Starting phenix.real_space_refine on Wed Jul 30 03:05:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fm1_50546/07_2025/9fm1_50546.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fm1_50546/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9fm1_50546/07_2025/9fm1_50546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fm1_50546/07_2025/9fm1_50546.map" model { file = "/net/cci-nas-00/data/ceres_data/9fm1_50546/07_2025/9fm1_50546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fm1_50546/07_2025/9fm1_50546.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 2, 'ARG: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: {'GLU:plan': 2, 'ARG: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: {'GLU:plan': 2, 'ARG: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: 8.07, per 1000 atoms: 0.70 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: 2.81 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.84 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: 4.12 Time building geometry restraints manager: 3.37 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: 0.03 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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.480 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.510 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), 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 TRP 0.014 0.001 TRP D 52A HIS 0.004 0.001 HIS C 99 PHE 0.009 0.001 PHE C 41 TYR 0.027 0.002 TYR E 98 ARG 0.004 0.000 ARG C 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 6) link_NAG-ASN : angle 2.50431 ( 18) hydrogen bonds : bond 0.18367 ( 415) hydrogen bonds : angle 8.77534 ( 1131) SS BOND : bond 0.00363 ( 18) SS BOND : angle 1.23641 ( 36) covalent geometry : bond 0.00385 (11841) covalent geometry : angle 0.70056 (16122) *********************** 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 : 1.312 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: 0.9475 time to fit residues: 304.5778 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 : 1.207 ------------------------------------------------------------------------------- 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 126 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 60 optimal weight: 0.4980 chunk 117 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 215 ASN A 239 GLN A 406 ASN A 439 GLN B 239 GLN B 395 ASN C 148 ASN ** C 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.109926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.090119 restraints weight = 20899.965| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.84 r_work: 0.3006 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11865 Z= 0.271 Angle : 0.762 8.712 16176 Z= 0.396 Chirality : 0.051 0.197 1854 Planarity : 0.006 0.053 2091 Dihedral : 6.773 59.693 1762 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.41 % Allowed : 13.09 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1515 helix: 1.29 (0.34), residues: 210 sheet: 0.15 (0.27), residues: 363 loop : -0.82 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 52A HIS 0.005 0.002 HIS C 99 PHE 0.016 0.003 PHE F 37 TYR 0.033 0.003 TYR E 100C ARG 0.005 0.001 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 6) link_NAG-ASN : angle 2.60948 ( 18) hydrogen bonds : bond 0.04678 ( 415) hydrogen bonds : angle 6.36717 ( 1131) SS BOND : bond 0.00650 ( 18) SS BOND : angle 2.39552 ( 36) covalent geometry : bond 0.00639 (11841) covalent geometry : angle 0.74968 (16122) *********************** 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 221 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8218 (ttpp) cc_final: 0.7982 (tttm) REVERT: B 69 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7720 (ttp80) REVERT: C 320 ILE cc_start: 0.8480 (mt) cc_final: 0.8225 (mt) REVERT: C 425 ASP cc_start: 0.8224 (t0) cc_final: 0.7840 (t0) REVERT: D 29 ASP cc_start: 0.8772 (t0) cc_final: 0.8546 (t0) REVERT: D 46 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7990 (pt0) REVERT: D 64 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7680 (mp0) REVERT: E 29 ASP cc_start: 0.8856 (t0) cc_final: 0.8346 (t0) REVERT: E 46 GLU cc_start: 0.8198 (mp0) cc_final: 0.7973 (mp0) REVERT: F 29 ASP cc_start: 0.8878 (t0) cc_final: 0.8493 (t0) REVERT: F 64 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7421 (mp0) outliers start: 30 outliers final: 16 residues processed: 210 average time/residue: 0.9476 time to fit residues: 221.2021 Evaluate side-chains 180 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain B residue 33 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 257 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 100 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 85 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN A 406 ASN A 439 GLN ** C 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.110553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.090596 restraints weight = 21002.875| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.87 r_work: 0.3020 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11865 Z= 0.193 Angle : 0.673 7.956 16176 Z= 0.348 Chirality : 0.047 0.182 1854 Planarity : 0.005 0.047 2091 Dihedral : 6.607 59.696 1761 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.57 % Allowed : 16.14 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.20), residues: 1515 helix: 1.40 (0.35), residues: 210 sheet: -0.12 (0.27), residues: 357 loop : -0.81 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 52A HIS 0.003 0.001 HIS C 99 PHE 0.015 0.002 PHE B 153 TYR 0.025 0.002 TYR D 98 ARG 0.003 0.000 ARG B 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 6) link_NAG-ASN : angle 2.55829 ( 18) hydrogen bonds : bond 0.04244 ( 415) hydrogen bonds : angle 5.91091 ( 1131) SS BOND : bond 0.00509 ( 18) SS BOND : angle 1.98632 ( 36) covalent geometry : bond 0.00458 (11841) covalent geometry : angle 0.66194 (16122) *********************** 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 213 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8228 (ttpp) cc_final: 0.8004 (tttm) REVERT: B 69 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7611 (ttp80) REVERT: C 69 ARG cc_start: 0.8339 (ttt180) cc_final: 0.7925 (ttm170) REVERT: C 320 ILE cc_start: 0.8522 (mt) cc_final: 0.8245 (mt) REVERT: C 425 ASP cc_start: 0.8214 (t0) cc_final: 0.7853 (t0) REVERT: D 29 ASP cc_start: 0.8749 (t0) cc_final: 0.8468 (t0) REVERT: D 46 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7998 (pt0) REVERT: D 64 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7668 (mp0) REVERT: E 29 ASP cc_start: 0.8795 (t0) cc_final: 0.8289 (t0) REVERT: E 46 GLU cc_start: 0.8187 (mp0) cc_final: 0.7898 (mp0) REVERT: F 29 ASP cc_start: 0.8826 (t0) cc_final: 0.8389 (t0) REVERT: F 64 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7466 (mp0) REVERT: F 101 ASP cc_start: 0.7207 (t0) cc_final: 0.7000 (t0) outliers start: 32 outliers final: 15 residues processed: 197 average time/residue: 0.9541 time to fit residues: 208.5019 Evaluate side-chains 181 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 249 VAL 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 249 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 249 VAL 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 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 81 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN A 406 ASN A 439 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.090685 restraints weight = 20989.140| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.85 r_work: 0.3022 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11865 Z= 0.183 Angle : 0.662 8.465 16176 Z= 0.342 Chirality : 0.047 0.236 1854 Planarity : 0.005 0.047 2091 Dihedral : 6.333 59.886 1761 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.29 % Allowed : 16.22 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.20), residues: 1515 helix: 1.42 (0.35), residues: 210 sheet: -0.17 (0.26), residues: 357 loop : -0.83 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 36 HIS 0.003 0.001 HIS C 99 PHE 0.017 0.002 PHE B 153 TYR 0.031 0.002 TYR E 98 ARG 0.005 0.000 ARG C 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 6) link_NAG-ASN : angle 2.60770 ( 18) hydrogen bonds : bond 0.04091 ( 415) hydrogen bonds : angle 5.74779 ( 1131) SS BOND : bond 0.00476 ( 18) SS BOND : angle 1.89505 ( 36) covalent geometry : bond 0.00436 (11841) covalent geometry : angle 0.65155 (16122) *********************** 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 215 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8239 (ttpp) cc_final: 0.8008 (tttm) REVERT: A 320 ILE cc_start: 0.8333 (mt) cc_final: 0.8082 (mt) REVERT: B 69 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7866 (ttm170) REVERT: C 320 ILE cc_start: 0.8536 (mt) cc_final: 0.8236 (mt) REVERT: C 393 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8630 (t) REVERT: C 432 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7754 (tpp80) REVERT: D 29 ASP cc_start: 0.8817 (t0) cc_final: 0.8529 (t0) REVERT: D 46 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7992 (pt0) REVERT: D 64 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7561 (mp0) REVERT: E 29 ASP cc_start: 0.8824 (t0) cc_final: 0.8274 (t0) REVERT: E 46 GLU cc_start: 0.8159 (mp0) cc_final: 0.7845 (mp0) REVERT: F 29 ASP cc_start: 0.8847 (t0) cc_final: 0.8423 (t0) REVERT: F 64 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7429 (mp0) REVERT: F 101 ASP cc_start: 0.7302 (t0) cc_final: 0.7064 (t0) outliers start: 41 outliers final: 18 residues processed: 198 average time/residue: 0.8751 time to fit residues: 193.2828 Evaluate side-chains 184 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 249 VAL Chi-restraints excluded: chain A residue 259 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 249 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 415 ASP 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 78 VAL Chi-restraints excluded: chain E residue 111 VAL 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 140 optimal weight: 0.2980 chunk 7 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 chunk 106 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN A 439 GLN D 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.113115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.093348 restraints weight = 20644.611| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.89 r_work: 0.3071 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11865 Z= 0.115 Angle : 0.614 9.086 16176 Z= 0.317 Chirality : 0.045 0.151 1854 Planarity : 0.005 0.055 2091 Dihedral : 5.842 59.417 1761 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.09 % Allowed : 18.31 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1515 helix: 1.59 (0.35), residues: 210 sheet: 0.10 (0.27), residues: 348 loop : -0.73 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 271 HIS 0.003 0.001 HIS C 311 PHE 0.014 0.001 PHE B 153 TYR 0.014 0.001 TYR E 98 ARG 0.003 0.000 ARG B 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 6) link_NAG-ASN : angle 2.46627 ( 18) hydrogen bonds : bond 0.03644 ( 415) hydrogen bonds : angle 5.46430 ( 1131) SS BOND : bond 0.00368 ( 18) SS BOND : angle 1.61281 ( 36) covalent geometry : bond 0.00266 (11841) covalent geometry : angle 0.60504 (16122) *********************** 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 208 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 THR cc_start: 0.8904 (p) cc_final: 0.8643 (t) REVERT: B 69 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7543 (ttp80) REVERT: B 98 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7395 (mtt) REVERT: C 320 ILE cc_start: 0.8531 (mt) cc_final: 0.8226 (mt) REVERT: C 432 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7565 (tpp80) REVERT: D 29 ASP cc_start: 0.8725 (t0) cc_final: 0.8412 (t0) REVERT: D 46 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7985 (pt0) REVERT: D 64 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7566 (mp0) REVERT: E 29 ASP cc_start: 0.8734 (t0) cc_final: 0.8179 (t0) REVERT: E 46 GLU cc_start: 0.8147 (mp0) cc_final: 0.7800 (mp0) REVERT: E 83 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7196 (mtp180) REVERT: F 29 ASP cc_start: 0.8744 (t0) cc_final: 0.8314 (t0) REVERT: F 64 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7343 (mp0) REVERT: F 101 ASP cc_start: 0.7235 (t0) cc_final: 0.7034 (t0) outliers start: 26 outliers final: 13 residues processed: 198 average time/residue: 0.9511 time to fit residues: 208.6773 Evaluate side-chains 185 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 69 ARG Chi-restraints excluded: chain B residue 98 MET 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 259 THR Chi-restraints excluded: chain C residue 432 ARG Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 83 ARG 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 104 optimal weight: 5.9990 chunk 43 optimal weight: 0.0870 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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 390 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.092519 restraints weight = 20925.602| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.91 r_work: 0.3056 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11865 Z= 0.138 Angle : 0.644 9.025 16176 Z= 0.331 Chirality : 0.045 0.159 1854 Planarity : 0.005 0.045 2091 Dihedral : 5.759 58.697 1761 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.49 % Allowed : 19.36 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.20), residues: 1515 helix: 1.56 (0.35), residues: 210 sheet: 0.09 (0.27), residues: 366 loop : -0.69 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 271 HIS 0.003 0.001 HIS C 311 PHE 0.015 0.002 PHE B 153 TYR 0.010 0.001 TYR F 100C ARG 0.007 0.000 ARG A 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 6) link_NAG-ASN : angle 2.43067 ( 18) hydrogen bonds : bond 0.03732 ( 415) hydrogen bonds : angle 5.44559 ( 1131) SS BOND : bond 0.00394 ( 18) SS BOND : angle 1.66051 ( 36) covalent geometry : bond 0.00327 (11841) covalent geometry : angle 0.63476 (16122) *********************** 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 204 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7534 (ttp80) REVERT: B 98 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7560 (mtt) REVERT: C 320 ILE cc_start: 0.8477 (mt) cc_final: 0.8155 (mt) REVERT: D 29 ASP cc_start: 0.8775 (t0) cc_final: 0.8449 (t0) REVERT: D 46 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7971 (pt0) REVERT: D 64 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7547 (mp0) REVERT: E 29 ASP cc_start: 0.8773 (t0) cc_final: 0.8194 (t0) REVERT: E 46 GLU cc_start: 0.8120 (mp0) cc_final: 0.7752 (mp0) REVERT: E 83 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7190 (mtp180) REVERT: F 29 ASP cc_start: 0.8806 (t0) cc_final: 0.8372 (t0) REVERT: F 64 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7348 (mp0) REVERT: F 101 ASP cc_start: 0.7290 (t0) cc_final: 0.7077 (t0) outliers start: 31 outliers final: 21 residues processed: 191 average time/residue: 0.9462 time to fit residues: 203.2548 Evaluate side-chains 192 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 259 THR 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 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 436 ILE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 83 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 130 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.112116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.091931 restraints weight = 20590.749| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.92 r_work: 0.3063 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11865 Z= 0.133 Angle : 0.635 9.188 16176 Z= 0.326 Chirality : 0.045 0.162 1854 Planarity : 0.004 0.042 2091 Dihedral : 5.726 58.066 1761 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.65 % Allowed : 20.24 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1515 helix: 1.42 (0.35), residues: 210 sheet: 0.11 (0.27), residues: 366 loop : -0.68 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 271 HIS 0.003 0.001 HIS A 311 PHE 0.016 0.002 PHE B 153 TYR 0.031 0.001 TYR D 98 ARG 0.006 0.000 ARG A 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 6) link_NAG-ASN : angle 2.37653 ( 18) hydrogen bonds : bond 0.03670 ( 415) hydrogen bonds : angle 5.40141 ( 1131) SS BOND : bond 0.00390 ( 18) SS BOND : angle 1.57998 ( 36) covalent geometry : bond 0.00314 (11841) covalent geometry : angle 0.62699 (16122) *********************** 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 214 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8164 (tm-30) REVERT: B 69 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7505 (ttp80) REVERT: B 98 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7586 (mtt) REVERT: C 198 MET cc_start: 0.8005 (mmm) cc_final: 0.7672 (mtp) REVERT: C 320 ILE cc_start: 0.8485 (mt) cc_final: 0.8164 (mt) REVERT: D 29 ASP cc_start: 0.8753 (t0) cc_final: 0.8418 (t0) REVERT: D 46 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: D 64 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7558 (mp0) REVERT: D 83 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7715 (mtp180) REVERT: E 29 ASP cc_start: 0.8753 (t0) cc_final: 0.8169 (t0) REVERT: E 46 GLU cc_start: 0.8132 (mp0) cc_final: 0.7754 (mp0) REVERT: E 83 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7172 (mtp180) REVERT: E 100 ASN cc_start: 0.8663 (m110) cc_final: 0.8427 (m-40) REVERT: F 29 ASP cc_start: 0.8781 (t0) cc_final: 0.8345 (t0) REVERT: F 64 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7348 (mp0) REVERT: F 101 ASP cc_start: 0.7314 (t0) cc_final: 0.7098 (t0) outliers start: 33 outliers final: 22 residues processed: 199 average time/residue: 0.8925 time to fit residues: 197.9241 Evaluate side-chains 189 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 249 VAL 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 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 249 VAL 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 83 ARG 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 100 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.112175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.092289 restraints weight = 21011.034| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.91 r_work: 0.3043 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11865 Z= 0.148 Angle : 0.666 11.263 16176 Z= 0.342 Chirality : 0.046 0.166 1854 Planarity : 0.005 0.041 2091 Dihedral : 5.789 59.814 1761 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.57 % Allowed : 21.20 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1515 helix: 1.23 (0.35), residues: 213 sheet: 0.26 (0.26), residues: 390 loop : -0.73 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 271 HIS 0.003 0.001 HIS C 99 PHE 0.017 0.002 PHE B 153 TYR 0.042 0.002 TYR F 98 ARG 0.009 0.000 ARG A 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 6) link_NAG-ASN : angle 2.39114 ( 18) hydrogen bonds : bond 0.03877 ( 415) hydrogen bonds : angle 5.53489 ( 1131) SS BOND : bond 0.00412 ( 18) SS BOND : angle 1.66090 ( 36) covalent geometry : bond 0.00353 (11841) covalent geometry : angle 0.65740 (16122) *********************** 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 199 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7832 (ttm170) REVERT: B 98 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7664 (mtt) REVERT: C 198 MET cc_start: 0.7999 (mmm) cc_final: 0.7717 (mtp) REVERT: C 320 ILE cc_start: 0.8489 (mt) cc_final: 0.8165 (mt) REVERT: D 29 ASP cc_start: 0.8808 (t0) cc_final: 0.8493 (t0) REVERT: D 46 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: D 64 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7572 (mp0) REVERT: D 83 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7738 (mtp180) REVERT: E 29 ASP cc_start: 0.8788 (t0) cc_final: 0.8211 (t0) REVERT: E 46 GLU cc_start: 0.8131 (mp0) cc_final: 0.7799 (mp0) REVERT: E 83 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7168 (mtp180) REVERT: F 29 ASP cc_start: 0.8806 (t0) cc_final: 0.8377 (t0) REVERT: F 64 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7345 (mp0) REVERT: F 101 ASP cc_start: 0.7323 (t0) cc_final: 0.7106 (t0) outliers start: 32 outliers final: 23 residues processed: 184 average time/residue: 0.9078 time to fit residues: 186.0983 Evaluate side-chains 194 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 249 VAL 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 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 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 249 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 436 ILE 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 83 ARG Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain F residue 2 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 21 optimal weight: 0.0770 chunk 121 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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 B 250 GLN D 3 GLN D 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.094029 restraints weight = 20940.071| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.92 r_work: 0.3078 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11865 Z= 0.118 Angle : 0.635 13.208 16176 Z= 0.326 Chirality : 0.045 0.170 1854 Planarity : 0.004 0.050 2091 Dihedral : 5.525 57.193 1761 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.49 % Allowed : 21.53 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1515 helix: 1.20 (0.35), residues: 213 sheet: 0.33 (0.26), residues: 378 loop : -0.67 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 271 HIS 0.002 0.001 HIS C 311 PHE 0.016 0.001 PHE B 153 TYR 0.035 0.001 TYR D 98 ARG 0.010 0.000 ARG C 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 6) link_NAG-ASN : angle 2.33673 ( 18) hydrogen bonds : bond 0.03578 ( 415) hydrogen bonds : angle 5.41644 ( 1131) SS BOND : bond 0.00366 ( 18) SS BOND : angle 1.47316 ( 36) covalent geometry : bond 0.00277 (11841) covalent geometry : angle 0.62789 (16122) *********************** 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 206 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8629 (tm) REVERT: B 69 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7483 (ttp80) REVERT: B 98 MET cc_start: 0.8043 (mtt) cc_final: 0.7529 (mtt) REVERT: C 198 MET cc_start: 0.7980 (mmm) cc_final: 0.7708 (mtp) REVERT: C 320 ILE cc_start: 0.8450 (mt) cc_final: 0.8131 (mt) REVERT: D 29 ASP cc_start: 0.8755 (t0) cc_final: 0.8426 (t0) REVERT: D 46 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: D 64 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7545 (mp0) REVERT: E 29 ASP cc_start: 0.8701 (t0) cc_final: 0.8114 (t0) REVERT: E 46 GLU cc_start: 0.8116 (mp0) cc_final: 0.7763 (mp0) REVERT: E 83 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7066 (mtp180) REVERT: E 100 ASN cc_start: 0.8591 (m110) cc_final: 0.8362 (m-40) REVERT: F 29 ASP cc_start: 0.8751 (t0) cc_final: 0.8349 (t0) REVERT: F 64 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7298 (mp0) REVERT: F 101 ASP cc_start: 0.7386 (t0) cc_final: 0.7174 (t0) outliers start: 31 outliers final: 22 residues processed: 191 average time/residue: 0.9239 time to fit residues: 196.1142 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 : 1.301 ------------------------------------------------------------------------------- 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 249 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 328 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 249 VAL 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 83 ARG Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain F residue 2 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 68 optimal weight: 0.1980 chunk 108 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 98 optimal weight: 5.9990 chunk 42 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 F 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.095328 restraints weight = 20844.166| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.90 r_work: 0.3102 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 11865 Z= 0.116 Angle : 0.639 13.877 16176 Z= 0.327 Chirality : 0.044 0.170 1854 Planarity : 0.004 0.057 2091 Dihedral : 5.377 55.822 1761 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.33 % Allowed : 21.93 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1515 helix: 1.26 (0.35), residues: 213 sheet: 0.37 (0.26), residues: 378 loop : -0.58 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 271 HIS 0.003 0.001 HIS A 311 PHE 0.016 0.001 PHE B 153 TYR 0.034 0.001 TYR D 98 ARG 0.011 0.000 ARG C 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 6) link_NAG-ASN : angle 2.24704 ( 18) hydrogen bonds : bond 0.03497 ( 415) hydrogen bonds : angle 5.35693 ( 1131) SS BOND : bond 0.00337 ( 18) SS BOND : angle 1.41955 ( 36) covalent geometry : bond 0.00275 (11841) covalent geometry : angle 0.63234 (16122) ********************** 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 212 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8366 (ttt180) cc_final: 0.7884 (ttm170) REVERT: B 69 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7458 (ttp80) REVERT: B 98 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7465 (mtt) REVERT: B 136 GLU cc_start: 0.7727 (pt0) cc_final: 0.7522 (mm-30) REVERT: C 198 MET cc_start: 0.7969 (mmm) cc_final: 0.7691 (mtp) REVERT: C 320 ILE cc_start: 0.8393 (mt) cc_final: 0.8068 (mt) REVERT: D 29 ASP cc_start: 0.8761 (t0) cc_final: 0.8431 (t0) REVERT: D 46 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: D 64 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7532 (mp0) REVERT: E 29 ASP cc_start: 0.8697 (t0) cc_final: 0.8106 (t0) REVERT: E 46 GLU cc_start: 0.8105 (mp0) cc_final: 0.7751 (mp0) REVERT: E 83 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.6967 (mtp180) REVERT: E 100 ASN cc_start: 0.8557 (m110) cc_final: 0.8334 (t0) REVERT: F 29 ASP cc_start: 0.8738 (t0) cc_final: 0.8314 (t0) REVERT: F 64 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7282 (mp0) REVERT: F 101 ASP cc_start: 0.7368 (t0) cc_final: 0.7158 (t0) outliers start: 29 outliers final: 21 residues processed: 197 average time/residue: 0.9248 time to fit residues: 202.9989 Evaluate side-chains 200 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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 249 VAL 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 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 237 LEU Chi-restraints excluded: chain C residue 249 VAL 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 83 ARG 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 67 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.0170 chunk 28 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 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 = 0.3527 r_free = 0.3527 target = 0.114639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.094866 restraints weight = 20768.422| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.91 r_work: 0.3095 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 11865 Z= 0.121 Angle : 0.640 13.787 16176 Z= 0.327 Chirality : 0.044 0.173 1854 Planarity : 0.004 0.050 2091 Dihedral : 5.381 56.296 1761 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.49 % Allowed : 22.01 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1515 helix: 1.25 (0.36), residues: 213 sheet: 0.41 (0.26), residues: 378 loop : -0.56 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 271 HIS 0.002 0.001 HIS A 311 PHE 0.016 0.001 PHE B 153 TYR 0.046 0.002 TYR F 98 ARG 0.009 0.000 ARG C 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 6) link_NAG-ASN : angle 2.27634 ( 18) hydrogen bonds : bond 0.03490 ( 415) hydrogen bonds : angle 5.38818 ( 1131) SS BOND : bond 0.00340 ( 18) SS BOND : angle 1.48011 ( 36) covalent geometry : bond 0.00287 (11841) covalent geometry : angle 0.63260 (16122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8051.93 seconds wall clock time: 138 minutes 13.23 seconds (8293.23 seconds total)