Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 14:47:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgr_31977/04_2023/7vgr_31977.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgr_31977/04_2023/7vgr_31977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgr_31977/04_2023/7vgr_31977.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgr_31977/04_2023/7vgr_31977.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgr_31977/04_2023/7vgr_31977.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgr_31977/04_2023/7vgr_31977.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5356 atoms to isotropic. 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 50 5.16 5 C 6320 2.51 5 N 1642 2.21 5 O 1860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9872 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1693 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1687 Chain: "D" Number of atoms: 1639 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1627 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 220, 1627 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 1656 Chain: "E" Number of atoms: 1693 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1687 Chain: "F" Number of atoms: 1639 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1627 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 220, 1627 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 1656 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1604 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 5, 'TRANS': 192} Chain: "B" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1604 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 5, 'TRANS': 192} Time building chain proxies: 8.30, per 1000 atoms: 0.84 Number of scatterers: 9872 At special positions: 0 Unit cell: (95.865, 140.685, 144.42, 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 50 16.00 O 1860 8.00 N 1642 7.00 C 6320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS D 147 " - pdb=" SG ACYS D 202 " distance=2.03 Simple disulfide: pdb=" SG BCYS D 147 " - pdb=" SG BCYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS F 147 " - pdb=" SG ACYS F 202 " distance=2.03 Simple disulfide: pdb=" SG BCYS F 147 " - pdb=" SG BCYS F 202 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 2.4 seconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 22 sheets defined 19.2% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'C' and resid 83 through 87 removed outlier: 4.179A pdb=" N VAL C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.639A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 83 through 87 removed outlier: 4.179A pdb=" N VAL E 87 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.639A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'A' and resid 10 through 37 Processing helix chain 'A' and resid 43 through 71 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 76 through 106 Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.734A pdb=" N SER A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 112 " --> pdb=" O MET A 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 37 Processing helix chain 'B' and resid 43 through 71 Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 76 through 106 Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.734A pdb=" N SER B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE B 112 " --> pdb=" O MET B 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.625A pdb=" N PHE C 75 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.426A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 122 removed outlier: 6.204A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 157 through 158 removed outlier: 3.893A pdb=" N ASN C 149 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR C 201 " --> pdb=" O ASN C 149 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS C 153 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR C 197 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N HIS C 202 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER C 207 " --> pdb=" O HIS C 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.505A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.598A pdb=" N GLU D 10 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 49 through 51 Processing sheet with id=AA8, first strand: chain 'D' and resid 127 through 131 removed outlier: 3.749A pdb=" N VAL D 143 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR D 182 " --> pdb=" O GLY D 151 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER D 185 " --> pdb=" O PRO D 174 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER D 187 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N THR D 172 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR D 189 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL D 170 " --> pdb=" O THR D 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.649A pdb=" N HIS D 206 " --> pdb=" O THR D 211 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.626A pdb=" N PHE E 75 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.427A pdb=" N LEU E 11 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS E 111 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL E 13 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N MET E 37 " --> pdb=" O TYR E 53 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR E 53 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP E 39 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 118 through 122 removed outlier: 6.203A pdb=" N TYR E 177 " --> pdb=" O ASN E 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 157 through 158 removed outlier: 3.893A pdb=" N ASN E 149 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR E 201 " --> pdb=" O ASN E 149 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS E 153 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR E 197 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N HIS E 202 " --> pdb=" O SER E 207 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N SER E 207 " --> pdb=" O HIS E 202 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.505A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.598A pdb=" N GLU F 10 " --> pdb=" O THR F 117 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 49 through 51 Processing sheet with id=AB8, first strand: chain 'F' and resid 127 through 131 removed outlier: 3.748A pdb=" N VAL F 143 " --> pdb=" O VAL F 190 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR F 182 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER F 185 " --> pdb=" O PRO F 174 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER F 187 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N THR F 172 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N THR F 189 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL F 170 " --> pdb=" O THR F 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 158 through 161 removed outlier: 3.650A pdb=" N HIS F 206 " --> pdb=" O THR F 211 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 128 through 133 removed outlier: 4.004A pdb=" N ILE A 118 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN A 121 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE A 168 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 200 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS A 180 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ARG A 198 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLY A 182 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR A 196 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.672A pdb=" N LEU A 149 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 128 through 133 removed outlier: 4.003A pdb=" N ILE B 118 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN B 121 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE B 168 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 200 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS B 180 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ARG B 198 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLY B 182 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N TYR B 196 " --> pdb=" O GLY B 182 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.671A pdb=" N LEU B 149 " --> pdb=" O LEU B 156 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1076 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: 2.65 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3097 1.34 - 1.46: 2528 1.46 - 1.58: 4439 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 10134 Sorted by residual: bond pdb=" CA LEU A 164 " pdb=" CB LEU A 164 " ideal model delta sigma weight residual 1.523 1.546 -0.023 1.83e-02 2.99e+03 1.60e+00 bond pdb=" CA LEU B 164 " pdb=" CB LEU B 164 " ideal model delta sigma weight residual 1.523 1.546 -0.023 1.83e-02 2.99e+03 1.57e+00 bond pdb=" N ARG A 174 " pdb=" CA ARG A 174 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.07e+00 bond pdb=" N ARG B 174 " pdb=" CA ARG B 174 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.97e-01 bond pdb=" CG PRO A 165 " pdb=" CD PRO A 165 " ideal model delta sigma weight residual 1.503 1.536 -0.033 3.40e-02 8.65e+02 9.64e-01 ... (remaining 10129 not shown) Histogram of bond angle deviations from ideal: 100.76 - 107.42: 385 107.42 - 114.09: 5715 114.09 - 120.75: 3893 120.75 - 127.42: 3708 127.42 - 134.08: 129 Bond angle restraints: 13830 Sorted by residual: angle pdb=" C ILE A 161 " pdb=" N LYS A 162 " pdb=" CA LYS A 162 " ideal model delta sigma weight residual 121.54 132.37 -10.83 1.91e+00 2.74e-01 3.22e+01 angle pdb=" C ILE B 161 " pdb=" N LYS B 162 " pdb=" CA LYS B 162 " ideal model delta sigma weight residual 121.54 132.36 -10.82 1.91e+00 2.74e-01 3.21e+01 angle pdb=" N ILE A 201 " pdb=" CA ILE A 201 " pdb=" C ILE A 201 " ideal model delta sigma weight residual 111.88 107.38 4.50 1.06e+00 8.90e-01 1.80e+01 angle pdb=" N ILE B 201 " pdb=" CA ILE B 201 " pdb=" C ILE B 201 " ideal model delta sigma weight residual 111.88 107.39 4.49 1.06e+00 8.90e-01 1.80e+01 angle pdb=" N LYS A 162 " pdb=" CA LYS A 162 " pdb=" CB LYS A 162 " ideal model delta sigma weight residual 110.49 115.32 -4.83 1.69e+00 3.50e-01 8.16e+00 ... (remaining 13825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 5690 16.91 - 33.83: 268 33.83 - 50.74: 41 50.74 - 67.66: 7 67.66 - 84.57: 12 Dihedral angle restraints: 6018 sinusoidal: 2278 harmonic: 3740 Sorted by residual: dihedral pdb=" CB ACYS F 147 " pdb=" SG ACYS F 147 " pdb=" SG ACYS F 202 " pdb=" CB ACYS F 202 " ideal model delta sinusoidal sigma weight residual 93.00 58.62 34.38 1 1.00e+01 1.00e-02 1.68e+01 dihedral pdb=" CB ACYS D 147 " pdb=" SG ACYS D 147 " pdb=" SG ACYS D 202 " pdb=" CB ACYS D 202 " ideal model delta sinusoidal sigma weight residual 93.00 58.85 34.15 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" CA SER E 71 " pdb=" C SER E 71 " pdb=" N ARG E 72 " pdb=" CA ARG E 72 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 6015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 923 0.027 - 0.054: 395 0.054 - 0.081: 137 0.081 - 0.108: 88 0.108 - 0.135: 27 Chirality restraints: 1570 Sorted by residual: chirality pdb=" CA ILE E 79 " pdb=" N ILE E 79 " pdb=" C ILE E 79 " pdb=" CB ILE E 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE B 201 " pdb=" N ILE B 201 " pdb=" C ILE B 201 " pdb=" CB ILE B 201 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 1567 not shown) Planarity restraints: 1742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 155 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO D 156 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 155 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO F 156 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO F 156 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 156 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 96 " -0.013 2.00e-02 2.50e+03 1.11e-02 2.16e+00 pdb=" CG PHE A 96 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 96 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 96 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 96 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 96 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 96 " -0.003 2.00e-02 2.50e+03 ... (remaining 1739 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2013 2.79 - 3.32: 8910 3.32 - 3.84: 16400 3.84 - 4.37: 18662 4.37 - 4.90: 32954 Nonbonded interactions: 78939 Sorted by model distance: nonbonded pdb=" O VAL A 139 " pdb=" NH1 ARG B 150 " model vdw 2.259 2.520 nonbonded pdb=" NH1 ARG A 150 " pdb=" O VAL B 139 " model vdw 2.295 2.520 nonbonded pdb=" NH1 ARG C 24 " pdb=" OD1 ASP C 74 " model vdw 2.302 2.520 nonbonded pdb=" NH1 ARG E 24 " pdb=" OD1 ASP E 74 " model vdw 2.302 2.520 nonbonded pdb=" OG SER E 166 " pdb=" O PRO F 174 " model vdw 2.309 2.440 ... (remaining 78934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 1 through 19 or resid 21 through 178 or resid 180 through \ 191 or resid 193 through 211 or resid 213 through 218)) selection = (chain 'E' and (resid 1 through 19 or resid 21 through 178 or resid 180 through \ 191 or resid 193 through 211 or resid 213 through 218)) } ncs_group { reference = (chain 'D' and (resid 1 through 146 or resid 148 through 154 or resid 156 throug \ h 201 or resid 203 through 220)) selection = (chain 'F' and (resid 1 through 146 or resid 148 through 154 or resid 156 throug \ h 201 or resid 203 through 220)) } 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=0.27 max=1.00 mean=0.99 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 3.940 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 30.960 Find NCS groups from input model: 0.570 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:10.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 : 0.002 0.043 10134 Z= 0.145 Angle : 0.554 10.835 13830 Z= 0.297 Chirality : 0.040 0.135 1570 Planarity : 0.004 0.038 1742 Dihedral : 10.586 84.569 3600 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.63 % Favored : 94.21 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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 (0.24), residues: 1274 helix: 1.41 (0.36), residues: 206 sheet: -0.07 (0.23), residues: 524 loop : -1.08 (0.27), residues: 544 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.106 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 282 average time/residue: 1.1225 time to fit residues: 339.9677 Evaluate side-chains 183 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2139 time to fit residues: 1.7271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN C 170 GLN D 6 GLN D 39 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS B 155 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.085 10134 Z= 0.634 Angle : 0.868 9.682 13830 Z= 0.446 Chirality : 0.055 0.237 1570 Planarity : 0.006 0.056 1742 Dihedral : 5.270 23.318 1406 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer Outliers : 3.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: -0.67 (0.23), residues: 1274 helix: 0.12 (0.33), residues: 212 sheet: 0.00 (0.23), residues: 532 loop : -1.05 (0.27), residues: 530 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 180 time to evaluate : 1.171 Fit side-chains outliers start: 40 outliers final: 16 residues processed: 200 average time/residue: 1.2328 time to fit residues: 264.0821 Evaluate side-chains 168 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 8 residues processed: 8 average time/residue: 0.3626 time to fit residues: 5.0677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 9.9990 chunk 34 optimal weight: 0.0070 chunk 93 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 162 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN E 214 ASN F 162 ASN A 113 ASN A 125 HIS B 113 ASN B 125 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 10134 Z= 0.204 Angle : 0.617 8.721 13830 Z= 0.315 Chirality : 0.044 0.253 1570 Planarity : 0.004 0.032 1742 Dihedral : 4.628 22.978 1406 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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 (0.24), residues: 1274 helix: 0.76 (0.35), residues: 212 sheet: 0.36 (0.23), residues: 528 loop : -0.98 (0.27), residues: 534 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 165 time to evaluate : 1.088 Fit side-chains outliers start: 29 outliers final: 13 residues processed: 181 average time/residue: 1.3094 time to fit residues: 253.1519 Evaluate side-chains 163 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.1157 time to fit residues: 1.9817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.076 10134 Z= 0.472 Angle : 0.760 9.232 13830 Z= 0.388 Chirality : 0.049 0.298 1570 Planarity : 0.005 0.031 1742 Dihedral : 5.189 24.358 1406 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer Outliers : 4.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: -0.37 (0.24), residues: 1274 helix: 0.46 (0.33), residues: 212 sheet: 0.20 (0.23), residues: 540 loop : -0.93 (0.27), residues: 522 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 149 time to evaluate : 1.200 Fit side-chains outliers start: 47 outliers final: 25 residues processed: 174 average time/residue: 1.2940 time to fit residues: 240.6829 Evaluate side-chains 175 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 17 residues processed: 8 average time/residue: 0.2873 time to fit residues: 4.3493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 ASN A 121 ASN B 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10134 Z= 0.211 Angle : 0.633 8.474 13830 Z= 0.321 Chirality : 0.043 0.213 1570 Planarity : 0.004 0.032 1742 Dihedral : 4.698 23.420 1406 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer Outliers : 3.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: -0.11 (0.24), residues: 1274 helix: 0.89 (0.34), residues: 212 sheet: 0.38 (0.23), residues: 532 loop : -0.89 (0.27), residues: 530 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 1.122 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 19 residues processed: 178 average time/residue: 1.2930 time to fit residues: 246.0139 Evaluate side-chains 160 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 0.4975 time to fit residues: 3.8536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN E 141 ASN ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.068 10134 Z= 0.471 Angle : 0.749 8.914 13830 Z= 0.383 Chirality : 0.049 0.242 1570 Planarity : 0.005 0.034 1742 Dihedral : 5.215 22.686 1406 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer Outliers : 4.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: -0.21 (0.24), residues: 1274 helix: 0.60 (0.34), residues: 212 sheet: 0.29 (0.23), residues: 540 loop : -0.81 (0.27), residues: 522 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 143 time to evaluate : 1.215 Fit side-chains outliers start: 45 outliers final: 30 residues processed: 167 average time/residue: 1.4180 time to fit residues: 252.0327 Evaluate side-chains 171 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 19 residues processed: 11 average time/residue: 0.1353 time to fit residues: 3.9146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7962 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 10134 Z= 0.208 Angle : 0.626 8.768 13830 Z= 0.317 Chirality : 0.043 0.243 1570 Planarity : 0.004 0.032 1742 Dihedral : 4.750 22.769 1406 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer Outliers : 3.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.04 (0.24), residues: 1274 helix: 0.99 (0.35), residues: 212 sheet: 0.42 (0.23), residues: 536 loop : -0.72 (0.28), residues: 526 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 1.143 Fit side-chains outliers start: 33 outliers final: 21 residues processed: 167 average time/residue: 1.3722 time to fit residues: 244.4930 Evaluate side-chains 158 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 1 average time/residue: 0.1450 time to fit residues: 1.7451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 0.0370 chunk 71 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 10134 Z= 0.222 Angle : 0.623 9.098 13830 Z= 0.314 Chirality : 0.043 0.248 1570 Planarity : 0.004 0.032 1742 Dihedral : 4.610 22.646 1406 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.15 (0.24), residues: 1274 helix: 1.18 (0.35), residues: 210 sheet: 0.52 (0.23), residues: 536 loop : -0.73 (0.28), residues: 528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 1.245 Fit side-chains outliers start: 30 outliers final: 24 residues processed: 160 average time/residue: 1.3470 time to fit residues: 229.7653 Evaluate side-chains 162 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 4 average time/residue: 0.1312 time to fit residues: 2.3394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 10134 Z= 0.261 Angle : 0.655 9.304 13830 Z= 0.330 Chirality : 0.044 0.224 1570 Planarity : 0.004 0.032 1742 Dihedral : 4.689 22.713 1406 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 3.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.17 (0.24), residues: 1274 helix: 1.14 (0.35), residues: 210 sheet: 0.58 (0.23), residues: 534 loop : -0.74 (0.28), residues: 530 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 1.190 Fit side-chains outliers start: 31 outliers final: 22 residues processed: 165 average time/residue: 1.3456 time to fit residues: 236.8103 Evaluate side-chains 161 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 3 average time/residue: 0.4345 time to fit residues: 3.0943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 75 optimal weight: 0.0040 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 10134 Z= 0.176 Angle : 0.614 9.607 13830 Z= 0.307 Chirality : 0.042 0.221 1570 Planarity : 0.004 0.033 1742 Dihedral : 4.423 22.692 1406 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.34 (0.25), residues: 1274 helix: 1.36 (0.35), residues: 210 sheet: 0.70 (0.24), residues: 534 loop : -0.69 (0.28), residues: 530 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 1.120 Fit side-chains outliers start: 26 outliers final: 17 residues processed: 161 average time/residue: 1.3659 time to fit residues: 234.2331 Evaluate side-chains 155 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.1330 time to fit residues: 1.6458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.144450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.092597 restraints weight = 54865.396| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.87 r_work: 0.2980 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10134 Z= 0.209 Angle : 0.629 9.920 13830 Z= 0.314 Chirality : 0.043 0.327 1570 Planarity : 0.004 0.038 1742 Dihedral : 4.443 23.135 1406 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.39 (0.25), residues: 1274 helix: 1.37 (0.35), residues: 210 sheet: 0.73 (0.24), residues: 536 loop : -0.66 (0.28), residues: 528 =============================================================================== Job complete usr+sys time: 4341.27 seconds wall clock time: 77 minutes 42.34 seconds (4662.34 seconds total)