905A pdb=" N VAL B 278 " --> pdb=" O GLN B 274 " (cutoff:3.500A) Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 297 through 300 No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.987A pdb=" N ILE B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 Processing helix chain 'B' and resid 343 through 353 removed outlier: 3.516A pdb=" N CYS B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 10 Processing helix chain 'C' and resid 33 through 54 Proline residue: C 46 - end of helix removed outlier: 3.682A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 86 Processing helix chain 'C' and resid 101 through 107 Processing helix chain 'C' and resid 109 through 130 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 132 through 157 removed outlier: 3.627A pdb=" N PHE C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 4.172A pdb=" N ASN C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 236 Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 271 through 295 removed outlier: 3.905A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 297 through 300 No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 307 through 311 removed outlier: 3.987A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 338 Processing helix chain 'C' and resid 343 through 353 removed outlier: 3.516A pdb=" N CYS C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 10 Processing helix chain 'D' and resid 33 through 54 Proline residue: D 46 - end of helix removed outlier: 3.682A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 86 Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 109 through 130 Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 132 through 157 removed outlier: 3.627A pdb=" N PHE D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 4.172A pdb=" N ASN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 236 Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 271 through 295 removed outlier: 3.906A pdb=" N VAL D 278 " --> pdb=" O GLN D 274 " (cutoff:3.500A) Proline residue: D 289 - end of helix Processing helix chain 'D' and resid 297 through 300 No H-bonds generated for 'chain 'D' and resid 297 through 300' Processing helix chain 'D' and resid 307 through 311 removed outlier: 3.988A pdb=" N ILE D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 338 Processing helix chain 'D' and resid 343 through 353 removed outlier: 3.516A pdb=" N CYS D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 10 Processing helix chain 'E' and resid 33 through 54 Proline residue: E 46 - end of helix removed outlier: 3.681A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 86 Processing helix chain 'E' and resid 101 through 107 Processing helix chain 'E' and resid 109 through 130 Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 132 through 157 removed outlier: 3.627A pdb=" N PHE E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 4.172A pdb=" N ASN E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 236 Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 271 through 295 removed outlier: 3.906A pdb=" N VAL E 278 " --> pdb=" O GLN E 274 " (cutoff:3.500A) Proline residue: E 289 - end of helix Processing helix chain 'E' and resid 297 through 300 No H-bonds generated for 'chain 'E' and resid 297 through 300' Processing helix chain 'E' and resid 307 through 311 removed outlier: 3.988A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 338 Processing helix chain 'E' and resid 343 through 353 removed outlier: 3.516A pdb=" N CYS E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 10 Processing helix chain 'F' and resid 33 through 54 Proline residue: F 46 - end of helix removed outlier: 3.682A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 101 through 107 Processing helix chain 'F' and resid 109 through 130 Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 132 through 157 removed outlier: 3.626A pdb=" N PHE F 141 " --> pdb=" O SER F 137 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 removed outlier: 4.172A pdb=" N ASN F 205 " --> pdb=" O LYS F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 236 Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 271 through 295 removed outlier: 3.906A pdb=" N VAL F 278 " --> pdb=" O GLN F 274 " (cutoff:3.500A) Proline residue: F 289 - end of helix Processing helix chain 'F' and resid 297 through 300 No H-bonds generated for 'chain 'F' and resid 297 through 300' Processing helix chain 'F' and resid 307 through 311 removed outlier: 3.988A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 338 Processing helix chain 'F' and resid 343 through 353 removed outlier: 3.516A pdb=" N CYS F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 10 Processing helix chain 'G' and resid 33 through 54 Proline residue: G 46 - end of helix removed outlier: 3.681A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 86 Processing helix chain 'G' and resid 101 through 107 Processing helix chain 'G' and resid 109 through 130 Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 132 through 157 removed outlier: 3.626A pdb=" N PHE G 141 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 removed outlier: 4.173A pdb=" N ASN G 205 " --> pdb=" O LYS G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 236 Processing helix chain 'G' and resid 253 through 255 No H-bonds generated for 'chain 'G' and resid 253 through 255' Processing helix chain 'G' and resid 271 through 295 removed outlier: 3.905A pdb=" N VAL G 278 " --> pdb=" O GLN G 274 " (cutoff:3.500A) Proline residue: G 289 - end of helix Processing helix chain 'G' and resid 297 through 300 No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 307 through 311 removed outlier: 3.988A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 338 Processing helix chain 'G' and resid 343 through 353 removed outlier: 3.517A pdb=" N CYS G 347 " --> pdb=" O LYS G 343 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 64 through 67 removed outlier: 4.583A pdb=" N GLN A 264 " --> pdb=" O PHE A 67 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 64 through 67 removed outlier: 4.584A pdb=" N GLN B 264 " --> pdb=" O PHE B 67 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 64 through 67 removed outlier: 4.583A pdb=" N GLN C 264 " --> pdb=" O PHE C 67 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 64 through 67 removed outlier: 4.583A pdb=" N GLN D 264 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 64 through 67 removed outlier: 4.583A pdb=" N GLN E 264 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 64 through 67 removed outlier: 4.583A pdb=" N GLN F 264 " --> pdb=" O PHE F 67 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 64 through 67 removed outlier: 4.583A pdb=" N GLN G 264 " --> pdb=" O PHE G 67 " (cutoff:3.500A) 931 hydrogen bonds defined for protein. 2751 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: 4.86 Time building geometry restraints manager: 7.83 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: 5364 1.34 - 1.46: 3039 1.46 - 1.57: 10819 1.57 - 1.69: 21 1.69 - 1.81: 119 Bond restraints: 19362 Sorted by residual: bond pdb=" C42 LBN B 506 " pdb=" C5 LBN B 506 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C42 LBN E 506 " pdb=" C5 LBN E 506 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C42 LBN D 504 " pdb=" C5 LBN D 504 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C42 LBN G 504 " pdb=" C5 LBN G 504 " ideal model delta sigma weight residual 1.333 1.551 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C42 LBN C 506 " pdb=" C5 LBN C 506 " ideal model delta sigma weight residual 1.333 1.551 -0.218 2.00e-02 2.50e+03 1.19e+02 ... (remaining 19357 not shown) Histogram of bond angle deviations from ideal: 73.67 - 89.32: 14 89.32 - 104.97: 357 104.97 - 120.62: 19505 120.62 - 136.28: 6122 136.28 - 151.93: 7 Bond angle restraints: 26005 Sorted by residual: angle pdb=" O7 LBN D 505 " pdb=" C34 LBN D 505 " pdb=" O8 LBN D 505 " ideal model delta sigma weight residual 123.50 73.67 49.83 3.00e+00 1.11e-01 2.76e+02 angle pdb=" O7 LBN E 501 " pdb=" C34 LBN E 501 " pdb=" O8 LBN E 501 " ideal model delta sigma weight residual 123.50 73.69 49.81 3.00e+00 1.11e-01 2.76e+02 angle pdb=" O7 LBN F 501 " pdb=" C34 LBN F 501 " pdb=" O8 LBN F 501 " ideal model delta sigma weight residual 123.50 73.69 49.81 3.00e+00 1.11e-01 2.76e+02 angle pdb=" O7 LBN B 501 " pdb=" C34 LBN B 501 " pdb=" O8 LBN B 501 " ideal model delta sigma weight residual 123.50 73.70 49.80 3.00e+00 1.11e-01 2.76e+02 angle pdb=" O7 LBN C 501 " pdb=" C34 LBN C 501 " pdb=" O8 LBN C 501 " ideal model delta sigma weight residual 123.50 73.70 49.80 3.00e+00 1.11e-01 2.76e+02 ... (remaining 26000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 11497 35.15 - 70.30: 280 70.30 - 105.45: 47 105.45 - 140.60: 14 140.60 - 175.76: 42 Dihedral angle restraints: 11880 sinusoidal: 5174 harmonic: 6706 Sorted by residual: dihedral pdb=" O5 LBN B 502 " pdb=" C2 LBN B 502 " pdb=" C3 LBN B 502 " pdb=" O7 LBN B 502 " ideal model delta sinusoidal sigma weight residual 62.67 -113.09 175.76 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN C 502 " pdb=" C2 LBN C 502 " pdb=" C3 LBN C 502 " pdb=" O7 LBN C 502 " ideal model delta sinusoidal sigma weight residual 62.67 -113.08 175.75 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN G 506 " pdb=" C2 LBN G 506 " pdb=" C3 LBN G 506 " pdb=" O7 LBN G 506 " ideal model delta sinusoidal sigma weight residual 62.67 -113.06 175.73 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 11877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2252 0.043 - 0.086: 570 0.086 - 0.128: 139 0.128 - 0.171: 7 0.171 - 0.214: 14 Chirality restraints: 2982 Sorted by residual: chirality pdb=" C2 LBN C 502 " pdb=" C1 LBN C 502 " pdb=" C3 LBN C 502 " pdb=" O7 LBN C 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C2 LBN B 502 " pdb=" C1 LBN B 502 " pdb=" C3 LBN B 502 " pdb=" O7 LBN B 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C2 LBN D 506 " pdb=" C1 LBN D 506 " pdb=" C3 LBN D 506 " pdb=" O7 LBN D 506 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2979 not shown) Planarity restraints: 3100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN D 504 " -0.078 2.00e-02 2.50e+03 7.75e-02 6.01e+01 pdb=" C42 LBN D 504 " 0.078 2.00e-02 2.50e+03 pdb=" C5 LBN D 504 " 0.077 2.00e-02 2.50e+03 pdb=" C8 LBN D 504 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN G 504 " 0.078 2.00e-02 2.50e+03 7.74e-02 5.99e+01 pdb=" C42 LBN G 504 " -0.078 2.00e-02 2.50e+03 pdb=" C5 LBN G 504 " -0.077 2.00e-02 2.50e+03 pdb=" C8 LBN G 504 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 506 " -0.077 2.00e-02 2.50e+03 7.73e-02 5.98e+01 pdb=" C42 LBN C 506 " 0.078 2.00e-02 2.50e+03 pdb=" C5 LBN C 506 " 0.077 2.00e-02 2.50e+03 pdb=" C8 LBN C 506 " -0.077 2.00e-02 2.50e+03 ... (remaining 3097 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2397 2.75 - 3.29: 19021 3.29 - 3.83: 29654 3.83 - 4.36: 36338 4.36 - 4.90: 63205 Nonbonded interactions: 150615 Sorted by model distance: nonbonded pdb=" O LEU C 52 " pdb=" OH TYR D 111 " model vdw 2.215 2.440 nonbonded pdb=" OH TYR G 309 " pdb=" OG SER G 344 " model vdw 2.249 2.440 nonbonded pdb=" OH TYR E 309 " pdb=" OG SER E 344 " model vdw 2.249 2.440 nonbonded pdb=" OH TYR C 309 " pdb=" OG SER C 344 " model vdw 2.249 2.440 nonbonded pdb=" OH TYR A 309 " pdb=" OG SER A 344 " model vdw 2.249 2.440 ... (remaining 150610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 356 or (resid 501 and (name C11 or name C14 or n \ ame C17 or name C20 or name C22 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name C5 or name C \ 8 )) or (resid 502 and (name C10 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C30 or name C31 or name C32 or name C33 or name C4 or name \ C7 )) or resid 504 or (resid 505 and (name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name O5 or name O6 or name O7 or name O8 )) or \ resid 506)) selection = (chain 'B' and (resid 2 through 356 or (resid 501 and (name C11 or name C14 or n \ ame C17 or name C20 or name C22 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name C5 or name C \ 8 )) or (resid 502 and (name C10 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C30 or name C31 or name C32 or name C33 or name C4 or name \ C7 )) or resid 504 or (resid 505 and (name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name O5 or name O6 or name O7 or name O8 )) or \ resid 506)) selection = (chain 'C' and (resid 2 through 356 or (resid 501 and (name C11 or name C14 or n \ ame C17 or name C20 or name C22 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name C5 or name C \ 8 )) or (resid 502 and (name C10 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C30 or name C31 or name C32 or name C33 or name C4 or name \ C7 )) or resid 504 or (resid 505 and (name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name O5 or name O6 or name O7 or name O8 )) or \ resid 506)) selection = (chain 'D' and (resid 2 through 356 or resid 501 through 502 or resid 504 or (re \ sid 505 and (name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name O5 or name O6 or name O7 or name O8 )) or (resid 506 and (name C10 \ or name C25 or name C26 or name C27 or name C28 or name C29 or name C30 or name \ C31 or name C32 or name C33 or name C4 or name C7 )))) selection = (chain 'E' and (resid 2 through 356 or (resid 501 and (name C11 or name C14 or n \ ame C17 or name C20 or name C22 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name C5 or name C \ 8 )) or (resid 502 and (name C10 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C30 or name C31 or name C32 or name C33 or name C4 or name \ C7 )) or resid 504 or (resid 505 and (name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name O5 or name O6 or name O7 or name O8 )) or \ resid 506)) selection = (chain 'F' and (resid 2 through 356 or (resid 501 and (name C11 or name C14 or n \ ame C17 or name C20 or name C22 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name C5 or name C \ 8 )) or (resid 502 and (name C10 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C30 or name C31 or name C32 or name C33 or name C4 or name \ C7 )) or resid 504 or (resid 505 and (name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name O5 or name O6 or name O7 or name O8 )) or \ resid 506)) selection = (chain 'G' and (resid 2 through 356 or resid 501 through 502 or resid 504 or (re \ sid 505 and (name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name O5 or name O6 or name O7 or name O8 )) or (resid 506 and (name C10 \ or name C25 or name C26 or name C27 or name C28 or name C29 or name C30 or name \ C31 or name C32 or name C33 or name C4 or name C7 )))) } 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: 0.940 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: 5.590 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 49.310 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 0.010 0.219 19362 Z= 0.614 Angle : 1.623 49.829 26005 Z= 0.581 Chirality : 0.040 0.214 2982 Planarity : 0.005 0.077 3100 Dihedral : 20.219 175.755 7470 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.04 % Allowed : 1.09 % Favored : 97.87 % 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: 0.64 (0.19), residues: 2212 helix: 1.67 (0.14), residues: 1498 sheet: None (None), residues: 0 loop : -2.44 (0.20), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 104 HIS 0.001 0.000 HIS D 106 PHE 0.010 0.001 PHE A 116 TYR 0.005 0.001 TYR C 83 ARG 0.002 0.000 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 222 time to evaluate : 1.917 Fit side-chains REVERT: A 29 ARG cc_start: 0.7862 (ptp90) cc_final: 0.7661 (ptt-90) REVERT: B 243 GLU cc_start: 0.8434 (pt0) cc_final: 0.7986 (pt0) REVERT: C 207 ASN cc_start: 0.8596 (p0) cc_final: 0.8388 (p0) REVERT: C 243 GLU cc_start: 0.8510 (pt0) cc_final: 0.8217 (pt0) REVERT: D 29 ARG cc_start: 0.7755 (ptp90) cc_final: 0.7516 (ptt-90) REVERT: E 29 ARG cc_start: 0.7749 (ptp90) cc_final: 0.7426 (ptt-90) REVERT: F 207 ASN cc_start: 0.8767 (p0) cc_final: 0.8563 (p0) REVERT: G 207 ASN cc_start: 0.8905 (p0) cc_final: 0.8668 (p0) REVERT: G 243 GLU cc_start: 0.8447 (pt0) cc_final: 0.8154 (pt0) outliers start: 21 outliers final: 16 residues processed: 241 average time/residue: 0.3977 time to fit residues: 135.7315 Evaluate side-chains 208 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 175 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN C 90 GLN C 151 ASN D 90 GLN E 90 GLN E 151 ASN F 90 GLN F 151 ASN G 90 GLN G 151 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19362 Z= 0.202 Angle : 1.416 45.995 26005 Z= 0.513 Chirality : 0.040 0.190 2982 Planarity : 0.004 0.033 3100 Dihedral : 22.864 177.425 3242 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.48 % Allowed : 5.73 % Favored : 92.78 % 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: 1.00 (0.18), residues: 2212 helix: 2.12 (0.14), residues: 1449 sheet: -1.56 (0.51), residues: 42 loop : -2.45 (0.21), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 74 HIS 0.001 0.001 HIS D 134 PHE 0.028 0.001 PHE F 116 TYR 0.013 0.001 TYR E 83 ARG 0.004 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 213 time to evaluate : 2.246 Fit side-chains REVERT: A 29 ARG cc_start: 0.7930 (ptp90) cc_final: 0.7603 (ptt-90) REVERT: A 40 CYS cc_start: 0.8694 (t) cc_final: 0.7877 (m) REVERT: A 207 ASN cc_start: 0.8997 (p0) cc_final: 0.8659 (p0) REVERT: C 58 ILE cc_start: 0.8596 (tp) cc_final: 0.8332 (tp) REVERT: D 40 CYS cc_start: 0.8717 (t) cc_final: 0.7947 (m) REVERT: D 207 ASN cc_start: 0.9077 (p0) cc_final: 0.8813 (p0) REVERT: E 40 CYS cc_start: 0.8707 (t) cc_final: 0.8415 (t) REVERT: E 207 ASN cc_start: 0.8946 (p0) cc_final: 0.8613 (p0) REVERT: G 207 ASN cc_start: 0.8885 (p0) cc_final: 0.8683 (p0) REVERT: G 243 GLU cc_start: 0.8473 (pt0) cc_final: 0.8167 (pt0) outliers start: 30 outliers final: 27 residues processed: 235 average time/residue: 0.3768 time to fit residues: 126.0323 Evaluate side-chains 223 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 196 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 169 optimal weight: 8.9990 chunk 138 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 203 optimal weight: 0.7980 chunk 220 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN C 90 GLN E 90 GLN F 90 GLN G 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19362 Z= 0.193 Angle : 1.406 46.027 26005 Z= 0.507 Chirality : 0.040 0.179 2982 Planarity : 0.004 0.033 3100 Dihedral : 20.804 179.548 3214 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.78 % Allowed : 8.55 % Favored : 89.67 % 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: 1.08 (0.19), residues: 2212 helix: 2.11 (0.14), residues: 1463 sheet: -0.42 (0.59), residues: 42 loop : -2.39 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 104 HIS 0.001 0.000 HIS F 106 PHE 0.023 0.001 PHE F 116 TYR 0.009 0.001 TYR D 83 ARG 0.005 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 207 time to evaluate : 2.013 Fit side-chains REVERT: A 207 ASN cc_start: 0.8983 (p0) cc_final: 0.8662 (p0) REVERT: B 243 GLU cc_start: 0.8511 (pt0) cc_final: 0.8230 (pt0) REVERT: C 243 GLU cc_start: 0.8525 (pt0) cc_final: 0.8179 (pt0) REVERT: D 207 ASN cc_start: 0.9029 (p0) cc_final: 0.8757 (p0) REVERT: E 207 ASN cc_start: 0.8917 (p0) cc_final: 0.8548 (p0) REVERT: F 207 ASN cc_start: 0.8990 (p0) cc_final: 0.8761 (p0) REVERT: F 337 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7487 (tm-30) outliers start: 36 outliers final: 27 residues processed: 237 average time/residue: 0.3920 time to fit residues: 132.5510 Evaluate side-chains 229 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 202 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 105 optimal weight: 0.0980 chunk 22 optimal weight: 0.0040 chunk 97 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 ASN E 90 GLN F 90 GLN G 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19362 Z= 0.148 Angle : 1.397 45.972 26005 Z= 0.500 Chirality : 0.039 0.165 2982 Planarity : 0.003 0.033 3100 Dihedral : 19.310 178.855 3214 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.08 % Allowed : 9.69 % Favored : 88.24 % 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: 1.23 (0.19), residues: 2212 helix: 2.16 (0.14), residues: 1470 sheet: -0.06 (0.62), residues: 42 loop : -2.24 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.001 0.000 HIS F 106 PHE 0.022 0.001 PHE D 116 TYR 0.008 0.001 TYR A 83 ARG 0.003 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 198 time to evaluate : 2.004 Fit side-chains REVERT: A 207 ASN cc_start: 0.8943 (p0) cc_final: 0.8653 (p0) REVERT: B 243 GLU cc_start: 0.8530 (pt0) cc_final: 0.8191 (pt0) REVERT: B 337 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7389 (tm-30) REVERT: C 58 ILE cc_start: 0.8514 (tp) cc_final: 0.8257 (tp) REVERT: C 207 ASN cc_start: 0.8927 (p0) cc_final: 0.8660 (p0) REVERT: D 207 ASN cc_start: 0.8985 (p0) cc_final: 0.8745 (p0) REVERT: E 207 ASN cc_start: 0.8906 (p0) cc_final: 0.8606 (p0) REVERT: F 207 ASN cc_start: 0.8934 (p0) cc_final: 0.8644 (p0) REVERT: F 337 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7286 (tm-30) REVERT: G 207 ASN cc_start: 0.9041 (p0) cc_final: 0.8809 (p0) REVERT: G 243 GLU cc_start: 0.8324 (pt0) cc_final: 0.8008 (pt0) outliers start: 42 outliers final: 32 residues processed: 226 average time/residue: 0.3658 time to fit residues: 118.8119 Evaluate side-chains 225 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 193 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 344 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 184 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 194 optimal weight: 0.0050 chunk 54 optimal weight: 0.6980 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN B 90 GLN B 338 ASN D 151 ASN E 90 GLN F 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19362 Z= 0.196 Angle : 1.404 45.985 26005 Z= 0.506 Chirality : 0.039 0.179 2982 Planarity : 0.004 0.034 3100 Dihedral : 18.306 177.499 3213 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.08 % Allowed : 10.03 % Favored : 87.89 % 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: 1.23 (0.19), residues: 2212 helix: 2.14 (0.14), residues: 1477 sheet: 0.76 (0.62), residues: 42 loop : -2.30 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 104 HIS 0.001 0.000 HIS F 106 PHE 0.024 0.001 PHE E 116 TYR 0.009 0.001 TYR C 83 ARG 0.004 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 204 time to evaluate : 2.248 Fit side-chains REVERT: A 207 ASN cc_start: 0.8914 (p0) cc_final: 0.8675 (p0) REVERT: B 243 GLU cc_start: 0.8527 (pt0) cc_final: 0.8201 (pt0) REVERT: B 337 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7538 (tm-30) REVERT: C 207 ASN cc_start: 0.9001 (p0) cc_final: 0.8723 (p0) REVERT: C 243 GLU cc_start: 0.8569 (pt0) cc_final: 0.8253 (pt0) REVERT: D 207 ASN cc_start: 0.8944 (p0) cc_final: 0.8717 (p0) REVERT: E 143 MET cc_start: 0.8054 (mtp) cc_final: 0.7725 (mmm) REVERT: E 207 ASN cc_start: 0.8895 (p0) cc_final: 0.8610 (p0) REVERT: F 207 ASN cc_start: 0.8963 (p0) cc_final: 0.8688 (p0) REVERT: F 337 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7589 (tm-30) REVERT: G 9 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6831 (tt0) REVERT: G 207 ASN cc_start: 0.9001 (p0) cc_final: 0.8719 (p0) REVERT: G 243 GLU cc_start: 0.8454 (pt0) cc_final: 0.8152 (pt0) outliers start: 42 outliers final: 33 residues processed: 230 average time/residue: 0.3768 time to fit residues: 124.4322 Evaluate side-chains 233 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 199 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 303 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 216 optimal weight: 0.7980 chunk 179 optimal weight: 0.7980 chunk 100 optimal weight: 0.0000 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 ASN E 90 GLN F 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19362 Z= 0.162 Angle : 1.397 45.998 26005 Z= 0.501 Chirality : 0.039 0.168 2982 Planarity : 0.004 0.034 3100 Dihedral : 17.799 173.889 3207 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.13 % Allowed : 11.17 % Favored : 86.70 % 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: 1.26 (0.19), residues: 2212 helix: 2.20 (0.14), residues: 1470 sheet: 1.08 (0.66), residues: 42 loop : -2.37 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 104 HIS 0.001 0.000 HIS F 106 PHE 0.022 0.001 PHE C 116 TYR 0.008 0.001 TYR D 83 ARG 0.006 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 186 time to evaluate : 2.086 Fit side-chains REVERT: A 207 ASN cc_start: 0.8909 (p0) cc_final: 0.8661 (p0) REVERT: A 243 GLU cc_start: 0.8493 (pt0) cc_final: 0.8123 (pt0) REVERT: B 243 GLU cc_start: 0.8561 (pt0) cc_final: 0.8197 (pt0) REVERT: B 337 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7602 (tm-30) REVERT: C 207 ASN cc_start: 0.8942 (p0) cc_final: 0.8654 (p0) REVERT: C 243 GLU cc_start: 0.8553 (pt0) cc_final: 0.8269 (pt0) REVERT: E 143 MET cc_start: 0.8048 (mtp) cc_final: 0.7746 (mmm) REVERT: E 207 ASN cc_start: 0.8856 (p0) cc_final: 0.8576 (p0) REVERT: F 207 ASN cc_start: 0.8915 (p0) cc_final: 0.8671 (p0) REVERT: F 243 GLU cc_start: 0.8586 (pt0) cc_final: 0.8346 (pt0) REVERT: G 9 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6842 (tt0) REVERT: G 207 ASN cc_start: 0.9042 (p0) cc_final: 0.8772 (p0) REVERT: G 243 GLU cc_start: 0.8439 (pt0) cc_final: 0.8165 (pt0) outliers start: 43 outliers final: 37 residues processed: 215 average time/residue: 0.3812 time to fit residues: 117.2715 Evaluate side-chains 219 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 181 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 303 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 338 ASN F 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19362 Z= 0.218 Angle : 1.405 46.021 26005 Z= 0.507 Chirality : 0.040 0.180 2982 Planarity : 0.004 0.035 3100 Dihedral : 17.375 168.552 3207 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.52 % Allowed : 10.97 % Favored : 86.51 % 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: 1.20 (0.19), residues: 2212 helix: 2.17 (0.14), residues: 1470 sheet: 1.29 (0.67), residues: 42 loop : -2.42 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 104 HIS 0.001 0.000 HIS F 106 PHE 0.023 0.001 PHE G 116 TYR 0.009 0.001 TYR E 83 ARG 0.007 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 195 time to evaluate : 1.938 Fit side-chains REVERT: A 207 ASN cc_start: 0.8917 (p0) cc_final: 0.8671 (p0) REVERT: A 243 GLU cc_start: 0.8536 (pt0) cc_final: 0.8177 (pt0) REVERT: B 29 ARG cc_start: 0.7286 (ptt-90) cc_final: 0.6810 (ptt-90) REVERT: B 243 GLU cc_start: 0.8585 (pt0) cc_final: 0.8235 (pt0) REVERT: B 337 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7627 (tm-30) REVERT: C 207 ASN cc_start: 0.8974 (p0) cc_final: 0.8663 (p0) REVERT: C 243 GLU cc_start: 0.8588 (pt0) cc_final: 0.8275 (pt0) REVERT: C 337 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7491 (tm-30) REVERT: E 9 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6782 (tt0) REVERT: E 143 MET cc_start: 0.8049 (mtp) cc_final: 0.7745 (mmm) REVERT: E 207 ASN cc_start: 0.8879 (p0) cc_final: 0.8616 (p0) REVERT: F 243 GLU cc_start: 0.8617 (pt0) cc_final: 0.8341 (pt0) REVERT: G 9 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6808 (tt0) REVERT: G 207 ASN cc_start: 0.9040 (p0) cc_final: 0.8758 (p0) REVERT: G 243 GLU cc_start: 0.8512 (pt0) cc_final: 0.8178 (pt0) outliers start: 51 outliers final: 42 residues processed: 230 average time/residue: 0.3764 time to fit residues: 124.4324 Evaluate side-chains 235 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 191 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 303 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.0570 chunk 86 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 0.0040 chunk 137 optimal weight: 6.9990 chunk 147 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 169 optimal weight: 0.7980 overall best weight: 0.3910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 ASN F 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19362 Z= 0.140 Angle : 1.396 46.032 26005 Z= 0.501 Chirality : 0.039 0.234 2982 Planarity : 0.004 0.034 3100 Dihedral : 16.351 161.701 3207 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.68 % Allowed : 12.31 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.19), residues: 2212 helix: 2.26 (0.14), residues: 1470 sheet: 1.20 (0.70), residues: 42 loop : -2.43 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.000 0.000 HIS F 106 PHE 0.023 0.001 PHE A 116 TYR 0.007 0.001 TYR A 10 ARG 0.007 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 180 time to evaluate : 1.933 Fit side-chains REVERT: A 243 GLU cc_start: 0.8486 (pt0) cc_final: 0.8138 (pt0) REVERT: B 29 ARG cc_start: 0.7217 (ptt-90) cc_final: 0.6681 (ptt-90) REVERT: B 243 GLU cc_start: 0.8553 (pt0) cc_final: 0.8083 (pt0) REVERT: B 337 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7619 (tm-30) REVERT: C 207 ASN cc_start: 0.8924 (p0) cc_final: 0.8628 (p0) REVERT: C 243 GLU cc_start: 0.8539 (pt0) cc_final: 0.7998 (pt0) REVERT: E 9 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6761 (tt0) REVERT: E 143 MET cc_start: 0.8017 (mtp) cc_final: 0.7746 (mmm) REVERT: E 207 ASN cc_start: 0.8822 (p0) cc_final: 0.8585 (p0) REVERT: F 243 GLU cc_start: 0.8575 (pt0) cc_final: 0.8305 (pt0) REVERT: G 9 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6901 (tt0) REVERT: G 207 ASN cc_start: 0.8992 (p0) cc_final: 0.8745 (p0) outliers start: 34 outliers final: 31 residues processed: 199 average time/residue: 0.3853 time to fit residues: 109.1165 Evaluate side-chains 210 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 177 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 303 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.0870 chunk 206 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 ASN F 90 GLN F 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19362 Z= 0.213 Angle : 1.407 46.000 26005 Z= 0.508 Chirality : 0.040 0.187 2982 Planarity : 0.004 0.036 3100 Dihedral : 15.918 159.885 3207 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.17 % Allowed : 12.16 % Favored : 85.66 % 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: 1.25 (0.19), residues: 2212 helix: 2.23 (0.14), residues: 1470 sheet: 1.24 (0.71), residues: 42 loop : -2.47 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 104 HIS 0.001 0.000 HIS F 106 PHE 0.024 0.001 PHE G 116 TYR 0.009 0.001 TYR D 83 ARG 0.007 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 184 time to evaluate : 2.101 Fit side-chains REVERT: A 243 GLU cc_start: 0.8555 (pt0) cc_final: 0.8211 (pt0) REVERT: B 29 ARG cc_start: 0.7336 (ptt-90) cc_final: 0.6780 (ptt-90) REVERT: B 243 GLU cc_start: 0.8594 (pt0) cc_final: 0.8133 (pt0) REVERT: B 337 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7581 (tm-30) REVERT: C 207 ASN cc_start: 0.8955 (p0) cc_final: 0.8651 (p0) REVERT: C 243 GLU cc_start: 0.8578 (pt0) cc_final: 0.8073 (pt0) REVERT: E 9 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6812 (tt0) REVERT: E 143 MET cc_start: 0.8041 (mtp) cc_final: 0.7754 (mmm) REVERT: E 207 ASN cc_start: 0.8849 (p0) cc_final: 0.8598 (p0) REVERT: F 243 GLU cc_start: 0.8625 (pt0) cc_final: 0.8367 (pt0) REVERT: G 9 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6904 (tt0) REVERT: G 207 ASN cc_start: 0.9008 (p0) cc_final: 0.8758 (p0) REVERT: G 243 GLU cc_start: 0.8536 (pt0) cc_final: 0.8221 (pt0) outliers start: 44 outliers final: 40 residues processed: 212 average time/residue: 0.3939 time to fit residues: 119.9459 Evaluate side-chains 225 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 183 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 338 ASN Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 303 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.5980 chunk 212 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 223 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 137 optimal weight: 0.0870 chunk 108 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 ASN F 90 GLN F 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19362 Z= 0.164 Angle : 1.402 46.017 26005 Z= 0.505 Chirality : 0.039 0.164 2982 Planarity : 0.004 0.035 3100 Dihedral : 15.657 158.105 3207 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.83 % Allowed : 12.80 % Favored : 85.37 % 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: 1.28 (0.19), residues: 2212 helix: 2.25 (0.14), residues: 1470 sheet: 1.35 (0.73), residues: 42 loop : -2.46 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 104 HIS 0.001 0.000 HIS F 106 PHE 0.023 0.001 PHE G 116 TYR 0.008 0.001 TYR D 83 ARG 0.005 0.000 ARG E 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 184 time to evaluate : 1.582 Fit side-chains REVERT: A 243 GLU cc_start: 0.8529 (pt0) cc_final: 0.8192 (pt0) REVERT: B 29 ARG cc_start: 0.7284 (ptt-90) cc_final: 0.6676 (ptt-90) REVERT: B 243 GLU cc_start: 0.8568 (pt0) cc_final: 0.8115 (pt0) REVERT: B 337 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7499 (tm-30) REVERT: B 338 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8129 (p0) REVERT: C 207 ASN cc_start: 0.8942 (p0) cc_final: 0.8650 (p0) REVERT: C 243 GLU cc_start: 0.8565 (pt0) cc_final: 0.8041 (pt0) REVERT: E 9 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6813 (tt0) REVERT: E 143 MET cc_start: 0.8012 (mtp) cc_final: 0.7744 (mmm) REVERT: E 207 ASN cc_start: 0.8844 (p0) cc_final: 0.8608 (p0) REVERT: F 243 GLU cc_start: 0.8604 (pt0) cc_final: 0.8352 (pt0) REVERT: G 9 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6909 (tt0) REVERT: G 207 ASN cc_start: 0.8990 (p0) cc_final: 0.8763 (p0) outliers start: 37 outliers final: 34 residues processed: 205 average time/residue: 0.3888 time to fit residues: 112.7834 Evaluate side-chains 220 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 183 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 338 ASN Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 303 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 182 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 ASN F 90 GLN F 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.145362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.110116 restraints weight = 19946.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.114324 restraints weight = 12251.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.116929 restraints weight = 8914.262| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19362 Z= 0.165 Angle : 1.401 46.010 26005 Z= 0.505 Chirality : 0.039 0.161 2982 Planarity : 0.004 0.035 3100 Dihedral : 15.371 156.193 3207 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.08 % Allowed : 12.61 % Favored : 85.32 % 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: 1.29 (0.19), residues: 2212 helix: 2.26 (0.14), residues: 1470 sheet: 1.27 (0.74), residues: 42 loop : -2.47 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 104 HIS 0.001 0.000 HIS F 106 PHE 0.023 0.001 PHE G 116 TYR 0.008 0.001 TYR C 10 ARG 0.005 0.000 ARG E 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3252.56 seconds wall clock time: 60 minutes 37.87 seconds (3637.87 seconds total)