Starting phenix.real_space_refine on Wed Sep 17 22:41:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fm1_50546/09_2025/9fm1_50546.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fm1_50546/09_2025/9fm1_50546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fm1_50546/09_2025/9fm1_50546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fm1_50546/09_2025/9fm1_50546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fm1_50546/09_2025/9fm1_50546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fm1_50546/09_2025/9fm1_50546.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 54 5.16 5 C 7257 2.51 5 N 2007 2.21 5 O 2286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11604 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2901 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2901 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2901 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 939 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 939 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 939 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.89, per 1000 atoms: 0.25 Number of scatterers: 11604 At special positions: 0 Unit cell: (109.44, 105.84, 110.88, 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 54 16.00 O 2286 8.00 N 2007 7.00 C 7257 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 57 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 143 " distance=2.04 Simple disulfide: pdb=" SG CYS A 178 " - pdb=" SG CYS A 272 " distance=2.04 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 318 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 57 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 72 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 143 " distance=2.04 Simple disulfide: pdb=" SG CYS B 178 " - pdb=" SG CYS B 272 " distance=2.04 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 318 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 57 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 143 " distance=2.04 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 272 " distance=2.04 Simple disulfide: pdb=" SG CYS C 292 " - pdb=" SG CYS C 318 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 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 601 " - " ASN A 145 " " NAG A 602 " - " ASN A 194 " " NAG B 601 " - " ASN B 145 " " NAG B 602 " - " ASN B 194 " " NAG C 601 " - " ASN C 145 " " NAG C 602 " - " ASN C 194 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 517.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2772 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 36 sheets defined 18.1% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.639A pdb=" N ARG A 101 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR A 102 " --> pdb=" O HIS A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 98 through 102' Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.686A pdb=" N GLY A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.658A pdb=" N ALA A 130 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.709A pdb=" N ASN A 397 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 453 Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.621A pdb=" N ARG B 101 " --> pdb=" O MET B 98 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR B 102 " --> pdb=" O HIS B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 98 through 102' Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.668A pdb=" N ALA B 130 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 202 Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 419 through 453 Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.644A pdb=" N ARG C 101 " --> pdb=" O MET C 98 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR C 102 " --> pdb=" O HIS C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 102' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 106 through 113 removed outlier: 3.733A pdb=" N GLY C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.589A pdb=" N ALA C 130 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 202 Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.544A pdb=" N ASN C 397 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER C 398 " --> pdb=" O LYS C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 453 removed outlier: 3.861A pdb=" N LEU C 422 " --> pdb=" O HIS C 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.635A pdb=" N GLU D 64 " --> pdb=" O ASP D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.877A pdb=" N THR D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.825A pdb=" N GLU E 64 " --> pdb=" O ASP E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.899A pdb=" N THR E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.663A pdb=" N GLU F 64 " --> pdb=" O ASP F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.967A pdb=" N THR F 87 " --> pdb=" O PRO F 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 18 removed outlier: 3.913A pdb=" N HIS A 14 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 removed outlier: 5.901A pdb=" N ASN A 43 " --> pdb=" O ALA A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 119 removed outlier: 4.057A pdb=" N ARG A 118 " --> pdb=" O CYS A 272 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS A 272 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL A 187 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 189 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE A 264 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 119 removed outlier: 4.057A pdb=" N ARG A 118 " --> pdb=" O CYS A 272 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS A 272 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 170 through 174 Processing sheet with id=AA8, first strand: chain 'A' and resid 298 through 300 Processing sheet with id=AA9, first strand: chain 'A' and resid 306 through 308 removed outlier: 6.060A pdb=" N TYR A 307 " --> pdb=" O VAL A 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 14 through 16 removed outlier: 3.931A pdb=" N HIS B 14 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 29 through 31 Processing sheet with id=AB3, first strand: chain 'B' and resid 43 through 44 removed outlier: 5.902A pdb=" N ASN B 43 " --> pdb=" O ALA B 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AB5, first strand: chain 'B' and resid 116 through 119 removed outlier: 4.021A pdb=" N ARG B 118 " --> pdb=" O CYS B 272 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS B 272 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL B 187 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 189 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE B 264 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 116 through 119 removed outlier: 4.021A pdb=" N ARG B 118 " --> pdb=" O CYS B 272 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS B 272 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 170 through 174 Processing sheet with id=AB8, first strand: chain 'B' and resid 298 through 300 Processing sheet with id=AB9, first strand: chain 'B' and resid 306 through 308 removed outlier: 6.045A pdb=" N TYR B 307 " --> pdb=" O VAL B 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 14 through 16 removed outlier: 3.910A pdb=" N HIS C 14 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 44 removed outlier: 5.878A pdb=" N ASN C 43 " --> pdb=" O ALA C 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AC5, first strand: chain 'C' and resid 116 through 119 removed outlier: 4.030A pdb=" N ARG C 118 " --> pdb=" O CYS C 272 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS C 272 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL C 187 " --> pdb=" O PRO C 267 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 189 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE C 264 " --> pdb=" O ALA C 159 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 116 through 119 removed outlier: 4.030A pdb=" N ARG C 118 " --> pdb=" O CYS C 272 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS C 272 " --> pdb=" O ARG C 118 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 170 through 174 Processing sheet with id=AC8, first strand: chain 'C' and resid 298 through 300 Processing sheet with id=AC9, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.060A pdb=" N TYR C 307 " --> pdb=" O VAL C 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.610A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL D 5 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 70 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.339A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.339A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.661A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL E 5 " --> pdb=" O ALA E 23 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.314A pdb=" N GLY E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.314A pdb=" N GLY E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.632A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER F 70 " --> pdb=" O TYR F 79 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1131 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: 1.40 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2022 1.32 - 1.45: 3061 1.45 - 1.57: 6686 1.57 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 11841 Sorted by residual: bond pdb=" CA SER E 76 " pdb=" CB SER E 76 " ideal model delta sigma weight residual 1.529 1.458 0.071 1.58e-02 4.01e+03 2.00e+01 bond pdb=" CA SER D 76 " pdb=" CB SER D 76 " ideal model delta sigma weight residual 1.530 1.468 0.062 1.50e-02 4.44e+03 1.69e+01 bond pdb=" N GLN F 105 " pdb=" CA GLN F 105 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.23e-02 6.61e+03 1.40e+01 bond pdb=" CA SER F 76 " pdb=" CB SER F 76 " ideal model delta sigma weight residual 1.530 1.475 0.054 1.50e-02 4.44e+03 1.32e+01 bond pdb=" N GLN D 105 " pdb=" CA GLN D 105 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.23e-02 6.61e+03 1.27e+01 ... (remaining 11836 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 15672 1.91 - 3.82: 373 3.82 - 5.74: 58 5.74 - 7.65: 16 7.65 - 9.56: 3 Bond angle restraints: 16122 Sorted by residual: angle pdb=" N PRO C 36 " pdb=" CA PRO C 36 " pdb=" C PRO C 36 " ideal model delta sigma weight residual 111.22 120.12 -8.90 1.40e+00 5.10e-01 4.04e+01 angle pdb=" C PRO A 325 " pdb=" CA PRO A 325 " pdb=" CB PRO A 325 " ideal model delta sigma weight residual 111.56 102.00 9.56 1.65e+00 3.67e-01 3.36e+01 angle pdb=" C PRO B 325 " pdb=" CA PRO B 325 " pdb=" CB PRO B 325 " ideal model delta sigma weight residual 111.56 102.58 8.98 1.65e+00 3.67e-01 2.96e+01 angle pdb=" N GLY E 65 " pdb=" CA GLY E 65 " pdb=" C GLY E 65 " ideal model delta sigma weight residual 115.36 108.54 6.82 1.33e+00 5.65e-01 2.63e+01 angle pdb=" N VAL D 63 " pdb=" CA VAL D 63 " pdb=" CB VAL D 63 " ideal model delta sigma weight residual 112.28 105.61 6.67 1.33e+00 5.65e-01 2.51e+01 ... (remaining 16117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6646 17.97 - 35.94: 421 35.94 - 53.91: 66 53.91 - 71.88: 20 71.88 - 89.85: 11 Dihedral angle restraints: 7164 sinusoidal: 2811 harmonic: 4353 Sorted by residual: dihedral pdb=" CB CYS C 178 " pdb=" SG CYS C 178 " pdb=" SG CYS C 272 " pdb=" CB CYS C 272 " ideal model delta sinusoidal sigma weight residual 93.00 168.46 -75.46 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS A 178 " pdb=" SG CYS A 178 " pdb=" SG CYS A 272 " pdb=" CB CYS A 272 " ideal model delta sinusoidal sigma weight residual 93.00 155.32 -62.32 1 1.00e+01 1.00e-02 5.14e+01 dihedral pdb=" CB CYS B 178 " pdb=" SG CYS B 178 " pdb=" SG CYS B 272 " pdb=" CB CYS B 272 " ideal model delta sinusoidal sigma weight residual 93.00 152.03 -59.03 1 1.00e+01 1.00e-02 4.66e+01 ... (remaining 7161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1594 0.066 - 0.133: 232 0.133 - 0.199: 18 0.199 - 0.265: 8 0.265 - 0.331: 2 Chirality restraints: 1854 Sorted by residual: chirality pdb=" CA ALA D 60 " pdb=" N ALA D 60 " pdb=" C ALA D 60 " pdb=" CB ALA D 60 " both_signs ideal model delta sigma weight residual False 2.48 2.15 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA VAL E 63 " pdb=" N VAL E 63 " pdb=" C VAL E 63 " pdb=" CB VAL E 63 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA GLN E 105 " pdb=" N GLN E 105 " pdb=" C GLN E 105 " pdb=" CB GLN E 105 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 1851 not shown) Planarity restraints: 2097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 237 " -0.046 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO B 238 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 238 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 238 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 58 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.48e+00 pdb=" C ILE E 58 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE E 58 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR E 59 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 58 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C ILE F 58 " -0.042 2.00e-02 2.50e+03 pdb=" O ILE F 58 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR F 59 " 0.014 2.00e-02 2.50e+03 ... (remaining 2094 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 789 2.74 - 3.28: 10867 3.28 - 3.82: 17829 3.82 - 4.36: 21556 4.36 - 4.90: 39384 Nonbonded interactions: 90425 Sorted by model distance: nonbonded pdb=" OH TYR A 176 " pdb=" O GLU A 182 " model vdw 2.194 3.040 nonbonded pdb=" OH TYR C 176 " pdb=" O GLU C 182 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR B 176 " pdb=" O GLU B 182 " model vdw 2.206 3.040 nonbonded pdb=" OG1 THR B 61 " pdb=" OD2 ASP B 64 " model vdw 2.214 3.040 nonbonded pdb=" NH1 ARG B 69 " pdb=" O GLY B 93 " model vdw 2.235 3.120 ... (remaining 90420 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.060 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 0.071 11865 Z= 0.242 Angle : 0.707 9.562 16176 Z= 0.419 Chirality : 0.049 0.331 1854 Planarity : 0.005 0.071 2091 Dihedral : 12.507 89.848 4338 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.24 % Allowed : 0.56 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.21), residues: 1515 helix: 1.87 (0.37), residues: 204 sheet: 0.58 (0.28), residues: 369 loop : -0.66 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 432 TYR 0.027 0.002 TYR E 98 PHE 0.009 0.001 PHE C 41 TRP 0.014 0.001 TRP D 52A HIS 0.004 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00385 (11841) covalent geometry : angle 0.70056 (16122) SS BOND : bond 0.00363 ( 18) SS BOND : angle 1.23641 ( 36) hydrogen bonds : bond 0.18367 ( 415) hydrogen bonds : angle 8.77534 ( 1131) link_NAG-ASN : bond 0.00275 ( 6) link_NAG-ASN : angle 2.50431 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 291 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 ARG cc_start: 0.7714 (mmt90) cc_final: 0.7410 (mmt90) REVERT: B 453 ASN cc_start: 0.5731 (m110) cc_final: 0.5426 (m110) REVERT: C 425 ASP cc_start: 0.7180 (t0) cc_final: 0.6819 (t0) REVERT: E 29 ASP cc_start: 0.7662 (t0) cc_final: 0.7406 (t0) REVERT: F 29 ASP cc_start: 0.7787 (t0) cc_final: 0.7525 (t0) outliers start: 3 outliers final: 1 residues processed: 291 average time/residue: 0.4553 time to fit residues: 145.7440 Evaluate side-chains 189 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN A 239 GLN A 406 ASN A 439 GLN B 239 GLN ** C 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.116839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097103 restraints weight = 20576.529| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.88 r_work: 0.3123 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11865 Z= 0.124 Angle : 0.614 7.527 16176 Z= 0.318 Chirality : 0.046 0.180 1854 Planarity : 0.005 0.055 2091 Dihedral : 6.124 57.580 1762 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.88 % Allowed : 12.37 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.21), residues: 1515 helix: 1.81 (0.35), residues: 210 sheet: 0.41 (0.28), residues: 369 loop : -0.57 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 432 TYR 0.026 0.002 TYR E 98 PHE 0.010 0.002 PHE D 47 TRP 0.013 0.001 TRP B 271 HIS 0.003 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00279 (11841) covalent geometry : angle 0.60430 (16122) SS BOND : bond 0.00332 ( 18) SS BOND : angle 1.75663 ( 36) hydrogen bonds : bond 0.03835 ( 415) hydrogen bonds : angle 6.15062 ( 1131) link_NAG-ASN : bond 0.00216 ( 6) link_NAG-ASN : angle 2.44202 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 212 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8055 (ttpp) cc_final: 0.7814 (tttm) REVERT: A 69 ARG cc_start: 0.8452 (ttt180) cc_final: 0.7931 (ttm170) REVERT: C 21 GLN cc_start: 0.8449 (mp10) cc_final: 0.8209 (mp10) REVERT: C 425 ASP cc_start: 0.8132 (t0) cc_final: 0.7681 (t0) REVERT: D 64 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7627 (mp0) REVERT: E 29 ASP cc_start: 0.8724 (t0) cc_final: 0.8250 (t0) REVERT: E 46 GLU cc_start: 0.8119 (mp0) cc_final: 0.7879 (mp0) REVERT: E 64 GLU cc_start: 0.7540 (tt0) cc_final: 0.7188 (mt-10) REVERT: F 29 ASP cc_start: 0.8760 (t0) cc_final: 0.8376 (t0) outliers start: 11 outliers final: 8 residues processed: 218 average time/residue: 0.4184 time to fit residues: 101.5497 Evaluate side-chains 196 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 188 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain F residue 58 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 146 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 42 optimal weight: 0.0970 chunk 141 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 82 optimal weight: 0.2980 chunk 103 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 58 optimal weight: 0.0970 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 390 ASN A 406 ASN A 439 GLN B 395 ASN C 148 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.119326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.099531 restraints weight = 20664.215| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.93 r_work: 0.3170 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11865 Z= 0.097 Angle : 0.565 8.798 16176 Z= 0.288 Chirality : 0.044 0.252 1854 Planarity : 0.004 0.045 2091 Dihedral : 5.620 55.203 1761 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.37 % Allowed : 14.30 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.21), residues: 1515 helix: 1.98 (0.35), residues: 210 sheet: 0.38 (0.27), residues: 348 loop : -0.47 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 432 TYR 0.025 0.001 TYR D 98 PHE 0.008 0.001 PHE A 41 TRP 0.012 0.001 TRP C 271 HIS 0.002 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00214 (11841) covalent geometry : angle 0.55592 (16122) SS BOND : bond 0.00346 ( 18) SS BOND : angle 1.50288 ( 36) hydrogen bonds : bond 0.03210 ( 415) hydrogen bonds : angle 5.54256 ( 1131) link_NAG-ASN : bond 0.00405 ( 6) link_NAG-ASN : angle 2.36883 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8092 (ttpp) cc_final: 0.7864 (tttm) REVERT: A 69 ARG cc_start: 0.8386 (ttt180) cc_final: 0.7978 (ttm170) REVERT: A 432 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7694 (tpp80) REVERT: A 449 GLU cc_start: 0.8888 (tt0) cc_final: 0.8672 (tt0) REVERT: B 69 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7389 (ttp80) REVERT: C 425 ASP cc_start: 0.8091 (t0) cc_final: 0.7709 (t0) REVERT: C 432 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8301 (tpt90) REVERT: D 64 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7568 (mp0) REVERT: D 83 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7621 (mtp180) REVERT: E 29 ASP cc_start: 0.8661 (t0) cc_final: 0.8184 (t0) REVERT: E 46 GLU cc_start: 0.8161 (mp0) cc_final: 0.7893 (mp0) REVERT: F 29 ASP cc_start: 0.8725 (t0) cc_final: 0.8301 (t0) REVERT: F 64 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7477 (mp0) outliers start: 17 outliers final: 5 residues processed: 223 average time/residue: 0.4409 time to fit residues: 109.1023 Evaluate side-chains 202 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 193 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 432 ARG Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 116 optimal weight: 0.0000 chunk 64 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 15 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 406 ASN A 439 GLN C 148 ASN D 3 GLN D 32 ASN E 32 ASN F 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.117950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.098393 restraints weight = 20810.963| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.92 r_work: 0.3158 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11865 Z= 0.104 Angle : 0.576 8.817 16176 Z= 0.294 Chirality : 0.044 0.160 1854 Planarity : 0.004 0.049 2091 Dihedral : 5.370 56.782 1761 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.25 % Allowed : 15.66 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.21), residues: 1515 helix: 2.10 (0.36), residues: 210 sheet: 0.33 (0.27), residues: 366 loop : -0.39 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 242 TYR 0.031 0.001 TYR E 98 PHE 0.009 0.001 PHE B 190 TRP 0.009 0.001 TRP C 271 HIS 0.002 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00239 (11841) covalent geometry : angle 0.56715 (16122) SS BOND : bond 0.00310 ( 18) SS BOND : angle 1.51554 ( 36) hydrogen bonds : bond 0.03175 ( 415) hydrogen bonds : angle 5.38808 ( 1131) link_NAG-ASN : bond 0.00313 ( 6) link_NAG-ASN : angle 2.28729 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8370 (ttt180) cc_final: 0.8100 (ttm170) REVERT: A 393 THR cc_start: 0.8799 (p) cc_final: 0.8566 (t) REVERT: B 69 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7383 (ttp80) REVERT: B 98 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.6508 (mpp) REVERT: C 23 GLU cc_start: 0.8561 (mp0) cc_final: 0.8359 (mp0) REVERT: C 393 THR cc_start: 0.8762 (p) cc_final: 0.8492 (t) REVERT: C 425 ASP cc_start: 0.8081 (t0) cc_final: 0.7685 (t0) REVERT: D 64 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7626 (mp0) REVERT: D 83 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7644 (mtp180) REVERT: E 29 ASP cc_start: 0.8725 (t0) cc_final: 0.8225 (t0) REVERT: E 46 GLU cc_start: 0.8164 (mp0) cc_final: 0.7868 (mp0) REVERT: F 29 ASP cc_start: 0.8743 (t0) cc_final: 0.8324 (t0) REVERT: F 64 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7418 (mp0) outliers start: 28 outliers final: 9 residues processed: 216 average time/residue: 0.4048 time to fit residues: 97.6573 Evaluate side-chains 189 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 59 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 87 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 390 ASN A 406 ASN A 439 GLN D 32 ASN E 32 ASN F 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.113763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.093873 restraints weight = 20727.037| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.89 r_work: 0.3082 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11865 Z= 0.152 Angle : 0.648 8.755 16176 Z= 0.330 Chirality : 0.046 0.165 1854 Planarity : 0.004 0.048 2091 Dihedral : 5.565 58.934 1761 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.21 % Allowed : 15.66 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.21), residues: 1515 helix: 1.72 (0.35), residues: 210 sheet: 0.36 (0.26), residues: 372 loop : -0.51 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 432 TYR 0.027 0.002 TYR D 98 PHE 0.014 0.002 PHE B 153 TRP 0.006 0.001 TRP A 321 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00362 (11841) covalent geometry : angle 0.63805 (16122) SS BOND : bond 0.00395 ( 18) SS BOND : angle 1.83697 ( 36) hydrogen bonds : bond 0.03696 ( 415) hydrogen bonds : angle 5.48966 ( 1131) link_NAG-ASN : bond 0.00255 ( 6) link_NAG-ASN : angle 2.43352 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8459 (ttt180) cc_final: 0.8135 (ttm170) REVERT: B 69 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7495 (ttp80) REVERT: B 432 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7574 (tpp80) REVERT: C 198 MET cc_start: 0.7838 (mmm) cc_final: 0.7552 (mtp) REVERT: C 320 ILE cc_start: 0.8501 (mt) cc_final: 0.8223 (mt) REVERT: D 64 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7589 (mp0) REVERT: D 83 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7685 (mtp180) REVERT: E 29 ASP cc_start: 0.8799 (t0) cc_final: 0.8284 (t0) REVERT: E 46 GLU cc_start: 0.8098 (mp0) cc_final: 0.7774 (mp0) REVERT: F 29 ASP cc_start: 0.8772 (t0) cc_final: 0.8386 (t0) REVERT: F 64 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7495 (mp0) outliers start: 40 outliers final: 21 residues processed: 205 average time/residue: 0.4603 time to fit residues: 104.3535 Evaluate side-chains 194 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 85 optimal weight: 0.5980 chunk 71 optimal weight: 0.0770 chunk 129 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 19 optimal weight: 0.0770 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 390 ASN A 406 ASN A 439 GLN C 390 ASN D 3 GLN D 32 ASN E 32 ASN F 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.116749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.096876 restraints weight = 20695.353| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.93 r_work: 0.3130 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11865 Z= 0.103 Angle : 0.597 9.268 16176 Z= 0.301 Chirality : 0.044 0.166 1854 Planarity : 0.004 0.035 2091 Dihedral : 5.253 55.555 1761 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.65 % Allowed : 17.43 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.21), residues: 1515 helix: 1.84 (0.36), residues: 210 sheet: 0.46 (0.26), residues: 372 loop : -0.45 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 432 TYR 0.037 0.001 TYR E 98 PHE 0.014 0.001 PHE B 153 TRP 0.010 0.001 TRP C 271 HIS 0.002 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00235 (11841) covalent geometry : angle 0.58923 (16122) SS BOND : bond 0.00314 ( 18) SS BOND : angle 1.37608 ( 36) hydrogen bonds : bond 0.03272 ( 415) hydrogen bonds : angle 5.25302 ( 1131) link_NAG-ASN : bond 0.00284 ( 6) link_NAG-ASN : angle 2.39984 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7475 (ttp80) REVERT: C 198 MET cc_start: 0.7833 (mmm) cc_final: 0.7493 (mtp) REVERT: C 320 ILE cc_start: 0.8486 (mt) cc_final: 0.8212 (mt) REVERT: C 425 ASP cc_start: 0.8083 (t0) cc_final: 0.7737 (t0) REVERT: C 432 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7806 (tpp80) REVERT: D 64 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7551 (mp0) REVERT: D 83 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8277 (mtt90) REVERT: E 29 ASP cc_start: 0.8737 (t0) cc_final: 0.8207 (t0) REVERT: E 46 GLU cc_start: 0.8144 (mp0) cc_final: 0.7803 (mp0) REVERT: F 29 ASP cc_start: 0.8741 (t0) cc_final: 0.8307 (t0) REVERT: F 64 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7357 (mp0) outliers start: 33 outliers final: 17 residues processed: 201 average time/residue: 0.4300 time to fit residues: 96.1499 Evaluate side-chains 188 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 432 ARG Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 41 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 107 optimal weight: 0.0030 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 0.0570 chunk 128 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 overall best weight: 1.2112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 406 ASN A 439 GLN D 32 ASN E 32 ASN F 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.094503 restraints weight = 20671.782| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.90 r_work: 0.3082 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11865 Z= 0.139 Angle : 0.648 8.963 16176 Z= 0.330 Chirality : 0.045 0.171 1854 Planarity : 0.004 0.045 2091 Dihedral : 5.466 57.602 1761 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.81 % Allowed : 17.91 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.21), residues: 1515 helix: 1.72 (0.36), residues: 210 sheet: 0.48 (0.27), residues: 342 loop : -0.49 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 432 TYR 0.035 0.001 TYR D 98 PHE 0.015 0.002 PHE B 153 TRP 0.005 0.001 TRP B 271 HIS 0.003 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00332 (11841) covalent geometry : angle 0.63916 (16122) SS BOND : bond 0.00352 ( 18) SS BOND : angle 1.71460 ( 36) hydrogen bonds : bond 0.03634 ( 415) hydrogen bonds : angle 5.35235 ( 1131) link_NAG-ASN : bond 0.00221 ( 6) link_NAG-ASN : angle 2.39791 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7507 (ttp80) REVERT: B 98 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7690 (mtt) REVERT: C 198 MET cc_start: 0.7887 (mmm) cc_final: 0.7581 (mtp) REVERT: C 320 ILE cc_start: 0.8524 (mt) cc_final: 0.8257 (mt) REVERT: C 432 ARG cc_start: 0.8612 (tpp80) cc_final: 0.7861 (tpp80) REVERT: D 64 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7591 (mp0) REVERT: D 83 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8329 (mtt90) REVERT: E 29 ASP cc_start: 0.8801 (t0) cc_final: 0.8250 (t0) REVERT: E 46 GLU cc_start: 0.8113 (mp0) cc_final: 0.7765 (mp0) REVERT: F 29 ASP cc_start: 0.8776 (t0) cc_final: 0.8360 (t0) REVERT: F 64 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7356 (mp0) outliers start: 35 outliers final: 22 residues processed: 193 average time/residue: 0.4282 time to fit residues: 91.7308 Evaluate side-chains 190 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 78 optimal weight: 0.2980 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 30 optimal weight: 0.0020 chunk 22 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 11 optimal weight: 0.0370 chunk 114 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.4468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 406 ASN A 439 GLN D 3 GLN D 32 ASN E 32 ASN F 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.116960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.097088 restraints weight = 20685.973| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.93 r_work: 0.3123 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11865 Z= 0.104 Angle : 0.610 9.560 16176 Z= 0.309 Chirality : 0.044 0.171 1854 Planarity : 0.004 0.037 2091 Dihedral : 5.234 54.835 1761 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.41 % Allowed : 18.88 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.21), residues: 1515 helix: 1.70 (0.36), residues: 213 sheet: 0.46 (0.27), residues: 366 loop : -0.38 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 432 TYR 0.052 0.001 TYR E 98 PHE 0.015 0.001 PHE B 153 TRP 0.010 0.001 TRP C 271 HIS 0.002 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00236 (11841) covalent geometry : angle 0.60250 (16122) SS BOND : bond 0.00319 ( 18) SS BOND : angle 1.37561 ( 36) hydrogen bonds : bond 0.03220 ( 415) hydrogen bonds : angle 5.17164 ( 1131) link_NAG-ASN : bond 0.00256 ( 6) link_NAG-ASN : angle 2.32449 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7471 (ttp80) REVERT: C 198 MET cc_start: 0.7840 (mmm) cc_final: 0.7540 (mtp) REVERT: C 320 ILE cc_start: 0.8499 (mt) cc_final: 0.8235 (mt) REVERT: C 432 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7843 (tpp80) REVERT: D 64 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7547 (mp0) REVERT: E 29 ASP cc_start: 0.8702 (t0) cc_final: 0.8145 (t0) REVERT: E 46 GLU cc_start: 0.8112 (mp0) cc_final: 0.7713 (mp0) REVERT: F 29 ASP cc_start: 0.8729 (t0) cc_final: 0.8301 (t0) REVERT: F 64 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7291 (mp0) outliers start: 30 outliers final: 20 residues processed: 193 average time/residue: 0.4075 time to fit residues: 87.5957 Evaluate side-chains 191 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 432 ARG Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 23 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 406 ASN A 439 GLN D 32 ASN E 32 ASN E 100GASN F 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.113752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.093727 restraints weight = 20505.476| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.89 r_work: 0.3080 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11865 Z= 0.148 Angle : 0.654 9.156 16176 Z= 0.333 Chirality : 0.045 0.177 1854 Planarity : 0.004 0.036 2091 Dihedral : 5.496 57.734 1761 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.09 % Allowed : 19.12 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.21), residues: 1515 helix: 1.57 (0.36), residues: 213 sheet: 0.74 (0.27), residues: 357 loop : -0.56 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 432 TYR 0.038 0.002 TYR D 98 PHE 0.017 0.002 PHE B 153 TRP 0.006 0.001 TRP A 321 HIS 0.003 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00352 (11841) covalent geometry : angle 0.64507 (16122) SS BOND : bond 0.00350 ( 18) SS BOND : angle 1.74244 ( 36) hydrogen bonds : bond 0.03572 ( 415) hydrogen bonds : angle 5.32436 ( 1131) link_NAG-ASN : bond 0.00192 ( 6) link_NAG-ASN : angle 2.42433 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7517 (ttp80) REVERT: C 320 ILE cc_start: 0.8526 (mt) cc_final: 0.8270 (mt) REVERT: D 64 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7592 (mp0) REVERT: E 29 ASP cc_start: 0.8783 (t0) cc_final: 0.8223 (t0) REVERT: E 46 GLU cc_start: 0.8115 (mp0) cc_final: 0.7758 (mp0) REVERT: F 29 ASP cc_start: 0.8782 (t0) cc_final: 0.8360 (t0) REVERT: F 64 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7342 (mp0) outliers start: 26 outliers final: 21 residues processed: 183 average time/residue: 0.4575 time to fit residues: 92.9174 Evaluate side-chains 188 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 112 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 406 ASN A 439 GLN D 3 GLN D 32 ASN E 32 ASN E 100GASN F 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.114510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.094553 restraints weight = 20721.189| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.90 r_work: 0.3090 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11865 Z= 0.134 Angle : 0.651 9.379 16176 Z= 0.334 Chirality : 0.045 0.172 1854 Planarity : 0.004 0.070 2091 Dihedral : 5.483 57.276 1761 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.17 % Allowed : 18.80 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.21), residues: 1515 helix: 1.47 (0.35), residues: 213 sheet: 0.57 (0.26), residues: 384 loop : -0.55 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 432 TYR 0.046 0.002 TYR E 98 PHE 0.018 0.002 PHE B 153 TRP 0.007 0.001 TRP C 271 HIS 0.003 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00317 (11841) covalent geometry : angle 0.64261 (16122) SS BOND : bond 0.00342 ( 18) SS BOND : angle 1.58758 ( 36) hydrogen bonds : bond 0.03613 ( 415) hydrogen bonds : angle 5.33092 ( 1131) link_NAG-ASN : bond 0.00226 ( 6) link_NAG-ASN : angle 2.47925 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7526 (ttp80) REVERT: B 98 MET cc_start: 0.8561 (mpp) cc_final: 0.7669 (mtt) REVERT: C 320 ILE cc_start: 0.8519 (mt) cc_final: 0.8251 (mt) REVERT: D 64 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7553 (mp0) REVERT: E 29 ASP cc_start: 0.8723 (t0) cc_final: 0.8164 (t0) REVERT: E 46 GLU cc_start: 0.8107 (mp0) cc_final: 0.7747 (mp0) REVERT: E 100 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7780 (t0) REVERT: F 29 ASP cc_start: 0.8764 (t0) cc_final: 0.8330 (t0) REVERT: F 64 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7350 (mp0) outliers start: 27 outliers final: 21 residues processed: 184 average time/residue: 0.4526 time to fit residues: 92.0246 Evaluate side-chains 189 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 106 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 406 ASN A 439 GLN D 32 ASN E 32 ASN F 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.094462 restraints weight = 20834.728| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.94 r_work: 0.3085 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 11865 Z= 0.179 Angle : 0.890 59.191 16176 Z= 0.509 Chirality : 0.050 0.972 1854 Planarity : 0.005 0.081 2091 Dihedral : 5.496 57.280 1761 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.25 % Allowed : 19.04 % Favored : 78.71 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.21), residues: 1515 helix: 1.45 (0.35), residues: 213 sheet: 0.57 (0.26), residues: 384 loop : -0.53 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 432 TYR 0.039 0.002 TYR D 98 PHE 0.017 0.002 PHE B 153 TRP 0.007 0.001 TRP C 271 HIS 0.003 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00369 (11841) covalent geometry : angle 0.88481 (16122) SS BOND : bond 0.00341 ( 18) SS BOND : angle 1.58264 ( 36) hydrogen bonds : bond 0.03619 ( 415) hydrogen bonds : angle 5.32955 ( 1131) link_NAG-ASN : bond 0.00227 ( 6) link_NAG-ASN : angle 2.48002 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3983.15 seconds wall clock time: 68 minutes 44.84 seconds (4124.84 seconds total)