Starting phenix.real_space_refine on Fri Feb 16 11:33:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgr_31977/02_2024/7vgr_31977.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgr_31977/02_2024/7vgr_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_31977/02_2024/7vgr_31977.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgr_31977/02_2024/7vgr_31977.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgr_31977/02_2024/7vgr_31977.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgr_31977/02_2024/7vgr_31977.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 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-dev-5238/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: 8.11, per 1000 atoms: 0.82 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: 4.14 Conformation dependent library (CDL) restraints added in 2.8 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: 1.22 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: 2.89 Time building geometry restraints manager: 4.32 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 3.470 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 33.510 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.970 ------------------------------------------------------------------------------- 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 % Allowed : 0.37 % Favored : 99.45 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 58 HIS 0.002 0.000 HIS B 154 PHE 0.025 0.001 PHE A 96 TYR 0.007 0.001 TYR B 95 ARG 0.001 0.000 ARG D 220 *********************** 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 : 0.999 Fit side-chains REVERT: C 36 PHE cc_start: 0.7922 (m-10) cc_final: 0.7694 (m-80) REVERT: C 46 GLN cc_start: 0.8048 (mt0) cc_final: 0.7807 (mt0) REVERT: C 85 ASP cc_start: 0.8004 (t0) cc_final: 0.7696 (OUTLIER) REVERT: C 107 LYS cc_start: 0.8359 (tttt) cc_final: 0.7851 (ttpt) REVERT: C 119 VAL cc_start: 0.8262 (t) cc_final: 0.7887 (t) REVERT: D 20 ILE cc_start: 0.8791 (mt) cc_final: 0.8279 (mp) REVERT: D 46 GLU cc_start: 0.7386 (tt0) cc_final: 0.7047 (mt-10) REVERT: D 211 THR cc_start: 0.7861 (m) cc_final: 0.7511 (p) REVERT: E 12 THR cc_start: 0.8973 (t) cc_final: 0.8716 (m) REVERT: E 107 LYS cc_start: 0.8339 (tttt) cc_final: 0.7993 (ttpt) REVERT: E 119 VAL cc_start: 0.8659 (t) cc_final: 0.8270 (t) REVERT: E 194 ASN cc_start: 0.7207 (t0) cc_final: 0.6960 (t0) REVERT: E 211 LYS cc_start: 0.7438 (mmtm) cc_final: 0.7222 (mptm) REVERT: F 20 ILE cc_start: 0.8829 (mt) cc_final: 0.8223 (mp) REVERT: F 150 LYS cc_start: 0.8208 (tttm) cc_final: 0.7970 (ttpp) REVERT: F 211 THR cc_start: 0.8111 (m) cc_final: 0.7779 (p) REVERT: B 127 THR cc_start: 0.8055 (p) cc_final: 0.7783 (t) outliers start: 0 outliers final: 1 residues processed: 282 average time/residue: 1.1301 time to fit residues: 341.9836 Evaluate side-chains 187 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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: 8.9990 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN C 170 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN E 214 ASN 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: 0.7934 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 10134 Z= 0.488 Angle : 0.763 8.939 13830 Z= 0.390 Chirality : 0.050 0.227 1570 Planarity : 0.005 0.040 1742 Dihedral : 4.703 21.947 1406 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.51 % Allowed : 11.16 % Favored : 85.33 % 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: -0.40 (0.24), residues: 1274 helix: 0.64 (0.35), residues: 212 sheet: 0.13 (0.23), residues: 530 loop : -0.96 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 58 HIS 0.006 0.002 HIS E 202 PHE 0.016 0.003 PHE B 26 TYR 0.021 0.003 TYR F 129 ARG 0.005 0.001 ARG E 65 *********************** 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 222 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 186 time to evaluate : 1.187 Fit side-chains REVERT: C 42 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: C 72 ARG cc_start: 0.7244 (ttp-110) cc_final: 0.6863 (ptm-80) REVERT: C 107 LYS cc_start: 0.8631 (tttt) cc_final: 0.7950 (ttpt) REVERT: C 128 GLN cc_start: 0.8470 (mm-40) cc_final: 0.7833 (tm-30) REVERT: C 214 ASN cc_start: 0.7198 (m-40) cc_final: 0.6915 (m-40) REVERT: D 20 ILE cc_start: 0.8783 (mt) cc_final: 0.8552 (mt) REVERT: D 46 GLU cc_start: 0.7809 (tt0) cc_final: 0.7584 (tt0) REVERT: D 74 LYS cc_start: 0.7839 (mtpt) cc_final: 0.7478 (mtmm) REVERT: D 211 THR cc_start: 0.7486 (m) cc_final: 0.7218 (m) REVERT: E 12 THR cc_start: 0.9174 (t) cc_final: 0.8703 (m) REVERT: E 59 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: E 72 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.6891 (ptm-80) REVERT: E 107 LYS cc_start: 0.8574 (tttt) cc_final: 0.7920 (ttpt) REVERT: E 141 ASN cc_start: 0.8234 (m110) cc_final: 0.7926 (m110) REVERT: F 20 ILE cc_start: 0.8771 (mt) cc_final: 0.8427 (mt) REVERT: F 74 LYS cc_start: 0.7780 (mtpt) cc_final: 0.7456 (mtmm) REVERT: F 150 LYS cc_start: 0.8024 (tttm) cc_final: 0.7690 (ttpp) REVERT: F 211 THR cc_start: 0.7720 (m) cc_final: 0.7442 (m) REVERT: A 74 ASN cc_start: 0.7734 (p0) cc_final: 0.7499 (p0) REVERT: A 91 MET cc_start: 0.8166 (mtm) cc_final: 0.7918 (mtm) REVERT: A 205 LYS cc_start: 0.6826 (mttt) cc_final: 0.6535 (mttt) REVERT: B 74 ASN cc_start: 0.7747 (p0) cc_final: 0.7493 (p0) REVERT: B 205 LYS cc_start: 0.6924 (mttt) cc_final: 0.6369 (mmtt) outliers start: 36 outliers final: 13 residues processed: 204 average time/residue: 1.2163 time to fit residues: 265.3235 Evaluate side-chains 173 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 164 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 162 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN A 113 ASN A 125 HIS B 113 ASN B 125 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3976 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= 0.220 Angle : 0.600 7.983 13830 Z= 0.305 Chirality : 0.043 0.144 1570 Planarity : 0.004 0.032 1742 Dihedral : 4.491 21.951 1406 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.60 % Allowed : 13.75 % Favored : 82.66 % 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: 0.95 (0.35), residues: 212 sheet: 0.29 (0.23), residues: 530 loop : -0.86 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 58 HIS 0.001 0.001 HIS A 148 PHE 0.010 0.001 PHE E 32 TYR 0.015 0.001 TYR E 196 ARG 0.003 0.000 ARG B 105 *********************** 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 206 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 1.173 Fit side-chains REVERT: C 27 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: C 42 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8832 (tt0) REVERT: C 72 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6949 (ptm-80) REVERT: C 107 LYS cc_start: 0.8615 (tttt) cc_final: 0.7892 (ttpt) REVERT: C 128 GLN cc_start: 0.8507 (mm-40) cc_final: 0.7856 (tm-30) REVERT: C 214 ASN cc_start: 0.7268 (m-40) cc_final: 0.6909 (m-40) REVERT: D 20 ILE cc_start: 0.8757 (mt) cc_final: 0.8235 (mp) REVERT: D 46 GLU cc_start: 0.7771 (tt0) cc_final: 0.7437 (tt0) REVERT: D 63 LYS cc_start: 0.8545 (mtpp) cc_final: 0.8274 (mtpt) REVERT: D 74 LYS cc_start: 0.7812 (mtpt) cc_final: 0.7510 (mtmm) REVERT: D 211 THR cc_start: 0.7491 (m) cc_final: 0.7220 (m) REVERT: E 12 THR cc_start: 0.9156 (t) cc_final: 0.8677 (m) REVERT: E 18 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7533 (ptp90) REVERT: E 27 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7992 (pm20) REVERT: E 72 ARG cc_start: 0.7143 (ttp-110) cc_final: 0.6797 (ptm-80) REVERT: E 107 LYS cc_start: 0.8572 (tttt) cc_final: 0.7837 (ttpt) REVERT: E 128 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7088 (tm-30) REVERT: F 20 ILE cc_start: 0.8763 (mt) cc_final: 0.8226 (mp) REVERT: F 74 LYS cc_start: 0.7768 (mtpt) cc_final: 0.7488 (mtmm) REVERT: F 150 LYS cc_start: 0.8088 (tttm) cc_final: 0.7783 (ttpp) REVERT: F 211 THR cc_start: 0.7580 (m) cc_final: 0.7322 (m) REVERT: A 74 ASN cc_start: 0.7839 (p0) cc_final: 0.7614 (p0) REVERT: A 91 MET cc_start: 0.8229 (mtm) cc_final: 0.7918 (mtm) REVERT: A 205 LYS cc_start: 0.6863 (mttt) cc_final: 0.6416 (mmtt) REVERT: B 74 ASN cc_start: 0.7819 (p0) cc_final: 0.7487 (p0) outliers start: 35 outliers final: 11 residues processed: 185 average time/residue: 1.3158 time to fit residues: 259.5849 Evaluate side-chains 171 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.9980 chunk 84 optimal weight: 0.0970 chunk 58 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4346 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= 0.278 Angle : 0.630 8.015 13830 Z= 0.319 Chirality : 0.044 0.161 1570 Planarity : 0.004 0.032 1742 Dihedral : 4.598 22.735 1406 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.87 % Allowed : 14.30 % Favored : 81.83 % 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: -0.16 (0.24), residues: 1274 helix: 0.99 (0.35), residues: 210 sheet: 0.30 (0.23), residues: 530 loop : -0.91 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 47 HIS 0.002 0.001 HIS B 148 PHE 0.012 0.002 PHE E 32 TYR 0.014 0.002 TYR E 196 ARG 0.003 0.000 ARG B 105 *********************** 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 200 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 162 time to evaluate : 1.117 Fit side-chains REVERT: C 27 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8043 (pm20) REVERT: C 42 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8310 (tt0) REVERT: C 59 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.7477 (tm-30) REVERT: C 72 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6686 (ptm-80) REVERT: C 107 LYS cc_start: 0.8645 (tttt) cc_final: 0.8394 (mtpm) REVERT: C 128 GLN cc_start: 0.8558 (mm-40) cc_final: 0.7967 (tm-30) REVERT: C 214 ASN cc_start: 0.7142 (m-40) cc_final: 0.6875 (m-40) REVERT: D 20 ILE cc_start: 0.8734 (mt) cc_final: 0.8190 (mp) REVERT: D 46 GLU cc_start: 0.7738 (tt0) cc_final: 0.7334 (tt0) REVERT: D 63 LYS cc_start: 0.8553 (mtpp) cc_final: 0.8238 (mtpt) REVERT: D 74 LYS cc_start: 0.7885 (mtpt) cc_final: 0.7547 (mtmm) REVERT: E 12 THR cc_start: 0.9179 (t) cc_final: 0.8585 (m) REVERT: E 18 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7668 (ptp90) REVERT: E 27 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8027 (pm20) REVERT: E 72 ARG cc_start: 0.7200 (ttp-110) cc_final: 0.6627 (ptm-80) REVERT: E 83 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7659 (mt-10) REVERT: E 107 LYS cc_start: 0.8624 (tttt) cc_final: 0.7888 (tptt) REVERT: E 128 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: F 20 ILE cc_start: 0.8746 (mt) cc_final: 0.8218 (mp) REVERT: F 74 LYS cc_start: 0.7798 (mtpt) cc_final: 0.7419 (mtmm) REVERT: F 150 LYS cc_start: 0.8066 (tttm) cc_final: 0.7715 (ttpp) REVERT: F 211 THR cc_start: 0.7482 (m) cc_final: 0.7213 (m) REVERT: A 74 ASN cc_start: 0.7946 (p0) cc_final: 0.7694 (p0) REVERT: A 128 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8693 (mm) REVERT: A 205 LYS cc_start: 0.6929 (mttt) cc_final: 0.6594 (mttt) REVERT: B 74 ASN cc_start: 0.7819 (p0) cc_final: 0.7445 (p0) REVERT: B 190 ASP cc_start: 0.7251 (m-30) cc_final: 0.7037 (t0) outliers start: 38 outliers final: 20 residues processed: 182 average time/residue: 1.3391 time to fit residues: 259.6184 Evaluate side-chains 177 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** A 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10134 Z= 0.238 Angle : 0.611 8.001 13830 Z= 0.309 Chirality : 0.043 0.148 1570 Planarity : 0.004 0.032 1742 Dihedral : 4.538 22.682 1406 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.69 % Allowed : 14.94 % Favored : 81.37 % 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: -0.07 (0.24), residues: 1274 helix: 1.08 (0.35), residues: 210 sheet: 0.41 (0.23), residues: 528 loop : -0.92 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 47 HIS 0.002 0.001 HIS D 171 PHE 0.010 0.001 PHE A 96 TYR 0.015 0.001 TYR E 196 ARG 0.003 0.000 ARG B 105 *********************** 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 189 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 1.208 Fit side-chains REVERT: C 27 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8057 (pm20) REVERT: C 42 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8843 (tt0) REVERT: C 72 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6712 (ptm-80) REVERT: C 107 LYS cc_start: 0.8626 (tttt) cc_final: 0.8383 (mtpm) REVERT: C 128 GLN cc_start: 0.8549 (mm-40) cc_final: 0.7957 (tm-30) REVERT: C 158 GLU cc_start: 0.8207 (mm-30) cc_final: 0.6931 (tm-30) REVERT: C 214 ASN cc_start: 0.7104 (m-40) cc_final: 0.6855 (m-40) REVERT: D 20 ILE cc_start: 0.8712 (mt) cc_final: 0.8173 (mp) REVERT: D 46 GLU cc_start: 0.7990 (tt0) cc_final: 0.7691 (tt0) REVERT: D 63 LYS cc_start: 0.8496 (mtpp) cc_final: 0.8240 (mtpt) REVERT: D 74 LYS cc_start: 0.7915 (mtpt) cc_final: 0.7556 (mtmm) REVERT: E 12 THR cc_start: 0.9186 (t) cc_final: 0.8571 (m) REVERT: E 18 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7638 (ptp90) REVERT: E 72 ARG cc_start: 0.7283 (ttp-110) cc_final: 0.6657 (ptm-80) REVERT: E 83 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7659 (mp0) REVERT: E 107 LYS cc_start: 0.8572 (tttt) cc_final: 0.7862 (tptt) REVERT: E 128 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7235 (tm-30) REVERT: E 153 LYS cc_start: 0.7659 (pttp) cc_final: 0.7443 (pttp) REVERT: E 158 GLU cc_start: 0.7970 (mm-30) cc_final: 0.6468 (tm-30) REVERT: F 20 ILE cc_start: 0.8741 (mt) cc_final: 0.8198 (mp) REVERT: F 74 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7522 (mtmm) REVERT: F 150 LYS cc_start: 0.8116 (tttm) cc_final: 0.7786 (ttpp) REVERT: F 211 THR cc_start: 0.7486 (m) cc_final: 0.7215 (m) REVERT: F 215 LYS cc_start: 0.7284 (tppp) cc_final: 0.6550 (tppt) REVERT: A 74 ASN cc_start: 0.7971 (p0) cc_final: 0.7699 (p0) REVERT: A 128 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8672 (mm) REVERT: A 205 LYS cc_start: 0.6967 (mttt) cc_final: 0.6632 (mttt) REVERT: B 74 ASN cc_start: 0.7876 (p0) cc_final: 0.7501 (p0) outliers start: 36 outliers final: 26 residues processed: 174 average time/residue: 1.3286 time to fit residues: 246.3771 Evaluate side-chains 181 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 149 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.7950 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10134 Z= 0.245 Angle : 0.617 8.979 13830 Z= 0.310 Chirality : 0.043 0.147 1570 Planarity : 0.004 0.036 1742 Dihedral : 4.534 23.002 1406 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.97 % Allowed : 14.85 % Favored : 81.18 % 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: 0.02 (0.24), residues: 1274 helix: 1.16 (0.35), residues: 210 sheet: 0.42 (0.23), residues: 528 loop : -0.81 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 47 HIS 0.002 0.001 HIS D 171 PHE 0.011 0.001 PHE A 96 TYR 0.008 0.001 TYR C 177 ARG 0.006 0.000 ARG C 159 *********************** 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 190 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 1.251 Fit side-chains revert: symmetry clash REVERT: C 27 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8041 (pm20) REVERT: C 42 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8854 (tt0) REVERT: C 59 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: C 72 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6776 (ptm-80) REVERT: C 107 LYS cc_start: 0.8617 (tttt) cc_final: 0.8374 (mtpm) REVERT: C 128 GLN cc_start: 0.8548 (mm-40) cc_final: 0.7939 (tm-30) REVERT: C 214 ASN cc_start: 0.6904 (m-40) cc_final: 0.6678 (m-40) REVERT: D 20 ILE cc_start: 0.8701 (mt) cc_final: 0.8159 (mp) REVERT: D 46 GLU cc_start: 0.8031 (tt0) cc_final: 0.7715 (tt0) REVERT: D 63 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8224 (mtpt) REVERT: D 74 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7567 (mtmm) REVERT: D 215 LYS cc_start: 0.7413 (tppt) cc_final: 0.6853 (tppt) REVERT: E 12 THR cc_start: 0.9199 (t) cc_final: 0.8575 (m) REVERT: E 18 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7650 (ptp90) REVERT: E 59 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: E 72 ARG cc_start: 0.7372 (ttp-110) cc_final: 0.6887 (ptm-80) REVERT: E 83 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7574 (mt-10) REVERT: E 107 LYS cc_start: 0.8562 (tttt) cc_final: 0.7844 (tptt) REVERT: E 128 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: F 20 ILE cc_start: 0.8705 (mt) cc_final: 0.8154 (mp) REVERT: F 74 LYS cc_start: 0.7747 (mtpt) cc_final: 0.7356 (mtmm) REVERT: F 150 LYS cc_start: 0.8099 (tttm) cc_final: 0.7755 (ttpp) REVERT: F 215 LYS cc_start: 0.7484 (tppp) cc_final: 0.6762 (tppt) REVERT: A 74 ASN cc_start: 0.7951 (p0) cc_final: 0.7673 (p0) REVERT: A 128 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8675 (mm) REVERT: A 205 LYS cc_start: 0.7001 (mttt) cc_final: 0.6669 (mttt) REVERT: B 74 ASN cc_start: 0.7983 (p0) cc_final: 0.7575 (p0) outliers start: 39 outliers final: 26 residues processed: 174 average time/residue: 1.3053 time to fit residues: 242.4413 Evaluate side-chains 183 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 148 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7936 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10134 Z= 0.212 Angle : 0.598 8.555 13830 Z= 0.300 Chirality : 0.042 0.139 1570 Planarity : 0.004 0.033 1742 Dihedral : 4.428 22.814 1406 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.87 % Allowed : 15.59 % Favored : 80.54 % 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: 0.09 (0.24), residues: 1274 helix: 1.24 (0.35), residues: 210 sheet: 0.45 (0.23), residues: 534 loop : -0.77 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.002 0.001 HIS D 171 PHE 0.009 0.001 PHE F 95 TYR 0.008 0.001 TYR E 53 ARG 0.008 0.000 ARG C 159 *********************** 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 191 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 GLU cc_start: 0.8428 (pt0) cc_final: 0.8056 (pm20) REVERT: C 42 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8808 (tt0) REVERT: C 107 LYS cc_start: 0.8602 (tttt) cc_final: 0.8366 (mtpm) REVERT: C 128 GLN cc_start: 0.8533 (mm-40) cc_final: 0.7929 (tm-30) REVERT: C 214 ASN cc_start: 0.6897 (m-40) cc_final: 0.6677 (m-40) REVERT: D 20 ILE cc_start: 0.8692 (mt) cc_final: 0.8150 (mp) REVERT: D 46 GLU cc_start: 0.8109 (tt0) cc_final: 0.7771 (tt0) REVERT: D 63 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8248 (mtpt) REVERT: D 74 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7523 (mtmm) REVERT: D 215 LYS cc_start: 0.7390 (tppt) cc_final: 0.6833 (tppt) REVERT: E 12 THR cc_start: 0.9230 (t) cc_final: 0.8711 (m) REVERT: E 18 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7618 (ptp90) REVERT: E 83 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7586 (mt-10) REVERT: E 107 LYS cc_start: 0.8557 (tttt) cc_final: 0.7839 (tptt) REVERT: E 128 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: F 20 ILE cc_start: 0.8689 (mt) cc_final: 0.8147 (mp) REVERT: F 74 LYS cc_start: 0.7781 (mtpt) cc_final: 0.7393 (mtmm) REVERT: F 150 LYS cc_start: 0.8101 (tttm) cc_final: 0.7771 (ttpp) REVERT: A 74 ASN cc_start: 0.7939 (p0) cc_final: 0.7590 (p0) REVERT: A 128 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8594 (mm) REVERT: A 205 LYS cc_start: 0.6923 (mttt) cc_final: 0.6604 (mttt) REVERT: B 74 ASN cc_start: 0.7928 (p0) cc_final: 0.7548 (p0) outliers start: 38 outliers final: 24 residues processed: 179 average time/residue: 1.3544 time to fit residues: 258.5345 Evaluate side-chains 180 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.0070 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 81 optimal weight: 0.0870 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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: 0.7912 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10134 Z= 0.180 Angle : 0.580 9.043 13830 Z= 0.289 Chirality : 0.042 0.132 1570 Planarity : 0.004 0.034 1742 Dihedral : 4.256 23.211 1406 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.68 % Allowed : 16.97 % Favored : 80.35 % 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 (0.25), residues: 1274 helix: 1.42 (0.36), residues: 210 sheet: 0.54 (0.23), residues: 534 loop : -0.75 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.001 0.000 HIS D 171 PHE 0.008 0.001 PHE F 95 TYR 0.009 0.001 TYR E 196 ARG 0.008 0.000 ARG C 159 *********************** 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 181 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.071 Fit side-chains REVERT: C 13 VAL cc_start: 0.8343 (m) cc_final: 0.8082 (m) REVERT: C 27 GLU cc_start: 0.8423 (pt0) cc_final: 0.8053 (pm20) REVERT: C 42 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8767 (tt0) REVERT: C 107 LYS cc_start: 0.8584 (tttt) cc_final: 0.8358 (mtpm) REVERT: C 128 GLN cc_start: 0.8506 (mm-40) cc_final: 0.7930 (tm-30) REVERT: C 159 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.7580 (mmm-85) REVERT: D 20 ILE cc_start: 0.8673 (mt) cc_final: 0.8155 (mp) REVERT: D 46 GLU cc_start: 0.8130 (tt0) cc_final: 0.7461 (mt-10) REVERT: D 74 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7559 (mtmm) REVERT: D 215 LYS cc_start: 0.7404 (tppt) cc_final: 0.6938 (tppt) REVERT: E 12 THR cc_start: 0.9121 (t) cc_final: 0.8628 (m) REVERT: E 107 LYS cc_start: 0.8545 (tttt) cc_final: 0.7821 (tptt) REVERT: E 128 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7242 (tm-30) REVERT: F 20 ILE cc_start: 0.8674 (mt) cc_final: 0.8155 (mp) REVERT: F 74 LYS cc_start: 0.7779 (mtpt) cc_final: 0.7420 (mtmm) REVERT: F 150 LYS cc_start: 0.8036 (tttm) cc_final: 0.7704 (ttpp) REVERT: A 74 ASN cc_start: 0.7972 (p0) cc_final: 0.7608 (p0) REVERT: A 128 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8525 (mm) REVERT: A 205 LYS cc_start: 0.6914 (mttt) cc_final: 0.6601 (mttt) REVERT: B 74 ASN cc_start: 0.7962 (p0) cc_final: 0.7538 (p0) outliers start: 25 outliers final: 17 residues processed: 174 average time/residue: 1.3318 time to fit residues: 246.9672 Evaluate side-chains 169 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4689 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= 0.219 Angle : 0.600 9.311 13830 Z= 0.299 Chirality : 0.042 0.140 1570 Planarity : 0.004 0.033 1742 Dihedral : 4.362 22.544 1406 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.95 % Allowed : 17.07 % Favored : 79.98 % 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: 0.24 (0.25), residues: 1274 helix: 1.37 (0.36), residues: 210 sheet: 0.54 (0.24), residues: 536 loop : -0.69 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 47 HIS 0.002 0.001 HIS D 171 PHE 0.010 0.001 PHE A 96 TYR 0.010 0.001 TYR C 177 ARG 0.007 0.000 ARG C 159 *********************** 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 178 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 1.014 Fit side-chains REVERT: C 13 VAL cc_start: 0.8395 (m) cc_final: 0.8140 (m) REVERT: C 27 GLU cc_start: 0.8417 (pt0) cc_final: 0.8039 (pm20) REVERT: C 42 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8844 (tt0) REVERT: C 107 LYS cc_start: 0.8551 (tttt) cc_final: 0.8318 (mtpm) REVERT: C 128 GLN cc_start: 0.8527 (mm-40) cc_final: 0.7936 (tm-30) REVERT: C 194 ASN cc_start: 0.7854 (t0) cc_final: 0.7512 (t0) REVERT: D 20 ILE cc_start: 0.8633 (mt) cc_final: 0.8106 (mp) REVERT: D 74 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7603 (mtmm) REVERT: D 215 LYS cc_start: 0.7400 (tppt) cc_final: 0.6922 (tppt) REVERT: E 12 THR cc_start: 0.9141 (t) cc_final: 0.8668 (m) REVERT: E 83 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7792 (OUTLIER) REVERT: E 107 LYS cc_start: 0.8551 (tttt) cc_final: 0.7830 (tptt) REVERT: E 128 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: F 20 ILE cc_start: 0.8661 (mt) cc_final: 0.8111 (mp) REVERT: F 74 LYS cc_start: 0.7826 (mtpt) cc_final: 0.7396 (mtmm) REVERT: F 150 LYS cc_start: 0.8076 (tttm) cc_final: 0.7748 (ttpp) REVERT: A 74 ASN cc_start: 0.7962 (p0) cc_final: 0.7608 (p0) REVERT: A 128 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8606 (mm) REVERT: A 205 LYS cc_start: 0.6936 (mttt) cc_final: 0.6631 (mttt) REVERT: B 74 ASN cc_start: 0.7992 (p0) cc_final: 0.7556 (p0) REVERT: B 128 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8620 (mm) outliers start: 28 outliers final: 22 residues processed: 171 average time/residue: 1.2597 time to fit residues: 230.3012 Evaluate side-chains 175 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** A 117 ASN B 19 GLN B 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 10134 Z= 0.429 Angle : 0.724 9.546 13830 Z= 0.364 Chirality : 0.048 0.174 1570 Planarity : 0.004 0.033 1742 Dihedral : 4.967 21.451 1406 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.32 % Allowed : 16.51 % Favored : 80.17 % 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: 0.03 (0.24), residues: 1274 helix: 0.95 (0.35), residues: 210 sheet: 0.37 (0.23), residues: 540 loop : -0.65 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 47 HIS 0.004 0.001 HIS B 148 PHE 0.014 0.002 PHE D 95 TYR 0.023 0.002 TYR C 177 ARG 0.007 0.001 ARG C 159 ********************** 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 182 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.180 Fit side-chains REVERT: C 27 GLU cc_start: 0.8435 (pt0) cc_final: 0.8060 (pm20) REVERT: C 42 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: C 83 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7359 (mt-10) REVERT: C 107 LYS cc_start: 0.8557 (tttt) cc_final: 0.8293 (mtpm) REVERT: C 128 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8019 (tm-30) REVERT: C 158 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7066 (tm-30) REVERT: C 194 ASN cc_start: 0.8054 (t0) cc_final: 0.7667 (t0) REVERT: D 20 ILE cc_start: 0.8729 (mt) cc_final: 0.8309 (mt) REVERT: D 46 GLU cc_start: 0.8018 (tt0) cc_final: 0.7302 (mt-10) REVERT: D 74 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7561 (mtmm) REVERT: D 215 LYS cc_start: 0.7318 (tppt) cc_final: 0.6715 (tppt) REVERT: E 12 THR cc_start: 0.9248 (t) cc_final: 0.8620 (m) REVERT: E 83 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: E 107 LYS cc_start: 0.8570 (tttt) cc_final: 0.7830 (tptt) REVERT: E 128 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: F 20 ILE cc_start: 0.8732 (mt) cc_final: 0.8333 (mt) REVERT: F 150 LYS cc_start: 0.8137 (tttm) cc_final: 0.7763 (ttpp) REVERT: A 74 ASN cc_start: 0.8012 (p0) cc_final: 0.7799 (p0) REVERT: A 205 LYS cc_start: 0.6977 (mttt) cc_final: 0.6600 (mmtt) REVERT: B 74 ASN cc_start: 0.7966 (p0) cc_final: 0.7643 (p0) REVERT: B 190 ASP cc_start: 0.7362 (m-30) cc_final: 0.7120 (t0) REVERT: B 205 LYS cc_start: 0.7126 (mttt) cc_final: 0.6576 (mmtt) outliers start: 32 outliers final: 24 residues processed: 173 average time/residue: 1.4132 time to fit residues: 259.7194 Evaluate side-chains 172 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 42 GLN Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.142356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.090450 restraints weight = 52850.982| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.81 r_work: 0.2940 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10134 Z= 0.262 Angle : 0.643 9.600 13830 Z= 0.323 Chirality : 0.044 0.151 1570 Planarity : 0.004 0.034 1742 Dihedral : 4.717 22.685 1406 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.32 % Allowed : 17.07 % Favored : 79.61 % 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: 0.13 (0.24), residues: 1274 helix: 1.11 (0.35), residues: 210 sheet: 0.40 (0.23), residues: 540 loop : -0.59 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 167 HIS 0.002 0.001 HIS D 171 PHE 0.011 0.002 PHE A 96 TYR 0.014 0.002 TYR C 177 ARG 0.010 0.001 ARG E 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4502.07 seconds wall clock time: 80 minutes 34.52 seconds (4834.52 seconds total)