Starting phenix.real_space_refine on Thu Feb 15 19:06:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/02_2024/8gmr_40231_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/02_2024/8gmr_40231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/02_2024/8gmr_40231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/02_2024/8gmr_40231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/02_2024/8gmr_40231_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmr_40231/02_2024/8gmr_40231_trim_updated.pdb" } resolution = 3.76 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= -0.010 sd= 0.445 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 96 5.16 5 C 8176 2.51 5 N 2048 2.21 5 O 2144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12472 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "A" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "C" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "D" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "E" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "F" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "G" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "H" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1507 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.28, per 1000 atoms: 0.58 Number of scatterers: 12472 At special positions: 0 Unit cell: (127.544, 127.544, 97.584, 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 96 16.00 P 8 15.00 O 2144 8.00 N 2048 7.00 C 8176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 127 " distance=2.03 Simple disulfide: pdb=" SG CYS F 42 " - pdb=" SG CYS F 127 " distance=2.03 Simple disulfide: pdb=" SG CYS G 42 " - pdb=" SG CYS G 127 " distance=2.03 Simple disulfide: pdb=" SG CYS H 42 " - pdb=" SG CYS H 127 " 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: 5.12 Conformation dependent library (CDL) restraints added in 2.4 seconds 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3296 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 0 sheets defined 60.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'B' and resid 34 through 37 No H-bonds generated for 'chain 'B' and resid 34 through 37' Processing helix chain 'B' and resid 49 through 70 removed outlier: 3.556A pdb=" N ILE B 56 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Proline residue: B 60 - end of helix removed outlier: 4.119A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 83 removed outlier: 3.893A pdb=" N GLU B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 110 through 121 removed outlier: 4.428A pdb=" N THR B 118 " --> pdb=" O TRP B 114 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 126 No H-bonds generated for 'chain 'B' and resid 123 through 126' Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 149 through 158 removed outlier: 4.812A pdb=" N ARG B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 214 through 220 removed outlier: 3.925A pdb=" N TRP B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 250 removed outlier: 4.002A pdb=" N GLU B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 241 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE B 242 " --> pdb=" O HIS B 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE B 250 " --> pdb=" O CYS B 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 37 No H-bonds generated for 'chain 'A' and resid 34 through 37' Processing helix chain 'A' and resid 49 through 70 removed outlier: 3.556A pdb=" N ILE A 56 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 4.119A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 83 removed outlier: 3.893A pdb=" N GLU A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 110 through 121 removed outlier: 4.428A pdb=" N THR A 118 " --> pdb=" O TRP A 114 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 129 through 132 Processing helix chain 'A' and resid 149 through 158 removed outlier: 4.812A pdb=" N ARG A 158 " --> pdb=" O ARG A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 176 No H-bonds generated for 'chain 'A' and resid 173 through 176' Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 214 through 220 removed outlier: 3.925A pdb=" N TRP A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 250 removed outlier: 4.002A pdb=" N GLU A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE A 242 " --> pdb=" O HIS A 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE A 250 " --> pdb=" O CYS A 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 37 No H-bonds generated for 'chain 'C' and resid 34 through 37' Processing helix chain 'C' and resid 49 through 70 removed outlier: 3.556A pdb=" N ILE C 56 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 57 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Proline residue: C 60 - end of helix removed outlier: 4.119A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 83 removed outlier: 3.893A pdb=" N GLU C 80 " --> pdb=" O SER C 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 110 through 121 removed outlier: 4.428A pdb=" N THR C 118 " --> pdb=" O TRP C 114 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 No H-bonds generated for 'chain 'C' and resid 123 through 126' Processing helix chain 'C' and resid 129 through 132 Processing helix chain 'C' and resid 149 through 158 removed outlier: 4.812A pdb=" N ARG C 158 " --> pdb=" O ARG C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 180 through 196 Processing helix chain 'C' and resid 198 through 200 No H-bonds generated for 'chain 'C' and resid 198 through 200' Processing helix chain 'C' and resid 214 through 220 removed outlier: 3.925A pdb=" N TRP C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 250 removed outlier: 4.002A pdb=" N GLU C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 240 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 241 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE C 242 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE C 250 " --> pdb=" O CYS C 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 37 No H-bonds generated for 'chain 'D' and resid 34 through 37' Processing helix chain 'D' and resid 49 through 70 removed outlier: 3.556A pdb=" N ILE D 56 " --> pdb=" O TYR D 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Proline residue: D 60 - end of helix removed outlier: 4.119A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 83 removed outlier: 3.893A pdb=" N GLU D 80 " --> pdb=" O SER D 76 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 110 through 121 removed outlier: 4.428A pdb=" N THR D 118 " --> pdb=" O TRP D 114 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 126 No H-bonds generated for 'chain 'D' and resid 123 through 126' Processing helix chain 'D' and resid 129 through 132 Processing helix chain 'D' and resid 149 through 158 removed outlier: 4.812A pdb=" N ARG D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 176 No H-bonds generated for 'chain 'D' and resid 173 through 176' Processing helix chain 'D' and resid 180 through 196 Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 214 through 220 removed outlier: 3.925A pdb=" N TRP D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 250 removed outlier: 4.002A pdb=" N GLU D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 240 " --> pdb=" O THR D 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE D 242 " --> pdb=" O HIS D 238 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN D 249 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE D 250 " --> pdb=" O CYS D 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 37 No H-bonds generated for 'chain 'E' and resid 34 through 37' Processing helix chain 'E' and resid 49 through 70 removed outlier: 3.556A pdb=" N ILE E 56 " --> pdb=" O TYR E 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU E 57 " --> pdb=" O SER E 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Proline residue: E 60 - end of helix removed outlier: 4.119A pdb=" N VAL E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 83 removed outlier: 3.893A pdb=" N GLU E 80 " --> pdb=" O SER E 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 110 through 121 removed outlier: 4.428A pdb=" N THR E 118 " --> pdb=" O TRP E 114 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU E 119 " --> pdb=" O VAL E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 No H-bonds generated for 'chain 'E' and resid 123 through 126' Processing helix chain 'E' and resid 129 through 132 Processing helix chain 'E' and resid 149 through 158 removed outlier: 4.812A pdb=" N ARG E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 176 No H-bonds generated for 'chain 'E' and resid 173 through 176' Processing helix chain 'E' and resid 180 through 196 Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 214 through 220 removed outlier: 3.925A pdb=" N TRP E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 250 removed outlier: 4.002A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS E 240 " --> pdb=" O THR E 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 241 " --> pdb=" O GLU E 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE E 242 " --> pdb=" O HIS E 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS E 244 " --> pdb=" O LYS E 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN E 248 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN E 249 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE E 250 " --> pdb=" O CYS E 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 37 No H-bonds generated for 'chain 'F' and resid 34 through 37' Processing helix chain 'F' and resid 49 through 70 removed outlier: 3.556A pdb=" N ILE F 56 " --> pdb=" O TYR F 52 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU F 57 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Proline residue: F 60 - end of helix removed outlier: 4.119A pdb=" N VAL F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 83 removed outlier: 3.893A pdb=" N GLU F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP F 82 " --> pdb=" O LEU F 78 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 110 through 121 removed outlier: 4.428A pdb=" N THR F 118 " --> pdb=" O TRP F 114 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU F 119 " --> pdb=" O VAL F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 No H-bonds generated for 'chain 'F' and resid 123 through 126' Processing helix chain 'F' and resid 129 through 132 Processing helix chain 'F' and resid 149 through 158 removed outlier: 4.812A pdb=" N ARG F 158 " --> pdb=" O ARG F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 176 No H-bonds generated for 'chain 'F' and resid 173 through 176' Processing helix chain 'F' and resid 180 through 196 Processing helix chain 'F' and resid 198 through 200 No H-bonds generated for 'chain 'F' and resid 198 through 200' Processing helix chain 'F' and resid 214 through 220 removed outlier: 3.925A pdb=" N TRP F 220 " --> pdb=" O LYS F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 250 removed outlier: 4.002A pdb=" N GLU F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR F 234 " --> pdb=" O LEU F 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS F 240 " --> pdb=" O THR F 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 241 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE F 242 " --> pdb=" O HIS F 238 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS F 244 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLN F 249 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE F 250 " --> pdb=" O CYS F 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 37 No H-bonds generated for 'chain 'G' and resid 34 through 37' Processing helix chain 'G' and resid 49 through 70 removed outlier: 3.556A pdb=" N ILE G 56 " --> pdb=" O TYR G 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU G 57 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Proline residue: G 60 - end of helix removed outlier: 4.119A pdb=" N VAL G 70 " --> pdb=" O LEU G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 83 removed outlier: 3.893A pdb=" N GLU G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 106 Processing helix chain 'G' and resid 110 through 121 removed outlier: 4.428A pdb=" N THR G 118 " --> pdb=" O TRP G 114 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU G 119 " --> pdb=" O VAL G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 126 No H-bonds generated for 'chain 'G' and resid 123 through 126' Processing helix chain 'G' and resid 129 through 132 Processing helix chain 'G' and resid 149 through 158 removed outlier: 4.812A pdb=" N ARG G 158 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 176 No H-bonds generated for 'chain 'G' and resid 173 through 176' Processing helix chain 'G' and resid 180 through 196 Processing helix chain 'G' and resid 198 through 200 No H-bonds generated for 'chain 'G' and resid 198 through 200' Processing helix chain 'G' and resid 214 through 220 removed outlier: 3.925A pdb=" N TRP G 220 " --> pdb=" O LYS G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 250 removed outlier: 4.003A pdb=" N GLU G 233 " --> pdb=" O LYS G 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR G 234 " --> pdb=" O LEU G 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS G 240 " --> pdb=" O THR G 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA G 241 " --> pdb=" O GLU G 237 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE G 242 " --> pdb=" O HIS G 238 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS G 244 " --> pdb=" O LYS G 240 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN G 249 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE G 250 " --> pdb=" O CYS G 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 37 No H-bonds generated for 'chain 'H' and resid 34 through 37' Processing helix chain 'H' and resid 49 through 70 removed outlier: 3.556A pdb=" N ILE H 56 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) Proline residue: H 60 - end of helix removed outlier: 4.119A pdb=" N VAL H 70 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 83 removed outlier: 3.893A pdb=" N GLU H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 106 Processing helix chain 'H' and resid 110 through 121 removed outlier: 4.428A pdb=" N THR H 118 " --> pdb=" O TRP H 114 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU H 119 " --> pdb=" O VAL H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 126 No H-bonds generated for 'chain 'H' and resid 123 through 126' Processing helix chain 'H' and resid 129 through 132 Processing helix chain 'H' and resid 149 through 158 removed outlier: 4.811A pdb=" N ARG H 158 " --> pdb=" O ARG H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 176 No H-bonds generated for 'chain 'H' and resid 173 through 176' Processing helix chain 'H' and resid 180 through 196 Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'H' and resid 214 through 220 removed outlier: 3.925A pdb=" N TRP H 220 " --> pdb=" O LYS H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 250 removed outlier: 4.002A pdb=" N GLU H 233 " --> pdb=" O LYS H 229 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR H 234 " --> pdb=" O LEU H 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS H 240 " --> pdb=" O THR H 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA H 241 " --> pdb=" O GLU H 237 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE H 242 " --> pdb=" O HIS H 238 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS H 244 " --> pdb=" O LYS H 240 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL H 245 " --> pdb=" O ALA H 241 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN H 248 " --> pdb=" O LYS H 244 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLN H 249 " --> pdb=" O VAL H 245 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE H 250 " --> pdb=" O CYS H 246 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1296 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: 3.00 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1904 1.31 - 1.44: 3312 1.44 - 1.56: 7376 1.56 - 1.69: 24 1.69 - 1.81: 120 Bond restraints: 12736 Sorted by residual: bond pdb=" C21 POV A 401 " pdb=" O21 POV A 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C21 POV H 401 " pdb=" O21 POV H 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C21 POV F 401 " pdb=" O21 POV F 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C21 POV B 401 " pdb=" O21 POV B 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C21 POV G 401 " pdb=" O21 POV G 401 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 ... (remaining 12731 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.49: 488 106.49 - 113.35: 7064 113.35 - 120.21: 4712 120.21 - 127.08: 4976 127.08 - 133.94: 168 Bond angle restraints: 17408 Sorted by residual: angle pdb=" C13 POV H 401 " pdb=" N POV H 401 " pdb=" C14 POV H 401 " ideal model delta sigma weight residual 108.80 128.17 -19.37 3.00e+00 1.11e-01 4.17e+01 angle pdb=" C13 POV A 401 " pdb=" N POV A 401 " pdb=" C14 POV A 401 " ideal model delta sigma weight residual 108.80 128.17 -19.37 3.00e+00 1.11e-01 4.17e+01 angle pdb=" C13 POV D 401 " pdb=" N POV D 401 " pdb=" C14 POV D 401 " ideal model delta sigma weight residual 108.80 128.16 -19.36 3.00e+00 1.11e-01 4.17e+01 angle pdb=" C13 POV E 401 " pdb=" N POV E 401 " pdb=" C14 POV E 401 " ideal model delta sigma weight residual 108.80 128.16 -19.36 3.00e+00 1.11e-01 4.16e+01 angle pdb=" C13 POV G 401 " pdb=" N POV G 401 " pdb=" C14 POV G 401 " ideal model delta sigma weight residual 108.80 128.16 -19.36 3.00e+00 1.11e-01 4.16e+01 ... (remaining 17403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 7056 22.84 - 45.68: 487 45.68 - 68.52: 81 68.52 - 91.36: 24 91.36 - 114.20: 8 Dihedral angle restraints: 7656 sinusoidal: 2616 harmonic: 5040 Sorted by residual: dihedral pdb=" CA VAL D 159 " pdb=" C VAL D 159 " pdb=" N PRO D 160 " pdb=" CA PRO D 160 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA VAL E 159 " pdb=" C VAL E 159 " pdb=" N PRO E 160 " pdb=" CA PRO E 160 " ideal model delta harmonic sigma weight residual 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA VAL C 159 " pdb=" C VAL C 159 " pdb=" N PRO C 160 " pdb=" CA PRO C 160 " ideal model delta harmonic sigma weight residual 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 7653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1265 0.034 - 0.068: 593 0.068 - 0.102: 175 0.102 - 0.136: 43 0.136 - 0.170: 12 Chirality restraints: 2088 Sorted by residual: chirality pdb=" CB THR D 236 " pdb=" CA THR D 236 " pdb=" OG1 THR D 236 " pdb=" CG2 THR D 236 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CB THR C 236 " pdb=" CA THR C 236 " pdb=" OG1 THR C 236 " pdb=" CG2 THR C 236 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CB THR E 236 " pdb=" CA THR E 236 " pdb=" OG1 THR E 236 " pdb=" CG2 THR E 236 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.08e-01 ... (remaining 2085 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 161 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO F 162 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO F 162 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 162 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS H 161 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO H 162 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO H 162 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 162 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 161 " 0.039 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO A 162 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 162 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 162 " 0.032 5.00e-02 4.00e+02 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 8 2.24 - 2.90: 5074 2.90 - 3.57: 17349 3.57 - 4.23: 24304 4.23 - 4.90: 39463 Nonbonded interactions: 86198 Sorted by model distance: nonbonded pdb=" CB ASN F 255 " pdb=" CE2 TYR H 219 " model vdw 1.574 3.740 nonbonded pdb=" CB ASN E 255 " pdb=" CE2 TYR G 219 " model vdw 1.574 3.740 nonbonded pdb=" CB ASN D 255 " pdb=" CE2 TYR F 219 " model vdw 1.575 3.740 nonbonded pdb=" CB ASN B 255 " pdb=" CE2 TYR C 219 " model vdw 1.575 3.740 nonbonded pdb=" CB ASN C 255 " pdb=" CE2 TYR E 219 " model vdw 1.575 3.740 ... (remaining 86193 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.580 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 35.640 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 : 0.006 0.090 12736 Z= 0.425 Angle : 1.181 19.371 17408 Z= 0.527 Chirality : 0.043 0.170 2088 Planarity : 0.006 0.058 2176 Dihedral : 17.020 114.197 4336 Min Nonbonded Distance : 1.574 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.56 % Favored : 86.96 % Rotamer: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % 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: -5.54 (0.17), residues: 1664 helix: -3.40 (0.12), residues: 912 sheet: None (None), residues: 0 loop : -4.03 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 220 HIS 0.005 0.003 HIS D 222 PHE 0.008 0.001 PHE A 40 TYR 0.013 0.001 TYR H 219 ARG 0.002 0.000 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.373 Fit side-chains REVERT: B 158 ARG cc_start: 0.8216 (mtt180) cc_final: 0.7855 (mtm180) REVERT: C 158 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7855 (mtm180) REVERT: E 158 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7854 (mtm180) REVERT: G 158 ARG cc_start: 0.8211 (mtt180) cc_final: 0.7855 (mtm180) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2692 time to fit residues: 83.5599 Evaluate side-chains 208 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12736 Z= 0.221 Angle : 0.796 10.528 17408 Z= 0.377 Chirality : 0.043 0.168 2088 Planarity : 0.006 0.045 2176 Dihedral : 13.108 108.730 2160 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.02 % Favored : 87.98 % Rotamer: Outliers : 1.65 % Allowed : 19.30 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -3.61 (0.20), residues: 1664 helix: -1.62 (0.15), residues: 1008 sheet: None (None), residues: 0 loop : -3.63 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 189 HIS 0.003 0.002 HIS D 222 PHE 0.018 0.001 PHE C 38 TYR 0.011 0.001 TYR D 219 ARG 0.002 0.000 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 214 time to evaluate : 1.456 Fit side-chains REVERT: B 158 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7707 (mtm180) REVERT: C 158 ARG cc_start: 0.8015 (mtt180) cc_final: 0.7707 (mtm180) REVERT: E 108 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8540 (tt) REVERT: E 158 ARG cc_start: 0.8019 (mtt180) cc_final: 0.7710 (mtm180) REVERT: G 108 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8542 (tt) REVERT: G 158 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7708 (mtm180) outliers start: 18 outliers final: 12 residues processed: 216 average time/residue: 0.2364 time to fit residues: 73.4992 Evaluate side-chains 206 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 192 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 74 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 0.0020 chunk 126 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 136 optimal weight: 0.1980 chunk 151 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN A 72 ASN C 72 ASN D 72 ASN E 72 ASN F 72 ASN G 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12736 Z= 0.318 Angle : 0.837 11.304 17408 Z= 0.392 Chirality : 0.045 0.131 2088 Planarity : 0.006 0.047 2176 Dihedral : 13.169 110.555 2160 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer: Outliers : 4.14 % Allowed : 24.91 % Favored : 70.96 % 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: -3.26 (0.20), residues: 1664 helix: -1.21 (0.16), residues: 1008 sheet: None (None), residues: 0 loop : -3.72 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 189 HIS 0.001 0.001 HIS E 222 PHE 0.015 0.002 PHE D 214 TYR 0.011 0.002 TYR H 223 ARG 0.002 0.000 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 192 time to evaluate : 1.327 Fit side-chains REVERT: B 108 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8569 (tt) REVERT: B 158 ARG cc_start: 0.8156 (mtt180) cc_final: 0.7836 (mtm180) REVERT: C 108 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8561 (tt) REVERT: C 158 ARG cc_start: 0.8155 (mtt180) cc_final: 0.7837 (mtm180) REVERT: E 108 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8566 (tt) REVERT: E 158 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7832 (mtm180) REVERT: G 108 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8565 (tt) REVERT: G 158 ARG cc_start: 0.8150 (mtt180) cc_final: 0.7833 (mtm180) outliers start: 45 outliers final: 26 residues processed: 219 average time/residue: 0.2358 time to fit residues: 74.0599 Evaluate side-chains 206 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 176 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 73 ASN Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 156 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12736 Z= 0.188 Angle : 0.745 10.689 17408 Z= 0.345 Chirality : 0.041 0.129 2088 Planarity : 0.005 0.049 2176 Dihedral : 12.081 108.123 2160 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.06 % Favored : 88.94 % Rotamer: Outliers : 4.04 % Allowed : 25.64 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.21), residues: 1664 helix: -0.86 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -3.38 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 169 HIS 0.000 0.000 HIS G 222 PHE 0.024 0.001 PHE H 38 TYR 0.008 0.001 TYR A 223 ARG 0.002 0.000 ARG G 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 200 time to evaluate : 1.440 Fit side-chains REVERT: B 108 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8568 (tt) REVERT: B 158 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7690 (mtm180) REVERT: C 108 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8563 (tt) REVERT: C 158 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7691 (mtm180) REVERT: E 108 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8581 (tt) REVERT: E 158 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7692 (mtm180) REVERT: F 66 LEU cc_start: 0.8805 (pp) cc_final: 0.8601 (tp) REVERT: G 108 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8581 (tt) REVERT: G 158 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7689 (mtm180) outliers start: 44 outliers final: 12 residues processed: 231 average time/residue: 0.2718 time to fit residues: 86.2237 Evaluate side-chains 197 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 74 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 4.9990 chunk 92 optimal weight: 0.0010 chunk 2 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 chunk 138 optimal weight: 0.4980 chunk 112 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN C 105 GLN D 105 GLN E 105 GLN G 105 GLN H 72 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12736 Z= 0.169 Angle : 0.721 10.504 17408 Z= 0.334 Chirality : 0.039 0.119 2088 Planarity : 0.005 0.050 2176 Dihedral : 10.944 106.468 2160 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 3.68 % Allowed : 26.84 % Favored : 69.49 % 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: -2.02 (0.22), residues: 1664 helix: -0.35 (0.17), residues: 1056 sheet: None (None), residues: 0 loop : -3.13 (0.28), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 169 HIS 0.000 0.000 HIS F 222 PHE 0.016 0.001 PHE H 38 TYR 0.005 0.001 TYR H 165 ARG 0.003 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 195 time to evaluate : 1.311 Fit side-chains REVERT: B 108 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8581 (tt) REVERT: B 198 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8583 (mp) REVERT: A 34 MET cc_start: 0.5992 (tpt) cc_final: 0.4796 (ttm) REVERT: A 71 MET cc_start: 0.8614 (mtt) cc_final: 0.8365 (tpp) REVERT: A 108 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8586 (tt) REVERT: C 108 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8567 (tt) REVERT: C 198 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8575 (mp) REVERT: D 34 MET cc_start: 0.5992 (tpt) cc_final: 0.4801 (ttm) REVERT: D 71 MET cc_start: 0.8631 (mtt) cc_final: 0.8329 (tpp) REVERT: D 108 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8585 (tt) REVERT: E 198 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8581 (mp) REVERT: F 34 MET cc_start: 0.6009 (tpt) cc_final: 0.4805 (ttm) REVERT: F 71 MET cc_start: 0.8635 (mtt) cc_final: 0.8386 (tpp) REVERT: F 108 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8684 (tt) REVERT: G 198 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8602 (mp) REVERT: H 108 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8592 (tt) outliers start: 40 outliers final: 18 residues processed: 220 average time/residue: 0.1952 time to fit residues: 65.4416 Evaluate side-chains 205 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 177 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 72 ASN Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 0.0870 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 0.4980 chunk 40 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 0.0970 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12736 Z= 0.160 Angle : 0.736 10.411 17408 Z= 0.332 Chirality : 0.039 0.121 2088 Planarity : 0.005 0.046 2176 Dihedral : 10.585 106.695 2160 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 2.85 % Allowed : 26.93 % Favored : 70.22 % 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: -1.39 (0.23), residues: 1664 helix: 0.23 (0.17), residues: 1040 sheet: None (None), residues: 0 loop : -3.00 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 169 HIS 0.000 0.000 HIS F 222 PHE 0.027 0.001 PHE H 38 TYR 0.022 0.001 TYR D 165 ARG 0.002 0.000 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 183 time to evaluate : 1.335 Fit side-chains REVERT: A 34 MET cc_start: 0.5984 (tpt) cc_final: 0.4818 (ttm) REVERT: A 71 MET cc_start: 0.8623 (mtt) cc_final: 0.8405 (tpp) REVERT: A 108 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8667 (tt) REVERT: D 34 MET cc_start: 0.5975 (tpt) cc_final: 0.4816 (ttm) REVERT: D 71 MET cc_start: 0.8630 (mtt) cc_final: 0.8406 (tpp) REVERT: D 108 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8664 (tt) REVERT: F 34 MET cc_start: 0.5982 (tpt) cc_final: 0.4815 (ttm) REVERT: F 71 MET cc_start: 0.8625 (mtt) cc_final: 0.8399 (tpp) REVERT: F 108 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8672 (tt) REVERT: H 108 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8676 (tt) REVERT: H 187 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8515 (tt) outliers start: 31 outliers final: 13 residues processed: 202 average time/residue: 0.1958 time to fit residues: 60.6216 Evaluate side-chains 197 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 179 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 187 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 4.9990 chunk 18 optimal weight: 0.0370 chunk 92 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 98 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12736 Z= 0.161 Angle : 0.696 10.633 17408 Z= 0.323 Chirality : 0.040 0.125 2088 Planarity : 0.005 0.044 2176 Dihedral : 10.314 106.684 2160 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 3.58 % Allowed : 25.09 % Favored : 71.32 % 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: -1.02 (0.23), residues: 1664 helix: 0.52 (0.17), residues: 1040 sheet: None (None), residues: 0 loop : -2.82 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 169 HIS 0.000 0.000 HIS C 222 PHE 0.021 0.001 PHE H 38 TYR 0.004 0.001 TYR F 223 ARG 0.001 0.000 ARG H 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 191 time to evaluate : 1.330 Fit side-chains REVERT: B 108 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8556 (tt) REVERT: B 198 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8587 (mp) REVERT: A 34 MET cc_start: 0.6039 (tpt) cc_final: 0.4929 (ttm) REVERT: A 71 MET cc_start: 0.8647 (mtt) cc_final: 0.8431 (tpp) REVERT: A 108 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8571 (tt) REVERT: A 187 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8527 (tt) REVERT: C 108 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8552 (tt) REVERT: C 198 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8579 (mp) REVERT: D 34 MET cc_start: 0.6035 (tpt) cc_final: 0.4927 (ttm) REVERT: D 71 MET cc_start: 0.8661 (mtt) cc_final: 0.8435 (tpp) REVERT: D 108 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8568 (tt) REVERT: D 187 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8518 (tt) REVERT: E 198 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8584 (mp) REVERT: F 71 MET cc_start: 0.8667 (mtt) cc_final: 0.8440 (tpp) REVERT: F 108 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8577 (tt) REVERT: F 187 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8529 (tt) REVERT: H 71 MET cc_start: 0.8669 (mtt) cc_final: 0.8384 (tpp) REVERT: H 108 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8584 (tt) outliers start: 39 outliers final: 21 residues processed: 214 average time/residue: 0.1995 time to fit residues: 65.0777 Evaluate side-chains 221 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 188 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 177 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 0.2980 chunk 48 optimal weight: 0.0570 chunk 31 optimal weight: 0.2980 chunk 102 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 127 optimal weight: 0.0570 chunk 147 optimal weight: 9.9990 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12736 Z= 0.157 Angle : 0.717 10.635 17408 Z= 0.325 Chirality : 0.039 0.125 2088 Planarity : 0.005 0.041 2176 Dihedral : 9.950 105.820 2160 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.31 % Allowed : 26.56 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.23), residues: 1664 helix: 0.82 (0.18), residues: 1040 sheet: None (None), residues: 0 loop : -2.66 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 169 HIS 0.002 0.001 HIS A 222 PHE 0.021 0.001 PHE F 38 TYR 0.020 0.001 TYR D 165 ARG 0.002 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 198 time to evaluate : 1.290 Fit side-chains REVERT: B 108 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8589 (tt) REVERT: A 34 MET cc_start: 0.5845 (tpt) cc_final: 0.4790 (ttm) REVERT: A 80 GLU cc_start: 0.6183 (tm-30) cc_final: 0.5943 (pp20) REVERT: A 108 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8571 (tt) REVERT: A 187 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8512 (tt) REVERT: C 108 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8588 (tt) REVERT: D 34 MET cc_start: 0.5839 (tpt) cc_final: 0.4794 (ttm) REVERT: D 80 GLU cc_start: 0.6185 (tm-30) cc_final: 0.5945 (pp20) REVERT: D 108 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8561 (tt) REVERT: D 187 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8513 (tt) REVERT: E 108 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8559 (tt) REVERT: F 34 MET cc_start: 0.5850 (tpt) cc_final: 0.4795 (ttm) REVERT: F 71 MET cc_start: 0.8636 (mtt) cc_final: 0.8435 (tpp) REVERT: F 80 GLU cc_start: 0.6187 (tm-30) cc_final: 0.5948 (pp20) REVERT: F 108 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8568 (tt) REVERT: F 187 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8508 (tt) REVERT: G 108 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8561 (tt) REVERT: H 71 MET cc_start: 0.8620 (mtt) cc_final: 0.8383 (tpp) REVERT: H 80 GLU cc_start: 0.6198 (tm-30) cc_final: 0.5955 (pp20) REVERT: H 108 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8551 (tt) REVERT: H 187 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8509 (tt) outliers start: 36 outliers final: 14 residues processed: 221 average time/residue: 0.2012 time to fit residues: 67.6963 Evaluate side-chains 224 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 198 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 187 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 150 optimal weight: 0.6980 chunk 90 optimal weight: 0.3980 chunk 65 optimal weight: 0.8980 chunk 118 optimal weight: 0.0870 chunk 46 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 142 optimal weight: 0.0050 chunk 99 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 overall best weight: 0.3772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12736 Z= 0.157 Angle : 0.676 10.669 17408 Z= 0.313 Chirality : 0.039 0.134 2088 Planarity : 0.005 0.037 2176 Dihedral : 9.721 105.840 2160 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.57 % Allowed : 25.74 % Favored : 71.69 % 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: -0.42 (0.23), residues: 1664 helix: 0.99 (0.18), residues: 1040 sheet: None (None), residues: 0 loop : -2.58 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 169 HIS 0.003 0.001 HIS G 222 PHE 0.027 0.001 PHE H 38 TYR 0.021 0.001 TYR B 165 ARG 0.001 0.000 ARG F 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 200 time to evaluate : 1.419 Fit side-chains REVERT: B 108 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8605 (tt) REVERT: A 80 GLU cc_start: 0.6203 (tm-30) cc_final: 0.5955 (pp20) REVERT: A 108 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8573 (tt) REVERT: A 187 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8533 (tt) REVERT: C 108 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8609 (tt) REVERT: D 80 GLU cc_start: 0.6200 (tm-30) cc_final: 0.5956 (pp20) REVERT: D 108 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8556 (tt) REVERT: D 187 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8538 (tt) REVERT: E 108 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8578 (tt) REVERT: F 80 GLU cc_start: 0.6191 (tm-30) cc_final: 0.5956 (pp20) REVERT: F 108 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8574 (tt) REVERT: F 187 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8538 (tt) REVERT: G 108 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8566 (tt) REVERT: H 71 MET cc_start: 0.8613 (mtt) cc_final: 0.8391 (tpp) REVERT: H 80 GLU cc_start: 0.6200 (tm-30) cc_final: 0.5952 (pp20) REVERT: H 108 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8571 (tt) REVERT: H 187 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8527 (tt) outliers start: 28 outliers final: 16 residues processed: 216 average time/residue: 0.2005 time to fit residues: 66.1723 Evaluate side-chains 221 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 193 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 187 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 167 optimal weight: 0.0070 chunk 154 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 overall best weight: 2.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12736 Z= 0.220 Angle : 0.744 10.907 17408 Z= 0.338 Chirality : 0.041 0.150 2088 Planarity : 0.005 0.036 2176 Dihedral : 10.613 109.420 2160 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 3.03 % Allowed : 25.74 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.23), residues: 1664 helix: 0.90 (0.17), residues: 1048 sheet: None (None), residues: 0 loop : -2.75 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 169 HIS 0.001 0.000 HIS G 222 PHE 0.027 0.001 PHE H 38 TYR 0.017 0.002 TYR B 165 ARG 0.002 0.000 ARG D 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 1.463 Fit side-chains REVERT: B 39 ASP cc_start: 0.7865 (t0) cc_final: 0.7644 (t0) REVERT: B 108 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8541 (tt) REVERT: B 158 ARG cc_start: 0.8076 (mtt180) cc_final: 0.7818 (mtm180) REVERT: A 39 ASP cc_start: 0.7887 (t0) cc_final: 0.7673 (t0) REVERT: A 108 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8593 (tt) REVERT: A 187 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8655 (tt) REVERT: C 39 ASP cc_start: 0.7855 (t0) cc_final: 0.7637 (t0) REVERT: C 108 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8530 (tt) REVERT: C 158 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7833 (mtm180) REVERT: C 187 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8468 (tt) REVERT: D 39 ASP cc_start: 0.7875 (t0) cc_final: 0.7665 (t0) REVERT: D 108 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8606 (tt) REVERT: D 187 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8654 (tt) REVERT: E 39 ASP cc_start: 0.7890 (t0) cc_final: 0.7663 (t0) REVERT: E 108 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8415 (tt) REVERT: E 158 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7835 (mtm180) REVERT: E 187 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8461 (tt) REVERT: F 39 ASP cc_start: 0.7885 (t0) cc_final: 0.7674 (t0) REVERT: F 108 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8614 (tt) REVERT: F 187 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8658 (tt) REVERT: G 39 ASP cc_start: 0.7887 (t0) cc_final: 0.7660 (t0) REVERT: G 108 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8446 (tt) REVERT: G 158 ARG cc_start: 0.8061 (mtt180) cc_final: 0.7813 (mtm180) REVERT: G 187 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8461 (tt) REVERT: H 108 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8606 (tt) REVERT: H 187 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8652 (tt) outliers start: 33 outliers final: 13 residues processed: 219 average time/residue: 0.2154 time to fit residues: 69.8976 Evaluate side-chains 228 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 200 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 187 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.0170 chunk 133 optimal weight: 3.9990 chunk 55 optimal weight: 0.0970 chunk 137 optimal weight: 3.9990 chunk 16 optimal weight: 0.0870 chunk 24 optimal weight: 3.9990 chunk 117 optimal weight: 0.0040 chunk 7 optimal weight: 4.9990 overall best weight: 0.2408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.150961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.127142 restraints weight = 25703.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.129478 restraints weight = 15738.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130921 restraints weight = 11110.894| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12736 Z= 0.158 Angle : 0.687 10.964 17408 Z= 0.315 Chirality : 0.039 0.136 2088 Planarity : 0.005 0.039 2176 Dihedral : 9.816 106.145 2160 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.48 % Allowed : 27.02 % Favored : 70.50 % 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: -0.10 (0.24), residues: 1664 helix: 1.20 (0.18), residues: 1040 sheet: None (None), residues: 0 loop : -2.37 (0.30), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 169 HIS 0.001 0.000 HIS D 222 PHE 0.021 0.001 PHE D 38 TYR 0.022 0.001 TYR G 223 ARG 0.002 0.000 ARG C 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2416.75 seconds wall clock time: 44 minutes 28.88 seconds (2668.88 seconds total)