Starting phenix.real_space_refine on Mon Dec 30 07:47:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bxb_16314/12_2024/8bxb_16314.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bxb_16314/12_2024/8bxb_16314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bxb_16314/12_2024/8bxb_16314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bxb_16314/12_2024/8bxb_16314.map" model { file = "/net/cci-nas-00/data/ceres_data/8bxb_16314/12_2024/8bxb_16314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bxb_16314/12_2024/8bxb_16314.cif" } resolution = 3.9 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= 0.001 sd= 0.031 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: 4 Type Number sf(0) Gaussians S 76 5.16 5 C 8320 2.51 5 N 2032 2.21 5 O 2119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12547 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2496 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 Chain: "B" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2499 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2493 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 Chain: "D" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2492 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 Chain: "E" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2493 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.72, per 1000 atoms: 0.77 Number of scatterers: 12547 At special positions: 0 Unit cell: (91.152, 91.152, 121.536, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 76 16.00 O 2119 8.00 N 2032 7.00 C 8320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.49 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.49 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.49 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 152 " distance=2.49 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 167 " " NAG B 501 " - " ASN B 167 " " NAG C 501 " - " ASN C 167 " " NAG D 501 " - " ASN D 167 " " NAG E 501 " - " ASN E 167 " Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.9 seconds 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3130 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 39.6% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.910A pdb=" N SER A 83 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 95 removed outlier: 3.546A pdb=" N ILE A 95 " --> pdb=" O VAL A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 removed outlier: 3.764A pdb=" N ARG A 144 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 225 through 239 Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.640A pdb=" N LYS A 247 " --> pdb=" O PRO A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 279 through 307 removed outlier: 3.600A pdb=" N MET A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 440 Processing helix chain 'B' and resid 13 through 19 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.911A pdb=" N SER B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 95 removed outlier: 3.545A pdb=" N ILE B 95 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.765A pdb=" N ARG B 144 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 225 through 239 Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.640A pdb=" N LYS B 247 " --> pdb=" O PRO B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 271 Processing helix chain 'B' and resid 279 through 307 removed outlier: 3.601A pdb=" N MET B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 440 Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.911A pdb=" N SER C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.545A pdb=" N ILE C 95 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 145 removed outlier: 3.764A pdb=" N ARG C 144 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 225 through 239 Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.641A pdb=" N LYS C 247 " --> pdb=" O PRO C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 279 through 307 removed outlier: 3.601A pdb=" N MET C 307 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 440 Processing helix chain 'D' and resid 13 through 19 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.910A pdb=" N SER D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 removed outlier: 3.546A pdb=" N ILE D 95 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 removed outlier: 3.765A pdb=" N ARG D 144 " --> pdb=" O ASP D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 225 through 239 Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.640A pdb=" N LYS D 247 " --> pdb=" O PRO D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 271 Processing helix chain 'D' and resid 279 through 307 removed outlier: 3.600A pdb=" N MET D 307 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 440 Processing helix chain 'E' and resid 13 through 19 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.911A pdb=" N SER E 83 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.545A pdb=" N ILE E 95 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 145 removed outlier: 3.764A pdb=" N ARG E 144 " --> pdb=" O ASP E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 225 Processing helix chain 'E' and resid 225 through 239 Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 243 through 247 removed outlier: 3.639A pdb=" N LYS E 247 " --> pdb=" O PRO E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 279 through 307 removed outlier: 3.600A pdb=" N MET E 307 " --> pdb=" O ILE E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 440 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL A 126 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 70 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL A 126 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 70 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL A 59 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP A 52 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N THR A 61 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN A 63 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.780A pdb=" N GLY A 207 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG A 194 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 209 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY A 211 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL B 126 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP B 70 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL B 126 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP B 70 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL B 59 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP B 52 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR B 61 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN B 63 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.780A pdb=" N GLY B 207 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG B 194 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE B 209 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY B 211 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL C 126 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP C 70 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL C 126 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP C 70 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL C 59 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP C 52 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR C 61 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL C 50 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN C 63 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 87 through 90 Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.781A pdb=" N GLY C 207 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG C 194 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE C 209 " --> pdb=" O PRO C 192 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY C 211 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL D 126 " --> pdb=" O TRP D 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 70 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 125 through 126 removed outlier: 3.658A pdb=" N VAL D 126 " --> pdb=" O TRP D 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 70 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL D 59 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP D 52 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR D 61 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASN D 63 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 87 through 90 Processing sheet with id=AB7, first strand: chain 'D' and resid 100 through 102 removed outlier: 6.780A pdb=" N GLY D 207 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG D 194 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE D 209 " --> pdb=" O PRO D 192 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY D 211 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 125 through 126 removed outlier: 3.659A pdb=" N VAL E 126 " --> pdb=" O TRP E 70 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 70 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 125 through 126 removed outlier: 3.659A pdb=" N VAL E 126 " --> pdb=" O TRP E 70 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 70 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL E 59 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP E 52 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR E 61 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL E 50 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASN E 63 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 87 through 90 Processing sheet with id=AC2, first strand: chain 'E' and resid 100 through 102 removed outlier: 6.781A pdb=" N GLY E 207 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG E 194 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE E 209 " --> pdb=" O PRO E 192 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY E 211 " --> pdb=" O VAL E 190 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1650 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: 3.92 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2498 1.33 - 1.45: 3056 1.45 - 1.57: 7181 1.57 - 1.69: 0 1.69 - 1.81: 133 Bond restraints: 12868 Sorted by residual: bond pdb=" N VAL A 113 " pdb=" CA VAL A 113 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.19e-02 7.06e+03 9.95e+00 bond pdb=" N VAL C 114 " pdb=" CA VAL C 114 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.95e+00 bond pdb=" N SER A 109 " pdb=" CA SER A 109 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.27e-02 6.20e+03 7.36e+00 bond pdb=" N ARG A 171 " pdb=" CA ARG A 171 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 6.90e+00 bond pdb=" N VAL C 113 " pdb=" CA VAL C 113 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.64e+00 ... (remaining 12863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 17225 2.24 - 4.49: 369 4.49 - 6.73: 41 6.73 - 8.98: 23 8.98 - 11.22: 1 Bond angle restraints: 17659 Sorted by residual: angle pdb=" N LEU C 285 " pdb=" CA LEU C 285 " pdb=" C LEU C 285 " ideal model delta sigma weight residual 111.82 100.60 11.22 1.16e+00 7.43e-01 9.36e+01 angle pdb=" CA LEU B 285 " pdb=" C LEU B 285 " pdb=" N ALA B 286 " ideal model delta sigma weight residual 118.14 110.15 7.99 1.31e+00 5.83e-01 3.72e+01 angle pdb=" CA LEU E 285 " pdb=" C LEU E 285 " pdb=" N ALA E 286 " ideal model delta sigma weight residual 118.14 110.40 7.74 1.31e+00 5.83e-01 3.49e+01 angle pdb=" N ALA A 286 " pdb=" CA ALA A 286 " pdb=" C ALA A 286 " ideal model delta sigma weight residual 111.82 105.03 6.79 1.16e+00 7.43e-01 3.43e+01 angle pdb=" N ALA E 286 " pdb=" CA ALA E 286 " pdb=" C ALA E 286 " ideal model delta sigma weight residual 112.23 105.08 7.15 1.26e+00 6.30e-01 3.22e+01 ... (remaining 17654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.98: 6503 11.98 - 23.95: 643 23.95 - 35.93: 219 35.93 - 47.90: 112 47.90 - 59.88: 47 Dihedral angle restraints: 7524 sinusoidal: 2679 harmonic: 4845 Sorted by residual: dihedral pdb=" CB CYS C 138 " pdb=" SG CYS C 138 " pdb=" SG CYS C 152 " pdb=" CB CYS C 152 " ideal model delta sinusoidal sigma weight residual 93.00 147.07 -54.07 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CB CYS D 138 " pdb=" SG CYS D 138 " pdb=" SG CYS D 152 " pdb=" CB CYS D 152 " ideal model delta sinusoidal sigma weight residual 93.00 147.05 -54.05 1 1.00e+01 1.00e-02 3.96e+01 dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual 93.00 147.03 -54.03 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 7521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1651 0.054 - 0.109: 373 0.109 - 0.163: 133 0.163 - 0.217: 12 0.217 - 0.272: 6 Chirality restraints: 2175 Sorted by residual: chirality pdb=" CA VAL E 114 " pdb=" N VAL E 114 " pdb=" C VAL E 114 " pdb=" CB VAL E 114 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL E 288 " pdb=" CA VAL E 288 " pdb=" CG1 VAL E 288 " pdb=" CG2 VAL E 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB VAL A 288 " pdb=" CA VAL A 288 " pdb=" CG1 VAL A 288 " pdb=" CG2 VAL A 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 2172 not shown) Planarity restraints: 2126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 285 " 0.027 2.00e-02 2.50e+03 5.83e-02 3.40e+01 pdb=" C LEU B 285 " -0.101 2.00e-02 2.50e+03 pdb=" O LEU B 285 " 0.040 2.00e-02 2.50e+03 pdb=" N ALA B 286 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 286 " 0.028 2.00e-02 2.50e+03 5.74e-02 3.30e+01 pdb=" C ALA D 286 " -0.099 2.00e-02 2.50e+03 pdb=" O ALA D 286 " 0.038 2.00e-02 2.50e+03 pdb=" N TYR D 287 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 285 " -0.026 2.00e-02 2.50e+03 5.58e-02 3.11e+01 pdb=" C LEU E 285 " 0.096 2.00e-02 2.50e+03 pdb=" O LEU E 285 " -0.038 2.00e-02 2.50e+03 pdb=" N ALA E 286 " -0.033 2.00e-02 2.50e+03 ... (remaining 2123 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2836 2.78 - 3.31: 10902 3.31 - 3.84: 20960 3.84 - 4.37: 22511 4.37 - 4.90: 39189 Nonbonded interactions: 96398 Sorted by model distance: nonbonded pdb=" CD1 LEU D 170 " pdb=" O ARG D 171 " model vdw 2.256 3.460 nonbonded pdb=" CD1 LEU C 170 " pdb=" O ARG C 171 " model vdw 2.259 3.460 nonbonded pdb=" OD1 ASN A 78 " pdb=" OG SER A 80 " model vdw 2.318 3.040 nonbonded pdb=" OD1 ASN D 78 " pdb=" OG SER D 80 " model vdw 2.319 3.040 nonbonded pdb=" OD1 ASN B 78 " pdb=" OG SER B 80 " model vdw 2.319 3.040 ... (remaining 96393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 304 or (resid 305 and (name N or n \ ame CA or name C or name O or name CB )) or resid 306 through 443 or resid 501)) \ selection = (chain 'B' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 269 or (resid 270 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name NE )) or res \ id 271 through 306 or (resid 307 and (name N or name CA or name C or name O or n \ ame CB )) or resid 414 through 443 or resid 501)) selection = (chain 'C' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 443 or resid 501)) selection = chain 'D' selection = (chain 'E' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 443 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 5.300 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.450 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12868 Z= 0.267 Angle : 0.779 11.225 17659 Z= 0.477 Chirality : 0.055 0.272 2175 Planarity : 0.006 0.098 2121 Dihedral : 13.499 59.880 4382 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.85 % Favored : 96.09 % Rotamer: Outliers : 5.55 % Allowed : 14.10 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.59 (0.19), residues: 1610 helix: -1.63 (0.18), residues: 535 sheet: -1.19 (0.28), residues: 410 loop : -1.98 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 159 HIS 0.005 0.001 HIS C 131 PHE 0.012 0.001 PHE B 289 TYR 0.014 0.002 TYR A 287 ARG 0.006 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 294 time to evaluate : 1.405 Fit side-chains REVERT: A 104 ASN cc_start: 0.7295 (OUTLIER) cc_final: 0.6791 (p0) REVERT: A 264 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8195 (tt) REVERT: A 265 MET cc_start: 0.8529 (ttp) cc_final: 0.8269 (ttt) REVERT: A 271 MET cc_start: 0.7761 (tmm) cc_final: 0.7490 (tmm) REVERT: B 17 LEU cc_start: 0.8255 (tp) cc_final: 0.7926 (tp) REVERT: B 264 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8260 (mt) REVERT: B 265 MET cc_start: 0.8577 (ttp) cc_final: 0.8194 (ttp) REVERT: B 271 MET cc_start: 0.7555 (tmm) cc_final: 0.7317 (tmm) REVERT: C 21 ILE cc_start: 0.9029 (tp) cc_final: 0.8672 (tt) REVERT: C 87 LYS cc_start: 0.8676 (mtpt) cc_final: 0.8433 (mtpt) REVERT: C 271 MET cc_start: 0.7734 (tmm) cc_final: 0.7467 (tmm) REVERT: D 21 ILE cc_start: 0.9018 (tp) cc_final: 0.8720 (tt) REVERT: D 104 ASN cc_start: 0.7232 (OUTLIER) cc_final: 0.6775 (p0) REVERT: D 264 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8191 (mt) REVERT: D 265 MET cc_start: 0.8430 (ttp) cc_final: 0.8105 (ttm) REVERT: D 271 MET cc_start: 0.7810 (tmm) cc_final: 0.7499 (tmm) REVERT: E 21 ILE cc_start: 0.9084 (tp) cc_final: 0.8711 (tt) REVERT: E 239 MET cc_start: 0.7409 (ttp) cc_final: 0.7156 (ttt) REVERT: E 264 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8254 (mt) REVERT: E 265 MET cc_start: 0.8441 (ttp) cc_final: 0.8111 (ttp) REVERT: E 271 MET cc_start: 0.7560 (tmm) cc_final: 0.7199 (tmm) outliers start: 70 outliers final: 8 residues processed: 354 average time/residue: 0.2003 time to fit residues: 111.7390 Evaluate side-chains 237 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 264 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 HIS C 58 HIS D 58 HIS E 58 HIS E 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12868 Z= 0.210 Angle : 0.557 5.855 17659 Z= 0.285 Chirality : 0.043 0.146 2175 Planarity : 0.004 0.029 2121 Dihedral : 5.238 56.869 1900 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.75 % Allowed : 18.54 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.52 (0.21), residues: 1610 helix: 0.04 (0.21), residues: 540 sheet: -0.76 (0.28), residues: 400 loop : -2.00 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 70 HIS 0.004 0.001 HIS E 58 PHE 0.017 0.001 PHE D 298 TYR 0.016 0.001 TYR B 287 ARG 0.003 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 249 time to evaluate : 1.514 Fit side-chains REVERT: A 104 ASN cc_start: 0.7372 (OUTLIER) cc_final: 0.6650 (p0) REVERT: A 214 LEU cc_start: 0.8050 (mt) cc_final: 0.7828 (mp) REVERT: A 265 MET cc_start: 0.8711 (ttp) cc_final: 0.8386 (ttt) REVERT: A 271 MET cc_start: 0.7765 (tmm) cc_final: 0.7523 (tmm) REVERT: A 275 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7753 (mt) REVERT: B 17 LEU cc_start: 0.8326 (tp) cc_final: 0.8071 (tp) REVERT: B 265 MET cc_start: 0.8667 (ttp) cc_final: 0.8360 (ttp) REVERT: B 271 MET cc_start: 0.7514 (tmm) cc_final: 0.7249 (tmm) REVERT: B 275 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7816 (mt) REVERT: C 21 ILE cc_start: 0.9135 (tp) cc_final: 0.8719 (tt) REVERT: C 127 MET cc_start: 0.8541 (mtp) cc_final: 0.8250 (mtp) REVERT: C 275 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7728 (mt) REVERT: D 21 ILE cc_start: 0.9104 (tp) cc_final: 0.8754 (tt) REVERT: D 275 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7780 (mt) REVERT: E 17 LEU cc_start: 0.8315 (tp) cc_final: 0.8044 (tp) REVERT: E 21 ILE cc_start: 0.9164 (tp) cc_final: 0.8787 (tt) REVERT: E 239 MET cc_start: 0.7704 (ttp) cc_final: 0.7363 (ttt) REVERT: E 265 MET cc_start: 0.8582 (ttp) cc_final: 0.8251 (ttp) REVERT: E 287 TYR cc_start: 0.7698 (t80) cc_final: 0.7244 (t80) outliers start: 60 outliers final: 33 residues processed: 281 average time/residue: 0.1878 time to fit residues: 83.9649 Evaluate side-chains 264 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 275 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 98 optimal weight: 0.0010 chunk 40 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 157 optimal weight: 0.0060 chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 0.4980 overall best weight: 0.6204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12868 Z= 0.181 Angle : 0.539 8.355 17659 Z= 0.274 Chirality : 0.043 0.161 2175 Planarity : 0.003 0.026 2121 Dihedral : 4.125 18.371 1878 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.12 % Allowed : 20.36 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.09 (0.21), residues: 1610 helix: 0.65 (0.21), residues: 545 sheet: -0.70 (0.28), residues: 400 loop : -1.87 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 185 HIS 0.004 0.001 HIS C 131 PHE 0.012 0.001 PHE D 298 TYR 0.017 0.001 TYR C 287 ARG 0.001 0.000 ARG E 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 243 time to evaluate : 1.738 Fit side-chains REVERT: A 214 LEU cc_start: 0.8116 (mt) cc_final: 0.7857 (mp) REVERT: A 265 MET cc_start: 0.8645 (ttp) cc_final: 0.8350 (ttt) REVERT: B 17 LEU cc_start: 0.8323 (tp) cc_final: 0.8052 (tp) REVERT: B 21 ILE cc_start: 0.9215 (tp) cc_final: 0.8819 (tt) REVERT: B 271 MET cc_start: 0.7570 (tmm) cc_final: 0.7292 (tmm) REVERT: C 21 ILE cc_start: 0.9150 (tp) cc_final: 0.8740 (tt) REVERT: C 291 MET cc_start: 0.8491 (tpt) cc_final: 0.8277 (tpp) REVERT: D 21 ILE cc_start: 0.9167 (tp) cc_final: 0.8801 (tt) REVERT: D 127 MET cc_start: 0.8428 (mtp) cc_final: 0.8161 (mtp) REVERT: E 17 LEU cc_start: 0.8375 (tp) cc_final: 0.8041 (tp) REVERT: E 21 ILE cc_start: 0.9200 (tp) cc_final: 0.8802 (tt) REVERT: E 265 MET cc_start: 0.8612 (ttp) cc_final: 0.8260 (ttp) outliers start: 52 outliers final: 28 residues processed: 276 average time/residue: 0.1895 time to fit residues: 82.3932 Evaluate side-chains 253 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 0.0570 chunk 41 optimal weight: 0.9980 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN E 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12868 Z= 0.208 Angle : 0.545 7.725 17659 Z= 0.278 Chirality : 0.044 0.171 2175 Planarity : 0.003 0.025 2121 Dihedral : 4.049 15.907 1876 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.55 % Allowed : 19.81 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.90 (0.21), residues: 1610 helix: 0.97 (0.21), residues: 545 sheet: -0.65 (0.28), residues: 400 loop : -1.89 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 185 HIS 0.004 0.001 HIS C 131 PHE 0.013 0.001 PHE A 298 TYR 0.014 0.001 TYR C 287 ARG 0.003 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 229 time to evaluate : 1.479 Fit side-chains REVERT: A 104 ASN cc_start: 0.7420 (OUTLIER) cc_final: 0.6669 (p0) REVERT: A 155 VAL cc_start: 0.9176 (t) cc_final: 0.8972 (m) REVERT: A 271 MET cc_start: 0.7878 (tmm) cc_final: 0.7626 (tmm) REVERT: B 17 LEU cc_start: 0.8358 (tp) cc_final: 0.8044 (tp) REVERT: B 21 ILE cc_start: 0.9220 (tp) cc_final: 0.8843 (tt) REVERT: B 271 MET cc_start: 0.7618 (tmm) cc_final: 0.7394 (tmm) REVERT: C 21 ILE cc_start: 0.9180 (tp) cc_final: 0.8801 (tt) REVERT: D 21 ILE cc_start: 0.9190 (tp) cc_final: 0.8830 (tt) REVERT: E 17 LEU cc_start: 0.8373 (tp) cc_final: 0.8049 (tp) REVERT: E 21 ILE cc_start: 0.9186 (tp) cc_final: 0.8810 (tt) REVERT: E 127 MET cc_start: 0.8179 (mtt) cc_final: 0.7919 (mtt) REVERT: E 264 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8263 (tt) REVERT: E 265 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8127 (ttp) outliers start: 70 outliers final: 43 residues processed: 283 average time/residue: 0.1778 time to fit residues: 80.7305 Evaluate side-chains 265 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 39 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN E 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12868 Z= 0.197 Angle : 0.552 9.003 17659 Z= 0.279 Chirality : 0.044 0.168 2175 Planarity : 0.003 0.024 2121 Dihedral : 4.026 15.404 1876 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.15 % Allowed : 20.76 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.87 (0.21), residues: 1610 helix: 1.08 (0.21), residues: 545 sheet: -0.63 (0.28), residues: 410 loop : -1.98 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 77 HIS 0.003 0.001 HIS B 68 PHE 0.011 0.001 PHE D 298 TYR 0.016 0.001 TYR C 252 ARG 0.002 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 235 time to evaluate : 1.444 Fit side-chains REVERT: A 21 ILE cc_start: 0.9171 (tp) cc_final: 0.8783 (tt) REVERT: A 104 ASN cc_start: 0.7401 (OUTLIER) cc_final: 0.6533 (p0) REVERT: A 127 MET cc_start: 0.8751 (mtp) cc_final: 0.8526 (mtp) REVERT: B 17 LEU cc_start: 0.8343 (tp) cc_final: 0.8047 (tp) REVERT: B 21 ILE cc_start: 0.9232 (tp) cc_final: 0.8969 (tt) REVERT: C 21 ILE cc_start: 0.9178 (tp) cc_final: 0.8822 (tt) REVERT: C 127 MET cc_start: 0.8360 (mtp) cc_final: 0.7977 (mtm) REVERT: D 21 ILE cc_start: 0.9159 (tp) cc_final: 0.8845 (tt) REVERT: E 17 LEU cc_start: 0.8399 (tp) cc_final: 0.8068 (tp) REVERT: E 21 ILE cc_start: 0.9183 (tp) cc_final: 0.8775 (tt) REVERT: E 127 MET cc_start: 0.8107 (mtt) cc_final: 0.7847 (mtm) REVERT: E 264 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8292 (tt) REVERT: E 265 MET cc_start: 0.8578 (ttp) cc_final: 0.8259 (ttp) REVERT: E 287 TYR cc_start: 0.7831 (t80) cc_final: 0.7496 (t80) outliers start: 65 outliers final: 44 residues processed: 281 average time/residue: 0.1829 time to fit residues: 82.1690 Evaluate side-chains 268 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 273 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.0050 chunk 38 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12868 Z= 0.212 Angle : 0.565 8.909 17659 Z= 0.285 Chirality : 0.044 0.172 2175 Planarity : 0.003 0.024 2121 Dihedral : 4.012 15.287 1876 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.39 % Allowed : 21.71 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1610 helix: 1.08 (0.21), residues: 545 sheet: -0.63 (0.28), residues: 410 loop : -2.00 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 77 HIS 0.003 0.001 HIS A 68 PHE 0.011 0.001 PHE D 298 TYR 0.017 0.001 TYR C 252 ARG 0.002 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 232 time to evaluate : 1.510 Fit side-chains REVERT: A 21 ILE cc_start: 0.9166 (tp) cc_final: 0.8798 (tt) REVERT: A 104 ASN cc_start: 0.7191 (OUTLIER) cc_final: 0.6573 (p0) REVERT: A 155 VAL cc_start: 0.9175 (t) cc_final: 0.8943 (m) REVERT: A 291 MET cc_start: 0.8124 (tpp) cc_final: 0.7864 (tpp) REVERT: B 17 LEU cc_start: 0.8366 (tp) cc_final: 0.8048 (tp) REVERT: B 21 ILE cc_start: 0.9225 (tp) cc_final: 0.8971 (tt) REVERT: C 21 ILE cc_start: 0.9151 (tp) cc_final: 0.8798 (tt) REVERT: D 21 ILE cc_start: 0.9183 (tp) cc_final: 0.8874 (tt) REVERT: D 264 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8368 (tt) REVERT: E 17 LEU cc_start: 0.8393 (tp) cc_final: 0.8057 (tp) REVERT: E 21 ILE cc_start: 0.9193 (tp) cc_final: 0.8803 (tt) REVERT: E 127 MET cc_start: 0.8243 (mtt) cc_final: 0.8012 (mtt) REVERT: E 227 MET cc_start: 0.7624 (tmm) cc_final: 0.7213 (tpt) REVERT: E 264 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8329 (tt) REVERT: E 265 MET cc_start: 0.8581 (ttp) cc_final: 0.8299 (ttp) outliers start: 68 outliers final: 48 residues processed: 281 average time/residue: 0.1770 time to fit residues: 79.7308 Evaluate side-chains 272 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 221 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 273 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 113 optimal weight: 0.0670 chunk 87 optimal weight: 0.5980 chunk 130 optimal weight: 0.0040 chunk 86 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 overall best weight: 0.4130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12868 Z= 0.176 Angle : 0.577 8.370 17659 Z= 0.289 Chirality : 0.044 0.171 2175 Planarity : 0.003 0.022 2121 Dihedral : 3.941 13.985 1876 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.20 % Allowed : 22.98 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.82 (0.21), residues: 1610 helix: 1.09 (0.21), residues: 545 sheet: -0.53 (0.28), residues: 410 loop : -1.97 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 77 HIS 0.002 0.001 HIS C 131 PHE 0.011 0.001 PHE A 234 TYR 0.015 0.001 TYR C 252 ARG 0.003 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 230 time to evaluate : 1.405 Fit side-chains REVERT: A 21 ILE cc_start: 0.9150 (tp) cc_final: 0.8791 (tt) REVERT: A 104 ASN cc_start: 0.7123 (OUTLIER) cc_final: 0.6526 (p0) REVERT: A 155 VAL cc_start: 0.9154 (t) cc_final: 0.8951 (m) REVERT: A 291 MET cc_start: 0.8100 (tpp) cc_final: 0.7689 (tpp) REVERT: B 17 LEU cc_start: 0.8334 (tp) cc_final: 0.8041 (tp) REVERT: B 21 ILE cc_start: 0.9184 (tp) cc_final: 0.8943 (tt) REVERT: C 21 ILE cc_start: 0.9126 (tp) cc_final: 0.8801 (tt) REVERT: D 21 ILE cc_start: 0.9157 (tp) cc_final: 0.8865 (tt) REVERT: D 127 MET cc_start: 0.8358 (mtp) cc_final: 0.8106 (mtp) REVERT: D 264 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8301 (tt) REVERT: E 17 LEU cc_start: 0.8376 (tp) cc_final: 0.8030 (tp) REVERT: E 21 ILE cc_start: 0.9170 (tp) cc_final: 0.8787 (tt) REVERT: E 127 MET cc_start: 0.8228 (mtt) cc_final: 0.7936 (mtt) REVERT: E 227 MET cc_start: 0.7622 (tmm) cc_final: 0.7238 (tpt) REVERT: E 264 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8359 (tt) REVERT: E 265 MET cc_start: 0.8553 (ttp) cc_final: 0.8347 (ttp) outliers start: 53 outliers final: 34 residues processed: 267 average time/residue: 0.1907 time to fit residues: 80.8447 Evaluate side-chains 253 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 273 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 0.0980 chunk 98 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12868 Z= 0.192 Angle : 0.586 8.507 17659 Z= 0.294 Chirality : 0.044 0.166 2175 Planarity : 0.003 0.023 2121 Dihedral : 3.913 14.210 1876 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.91 % Allowed : 22.66 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.83 (0.21), residues: 1610 helix: 1.09 (0.21), residues: 545 sheet: -0.59 (0.27), residues: 410 loop : -1.95 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 77 HIS 0.002 0.001 HIS C 131 PHE 0.010 0.001 PHE A 234 TYR 0.022 0.001 TYR A 112 ARG 0.002 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 222 time to evaluate : 1.522 Fit side-chains REVERT: A 21 ILE cc_start: 0.9152 (tp) cc_final: 0.8806 (tt) REVERT: A 104 ASN cc_start: 0.6887 (OUTLIER) cc_final: 0.6501 (p0) REVERT: B 17 LEU cc_start: 0.8330 (tp) cc_final: 0.8060 (tp) REVERT: B 21 ILE cc_start: 0.9146 (tp) cc_final: 0.8880 (tt) REVERT: B 127 MET cc_start: 0.8524 (mtt) cc_final: 0.8185 (mtt) REVERT: B 138 CYS cc_start: 0.7226 (p) cc_final: 0.7024 (m) REVERT: C 21 ILE cc_start: 0.9135 (tp) cc_final: 0.8806 (tt) REVERT: C 289 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8132 (t80) REVERT: D 21 ILE cc_start: 0.9164 (tp) cc_final: 0.8885 (tt) REVERT: D 127 MET cc_start: 0.8368 (mtp) cc_final: 0.8103 (mtp) REVERT: E 17 LEU cc_start: 0.8369 (tp) cc_final: 0.8023 (tp) REVERT: E 21 ILE cc_start: 0.9173 (tp) cc_final: 0.8795 (tt) REVERT: E 127 MET cc_start: 0.8272 (mtt) cc_final: 0.8023 (mtt) REVERT: E 227 MET cc_start: 0.7642 (tmm) cc_final: 0.7298 (tpt) REVERT: E 264 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8350 (tt) outliers start: 62 outliers final: 38 residues processed: 263 average time/residue: 0.1859 time to fit residues: 77.9354 Evaluate side-chains 256 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.4980 chunk 147 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 129 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12868 Z= 0.209 Angle : 0.610 8.761 17659 Z= 0.303 Chirality : 0.044 0.187 2175 Planarity : 0.003 0.021 2121 Dihedral : 3.905 13.653 1876 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.36 % Allowed : 22.98 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1610 helix: 1.10 (0.22), residues: 545 sheet: -0.47 (0.28), residues: 375 loop : -2.07 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 185 HIS 0.003 0.001 HIS C 131 PHE 0.016 0.001 PHE A 103 TYR 0.020 0.001 TYR C 252 ARG 0.003 0.000 ARG D 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 215 time to evaluate : 1.383 Fit side-chains REVERT: A 21 ILE cc_start: 0.9155 (tp) cc_final: 0.8811 (tt) REVERT: B 17 LEU cc_start: 0.8338 (tp) cc_final: 0.8034 (tp) REVERT: B 21 ILE cc_start: 0.9149 (tp) cc_final: 0.8887 (tt) REVERT: B 138 CYS cc_start: 0.7290 (p) cc_final: 0.7066 (m) REVERT: C 21 ILE cc_start: 0.9130 (tp) cc_final: 0.8811 (tt) REVERT: C 289 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8135 (t80) REVERT: D 21 ILE cc_start: 0.9189 (tp) cc_final: 0.8906 (tt) REVERT: D 127 MET cc_start: 0.8388 (mtp) cc_final: 0.8124 (mtp) REVERT: E 17 LEU cc_start: 0.8380 (tp) cc_final: 0.8026 (tp) REVERT: E 21 ILE cc_start: 0.9171 (tp) cc_final: 0.8812 (tt) REVERT: E 127 MET cc_start: 0.8294 (mtt) cc_final: 0.8041 (mtt) REVERT: E 227 MET cc_start: 0.7655 (tmm) cc_final: 0.7273 (tpt) outliers start: 55 outliers final: 42 residues processed: 252 average time/residue: 0.1854 time to fit residues: 74.5241 Evaluate side-chains 255 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 212 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 266 MET Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 268 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.0470 chunk 92 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 146 optimal weight: 0.0470 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 98 optimal weight: 0.0000 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12868 Z= 0.183 Angle : 0.629 13.337 17659 Z= 0.307 Chirality : 0.044 0.216 2175 Planarity : 0.003 0.023 2121 Dihedral : 3.829 12.852 1876 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.33 % Allowed : 24.09 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.81 (0.21), residues: 1610 helix: 1.10 (0.22), residues: 540 sheet: -0.56 (0.28), residues: 375 loop : -1.87 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 77 HIS 0.002 0.001 HIS C 131 PHE 0.011 0.001 PHE A 234 TYR 0.017 0.001 TYR C 252 ARG 0.005 0.000 ARG C 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 1.543 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.9146 (tp) cc_final: 0.8829 (tt) REVERT: B 21 ILE cc_start: 0.9128 (tp) cc_final: 0.8881 (tt) REVERT: C 21 ILE cc_start: 0.9107 (tp) cc_final: 0.8805 (tt) REVERT: C 289 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8088 (t80) REVERT: C 291 MET cc_start: 0.8358 (tpp) cc_final: 0.8109 (tpp) REVERT: D 21 ILE cc_start: 0.9167 (tp) cc_final: 0.8890 (tt) REVERT: D 127 MET cc_start: 0.8362 (mtp) cc_final: 0.8101 (mtp) REVERT: E 17 LEU cc_start: 0.8405 (tp) cc_final: 0.8047 (tp) REVERT: E 21 ILE cc_start: 0.9137 (tp) cc_final: 0.8793 (tt) REVERT: E 227 MET cc_start: 0.7642 (tmm) cc_final: 0.7314 (tpt) outliers start: 42 outliers final: 37 residues processed: 255 average time/residue: 0.1936 time to fit residues: 78.1171 Evaluate side-chains 257 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 289 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 266 MET Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 0.0970 chunk 111 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.144585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.115342 restraints weight = 21810.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.118693 restraints weight = 14582.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.121116 restraints weight = 11134.205| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12868 Z= 0.221 Angle : 0.643 10.936 17659 Z= 0.314 Chirality : 0.045 0.259 2175 Planarity : 0.003 0.024 2121 Dihedral : 3.861 13.155 1876 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.41 % Allowed : 23.93 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.83 (0.21), residues: 1610 helix: 1.16 (0.22), residues: 540 sheet: -0.69 (0.28), residues: 375 loop : -1.87 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 77 HIS 0.002 0.001 HIS D 68 PHE 0.010 0.001 PHE D 298 TYR 0.021 0.001 TYR C 252 ARG 0.004 0.000 ARG C 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2761.86 seconds wall clock time: 51 minutes 36.10 seconds (3096.10 seconds total)