Starting phenix.real_space_refine on Sat Dec 28 05:43:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gn8_34157/12_2024/8gn8_34157.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gn8_34157/12_2024/8gn8_34157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gn8_34157/12_2024/8gn8_34157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gn8_34157/12_2024/8gn8_34157.map" model { file = "/net/cci-nas-00/data/ceres_data/8gn8_34157/12_2024/8gn8_34157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gn8_34157/12_2024/8gn8_34157.cif" } resolution = 3.5 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= 0.006 sd= 0.116 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 70 5.16 5 C 5230 2.51 5 N 1340 2.21 5 O 1280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7920 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1584 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 1 Chain: "A" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1584 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 1 Chain: "B" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1584 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 1 Chain: "C" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1584 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 1 Chain: "E" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1584 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 1 Time building chain proxies: 5.18, per 1000 atoms: 0.65 Number of scatterers: 7920 At special positions: 0 Unit cell: (90.16, 90.16, 95.68, 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 70 16.00 O 1280 8.00 N 1340 7.00 C 5230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 180 " distance=2.04 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 180 " distance=2.04 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 180 " distance=2.04 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 180 " distance=2.04 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 175 " 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 Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1880 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 5 sheets defined 70.5% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'D' and resid 11 through 16 Processing helix chain 'D' and resid 19 through 32 Processing helix chain 'D' and resid 35 through 42 removed outlier: 3.959A pdb=" N ARG D 42 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 48 removed outlier: 4.408A pdb=" N ASP D 47 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU D 48 " --> pdb=" O TYR D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 102 removed outlier: 3.713A pdb=" N PHE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Proline residue: D 88 - end of helix removed outlier: 3.867A pdb=" N SER D 93 " --> pdb=" O SER D 89 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR D 102 " --> pdb=" O HIS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 4.198A pdb=" N LEU D 106 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 102 through 107' Processing helix chain 'D' and resid 140 through 166 removed outlier: 3.728A pdb=" N ILE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N HIS D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 155 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE D 157 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 219 removed outlier: 3.657A pdb=" N LYS D 194 " --> pdb=" O ARG D 190 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU D 216 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 227 removed outlier: 3.691A pdb=" N ARG D 227 " --> pdb=" O MET D 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 43 through 48 removed outlier: 4.423A pdb=" N ASP A 47 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 48 " --> pdb=" O TYR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 107 removed outlier: 3.724A pdb=" N PHE A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.835A pdb=" N SER A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 166 removed outlier: 3.739A pdb=" N ILE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 225 removed outlier: 3.648A pdb=" N LYS A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 16 Processing helix chain 'B' and resid 19 through 32 Processing helix chain 'B' and resid 35 through 41 Processing helix chain 'B' and resid 43 through 47 removed outlier: 4.389A pdb=" N ASP B 47 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 102 removed outlier: 3.718A pdb=" N PHE B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Proline residue: B 88 - end of helix removed outlier: 3.892A pdb=" N SER B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 102 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 removed outlier: 4.214A pdb=" N LEU B 106 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 102 through 107' Processing helix chain 'B' and resid 140 through 166 removed outlier: 3.730A pdb=" N ILE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 225 removed outlier: 3.647A pdb=" N LYS B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 16 Processing helix chain 'C' and resid 19 through 32 Processing helix chain 'C' and resid 35 through 42 removed outlier: 3.967A pdb=" N ARG C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 47 removed outlier: 4.411A pdb=" N ASP C 47 " --> pdb=" O VAL C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 102 removed outlier: 3.711A pdb=" N PHE C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Proline residue: C 88 - end of helix removed outlier: 3.898A pdb=" N SER C 93 " --> pdb=" O SER C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 removed outlier: 4.198A pdb=" N LEU C 106 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 102 through 107' Processing helix chain 'C' and resid 140 through 166 removed outlier: 3.761A pdb=" N ILE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 155 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 225 removed outlier: 3.649A pdb=" N LYS C 194 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 16 Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 35 through 42 removed outlier: 3.943A pdb=" N ARG E 42 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 47 removed outlier: 4.404A pdb=" N ASP E 47 " --> pdb=" O VAL E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 107 removed outlier: 3.713A pdb=" N PHE E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) Proline residue: E 88 - end of helix removed outlier: 3.991A pdb=" N SER E 93 " --> pdb=" O SER E 89 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR E 102 " --> pdb=" O HIS E 98 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU E 103 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA E 105 " --> pdb=" O ALA E 101 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU E 106 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 166 removed outlier: 3.725A pdb=" N ILE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS E 146 " --> pdb=" O GLY E 142 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 154 " --> pdb=" O ARG E 150 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA E 155 " --> pdb=" O THR E 151 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 225 removed outlier: 3.650A pdb=" N LYS E 194 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU E 216 " --> pdb=" O GLY E 212 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG E 221 " --> pdb=" O VAL E 217 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG E 225 " --> pdb=" O ARG E 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 172 through 175 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.889A pdb=" N VAL A 53 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.854A pdb=" N VAL B 53 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 172 through 175 Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.860A pdb=" N VAL E 53 " --> pdb=" O TYR E 187 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1278 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: 2.01 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2450 1.35 - 1.46: 1954 1.46 - 1.58: 3621 1.58 - 1.70: 0 1.70 - 1.82: 95 Bond restraints: 8120 Sorted by residual: bond pdb=" CA PHE D 9 " pdb=" C PHE D 9 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.34e-02 5.57e+03 1.41e+00 bond pdb=" CA PHE E 9 " pdb=" C PHE E 9 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.34e-02 5.57e+03 1.35e+00 bond pdb=" CA PHE A 9 " pdb=" C PHE A 9 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.34e-02 5.57e+03 1.28e+00 bond pdb=" CA PHE C 9 " pdb=" C PHE C 9 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.34e-02 5.57e+03 1.24e+00 bond pdb=" CA PHE B 9 " pdb=" C PHE B 9 " ideal model delta sigma weight residual 1.523 1.536 -0.013 1.34e-02 5.57e+03 9.51e-01 ... (remaining 8115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 10846 1.97 - 3.95: 160 3.95 - 5.92: 30 5.92 - 7.89: 9 7.89 - 9.87: 5 Bond angle restraints: 11050 Sorted by residual: angle pdb=" N GLY A 8 " pdb=" CA GLY A 8 " pdb=" C GLY A 8 " ideal model delta sigma weight residual 110.21 107.14 3.07 9.10e-01 1.21e+00 1.13e+01 angle pdb=" N GLY B 8 " pdb=" CA GLY B 8 " pdb=" C GLY B 8 " ideal model delta sigma weight residual 110.21 107.16 3.05 9.10e-01 1.21e+00 1.12e+01 angle pdb=" C PHE B 9 " pdb=" CA PHE B 9 " pdb=" CB PHE B 9 " ideal model delta sigma weight residual 110.42 116.63 -6.21 1.99e+00 2.53e-01 9.74e+00 angle pdb=" C PHE E 9 " pdb=" CA PHE E 9 " pdb=" CB PHE E 9 " ideal model delta sigma weight residual 110.42 116.55 -6.13 1.99e+00 2.53e-01 9.49e+00 angle pdb=" C PHE A 9 " pdb=" CA PHE A 9 " pdb=" CB PHE A 9 " ideal model delta sigma weight residual 110.42 116.42 -6.00 1.99e+00 2.53e-01 9.09e+00 ... (remaining 11045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.82: 3806 11.82 - 23.65: 530 23.65 - 35.47: 313 35.47 - 47.29: 124 47.29 - 59.12: 52 Dihedral angle restraints: 4825 sinusoidal: 1915 harmonic: 2910 Sorted by residual: dihedral pdb=" CA PRO D 178 " pdb=" C PRO D 178 " pdb=" N PRO D 179 " pdb=" CA PRO D 179 " ideal model delta harmonic sigma weight residual 180.00 133.93 46.07 0 5.00e+00 4.00e-02 8.49e+01 dihedral pdb=" CA PRO E 178 " pdb=" C PRO E 178 " pdb=" N PRO E 179 " pdb=" CA PRO E 179 " ideal model delta harmonic sigma weight residual 180.00 133.94 46.06 0 5.00e+00 4.00e-02 8.49e+01 dihedral pdb=" CA PRO A 178 " pdb=" C PRO A 178 " pdb=" N PRO A 179 " pdb=" CA PRO A 179 " ideal model delta harmonic sigma weight residual 180.00 134.14 45.86 0 5.00e+00 4.00e-02 8.41e+01 ... (remaining 4822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 676 0.024 - 0.048: 311 0.048 - 0.072: 223 0.072 - 0.096: 74 0.096 - 0.120: 26 Chirality restraints: 1310 Sorted by residual: chirality pdb=" CA VAL E 183 " pdb=" N VAL E 183 " pdb=" C VAL E 183 " pdb=" CB VAL E 183 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA VAL C 183 " pdb=" N VAL C 183 " pdb=" C VAL C 183 " pdb=" CB VAL C 183 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.54e-01 chirality pdb=" CA VAL A 183 " pdb=" N VAL A 183 " pdb=" C VAL A 183 " pdb=" CB VAL A 183 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 1307 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 9 " 0.021 2.00e-02 2.50e+03 2.82e-02 1.40e+01 pdb=" CG PHE B 9 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE B 9 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE B 9 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE B 9 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 9 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 9 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 9 " 0.020 2.00e-02 2.50e+03 2.73e-02 1.31e+01 pdb=" CG PHE E 9 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE E 9 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE E 9 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE E 9 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 9 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 9 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 178 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.72e+00 pdb=" N PRO C 179 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " -0.041 5.00e-02 4.00e+02 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1853 2.80 - 3.32: 6851 3.32 - 3.85: 12089 3.85 - 4.37: 12711 4.37 - 4.90: 23595 Nonbonded interactions: 57099 Sorted by model distance: nonbonded pdb=" O SER A 70 " pdb=" OG SER A 70 " model vdw 2.271 3.040 nonbonded pdb=" O SER B 70 " pdb=" OG SER B 70 " model vdw 2.272 3.040 nonbonded pdb=" O SER C 70 " pdb=" OG SER C 70 " model vdw 2.272 3.040 nonbonded pdb=" O SER D 70 " pdb=" OG SER D 70 " model vdw 2.275 3.040 nonbonded pdb=" O SER E 70 " pdb=" OG SER E 70 " model vdw 2.275 3.040 ... (remaining 57094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.790 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 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 : 0.003 0.029 8120 Z= 0.160 Angle : 0.658 9.866 11050 Z= 0.359 Chirality : 0.039 0.120 1310 Planarity : 0.006 0.074 1360 Dihedral : 16.612 58.699 2900 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.34 % Allowed : 31.61 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: 0.26 (0.30), residues: 990 helix: 1.09 (0.23), residues: 645 sheet: 1.60 (0.79), residues: 50 loop : -2.18 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 202 HIS 0.003 0.001 HIS A 74 PHE 0.065 0.002 PHE B 9 TYR 0.005 0.001 TYR C 162 ARG 0.004 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.830 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 85 average time/residue: 0.1505 time to fit residues: 19.4830 Evaluate side-chains 79 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 185 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 90 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8120 Z= 0.157 Angle : 0.583 8.031 11050 Z= 0.290 Chirality : 0.037 0.119 1310 Planarity : 0.005 0.069 1360 Dihedral : 4.804 44.718 1103 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.22 % Allowed : 27.59 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: 0.53 (0.30), residues: 990 helix: 1.39 (0.23), residues: 650 sheet: 1.74 (0.75), residues: 50 loop : -2.40 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 202 HIS 0.002 0.001 HIS C 74 PHE 0.014 0.001 PHE D 9 TYR 0.010 0.001 TYR D 162 ARG 0.003 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.787 Fit side-chains REVERT: B 6 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7042 (tt) REVERT: E 9 PHE cc_start: 0.9166 (t80) cc_final: 0.8941 (t80) REVERT: E 20 MET cc_start: 0.7273 (tpt) cc_final: 0.6963 (tpp) outliers start: 28 outliers final: 18 residues processed: 102 average time/residue: 0.1408 time to fit residues: 22.0363 Evaluate side-chains 101 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 183 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8120 Z= 0.252 Angle : 0.626 10.409 11050 Z= 0.311 Chirality : 0.041 0.143 1310 Planarity : 0.006 0.069 1360 Dihedral : 5.008 47.497 1100 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.86 % Allowed : 26.32 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: 0.36 (0.29), residues: 990 helix: 1.03 (0.22), residues: 670 sheet: 1.85 (0.75), residues: 50 loop : -2.12 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 202 HIS 0.006 0.002 HIS A 74 PHE 0.040 0.001 PHE B 9 TYR 0.009 0.001 TYR D 162 ARG 0.002 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 74 time to evaluate : 0.811 Fit side-chains REVERT: D 74 HIS cc_start: 0.6926 (OUTLIER) cc_final: 0.6268 (p-80) REVERT: A 6 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7614 (mm) REVERT: A 146 HIS cc_start: 0.8009 (OUTLIER) cc_final: 0.7359 (t-90) REVERT: B 74 HIS cc_start: 0.7118 (OUTLIER) cc_final: 0.6425 (p-80) outliers start: 51 outliers final: 31 residues processed: 113 average time/residue: 0.1767 time to fit residues: 28.3754 Evaluate side-chains 108 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 73 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 183 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 0.0670 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 0.0470 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8120 Z= 0.167 Angle : 0.562 9.142 11050 Z= 0.282 Chirality : 0.038 0.121 1310 Planarity : 0.005 0.068 1360 Dihedral : 4.823 45.715 1100 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.71 % Allowed : 28.51 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: 0.79 (0.30), residues: 990 helix: 1.45 (0.22), residues: 660 sheet: 1.95 (0.73), residues: 50 loop : -2.06 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 202 HIS 0.003 0.001 HIS C 74 PHE 0.042 0.001 PHE B 9 TYR 0.010 0.001 TYR D 162 ARG 0.002 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 81 time to evaluate : 0.841 Fit side-chains REVERT: D 74 HIS cc_start: 0.6813 (OUTLIER) cc_final: 0.6216 (p-80) REVERT: A 146 HIS cc_start: 0.8024 (OUTLIER) cc_final: 0.7606 (t-90) REVERT: B 74 HIS cc_start: 0.6938 (OUTLIER) cc_final: 0.6309 (p-80) outliers start: 41 outliers final: 30 residues processed: 108 average time/residue: 0.1408 time to fit residues: 23.1407 Evaluate side-chains 110 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 195 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 0.0270 chunk 82 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 0.0870 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8120 Z= 0.148 Angle : 0.552 8.832 11050 Z= 0.275 Chirality : 0.037 0.119 1310 Planarity : 0.005 0.065 1360 Dihedral : 4.674 44.961 1100 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 6.09 % Allowed : 27.59 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.30), residues: 990 helix: 1.63 (0.22), residues: 670 sheet: 1.94 (0.71), residues: 50 loop : -1.95 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 202 HIS 0.002 0.001 HIS C 74 PHE 0.045 0.001 PHE B 9 TYR 0.010 0.001 TYR D 162 ARG 0.002 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 85 time to evaluate : 0.929 Fit side-chains REVERT: D 74 HIS cc_start: 0.6704 (OUTLIER) cc_final: 0.6125 (p-80) REVERT: D 217 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8321 (p) REVERT: A 190 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7778 (ptp-170) REVERT: A 215 ASP cc_start: 0.8018 (t0) cc_final: 0.7791 (t70) REVERT: B 74 HIS cc_start: 0.6836 (OUTLIER) cc_final: 0.6328 (p-80) REVERT: B 190 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7444 (ptp-170) outliers start: 53 outliers final: 28 residues processed: 122 average time/residue: 0.1638 time to fit residues: 28.8689 Evaluate side-chains 112 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 79 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 183 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 50 optimal weight: 0.0570 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8120 Z= 0.170 Angle : 0.566 9.487 11050 Z= 0.280 Chirality : 0.038 0.118 1310 Planarity : 0.005 0.065 1360 Dihedral : 4.676 45.270 1100 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 6.44 % Allowed : 26.90 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.30), residues: 990 helix: 1.69 (0.22), residues: 670 sheet: 1.78 (0.70), residues: 50 loop : -1.88 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 202 HIS 0.003 0.001 HIS C 74 PHE 0.048 0.001 PHE B 9 TYR 0.007 0.001 TYR D 162 ARG 0.002 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 78 time to evaluate : 0.874 Fit side-chains REVERT: D 74 HIS cc_start: 0.6812 (OUTLIER) cc_final: 0.6226 (p-80) REVERT: D 217 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8337 (p) REVERT: A 215 ASP cc_start: 0.8047 (t0) cc_final: 0.7807 (t70) REVERT: B 74 HIS cc_start: 0.6911 (OUTLIER) cc_final: 0.6452 (p-80) REVERT: B 190 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7556 (ptp-170) REVERT: C 190 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7955 (ptp-170) REVERT: E 190 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8044 (ptt180) outliers start: 56 outliers final: 37 residues processed: 117 average time/residue: 0.1554 time to fit residues: 26.5871 Evaluate side-chains 119 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 76 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 74 HIS Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 195 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.0870 chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 0.0060 chunk 81 optimal weight: 0.0370 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 overall best weight: 0.2052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 17 ASN B 46 GLN E 17 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8120 Z= 0.134 Angle : 0.545 8.728 11050 Z= 0.271 Chirality : 0.037 0.122 1310 Planarity : 0.005 0.062 1360 Dihedral : 4.502 43.182 1100 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.83 % Allowed : 27.70 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.30), residues: 990 helix: 2.10 (0.22), residues: 665 sheet: 1.81 (0.67), residues: 50 loop : -1.79 (0.42), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 202 HIS 0.001 0.000 HIS E 74 PHE 0.052 0.001 PHE B 9 TYR 0.010 0.001 TYR D 162 ARG 0.001 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.880 Fit side-chains REVERT: D 171 LYS cc_start: 0.8277 (tppt) cc_final: 0.7970 (mttp) REVERT: A 190 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7688 (ptp-170) REVERT: B 47 ASP cc_start: 0.8672 (p0) cc_final: 0.8453 (p0) REVERT: B 74 HIS cc_start: 0.6692 (OUTLIER) cc_final: 0.6320 (p-80) REVERT: B 190 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7398 (ptp-170) REVERT: C 198 MET cc_start: 0.7828 (ttm) cc_final: 0.7536 (ttm) REVERT: E 190 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7904 (ptt180) outliers start: 42 outliers final: 24 residues processed: 123 average time/residue: 0.1900 time to fit residues: 32.8440 Evaluate side-chains 112 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 190 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8120 Z= 0.182 Angle : 0.571 10.253 11050 Z= 0.283 Chirality : 0.039 0.131 1310 Planarity : 0.005 0.063 1360 Dihedral : 4.619 45.021 1100 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.06 % Allowed : 27.47 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.30), residues: 990 helix: 1.98 (0.22), residues: 670 sheet: 1.59 (0.66), residues: 50 loop : -1.81 (0.43), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 78 HIS 0.004 0.001 HIS C 74 PHE 0.052 0.001 PHE E 9 TYR 0.005 0.001 TYR D 162 ARG 0.003 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 80 time to evaluate : 0.754 Fit side-chains REVERT: A 215 ASP cc_start: 0.7968 (t0) cc_final: 0.7699 (t70) REVERT: B 74 HIS cc_start: 0.6864 (OUTLIER) cc_final: 0.6461 (p-80) REVERT: E 190 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8021 (ptt180) outliers start: 44 outliers final: 35 residues processed: 110 average time/residue: 0.1466 time to fit residues: 24.1342 Evaluate side-chains 115 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 195 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 0.0470 chunk 57 optimal weight: 0.8980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8120 Z= 0.161 Angle : 0.561 9.853 11050 Z= 0.279 Chirality : 0.038 0.122 1310 Planarity : 0.005 0.063 1360 Dihedral : 4.609 44.272 1100 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.83 % Allowed : 27.47 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.30), residues: 990 helix: 2.05 (0.22), residues: 670 sheet: 1.49 (0.65), residues: 50 loop : -1.85 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 202 HIS 0.003 0.001 HIS C 74 PHE 0.056 0.001 PHE B 9 TYR 0.007 0.001 TYR D 162 ARG 0.004 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 83 time to evaluate : 0.897 Fit side-chains REVERT: B 74 HIS cc_start: 0.6807 (OUTLIER) cc_final: 0.6431 (p-80) REVERT: E 190 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8047 (ptt180) outliers start: 42 outliers final: 35 residues processed: 113 average time/residue: 0.1403 time to fit residues: 24.2225 Evaluate side-chains 117 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 80 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 195 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8120 Z= 0.198 Angle : 0.585 10.191 11050 Z= 0.289 Chirality : 0.039 0.159 1310 Planarity : 0.005 0.063 1360 Dihedral : 4.707 45.029 1100 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.60 % Allowed : 27.59 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.30), residues: 990 helix: 1.97 (0.22), residues: 670 sheet: 1.29 (0.64), residues: 50 loop : -1.87 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 202 HIS 0.004 0.001 HIS C 74 PHE 0.057 0.001 PHE B 9 TYR 0.005 0.001 TYR D 45 ARG 0.004 0.000 ARG E 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 78 time to evaluate : 0.863 Fit side-chains REVERT: B 74 HIS cc_start: 0.6948 (OUTLIER) cc_final: 0.6566 (p-80) REVERT: E 190 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8069 (ptt180) outliers start: 40 outliers final: 35 residues processed: 107 average time/residue: 0.1416 time to fit residues: 22.9616 Evaluate side-chains 113 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 76 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 195 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.091277 restraints weight = 9823.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.094158 restraints weight = 5770.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.095861 restraints weight = 4251.496| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8120 Z= 0.259 Angle : 0.626 11.071 11050 Z= 0.312 Chirality : 0.041 0.174 1310 Planarity : 0.005 0.065 1360 Dihedral : 4.997 47.171 1100 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.94 % Allowed : 27.47 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.29), residues: 990 helix: 1.76 (0.22), residues: 665 sheet: 1.02 (0.62), residues: 50 loop : -1.90 (0.42), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 25 HIS 0.006 0.002 HIS C 74 PHE 0.058 0.002 PHE B 9 TYR 0.006 0.001 TYR B 143 ARG 0.003 0.000 ARG E 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1505.83 seconds wall clock time: 28 minutes 27.33 seconds (1707.33 seconds total)