Starting phenix.real_space_refine on Mon Dec 30 03:21:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uad_42060/12_2024/8uad_42060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uad_42060/12_2024/8uad_42060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uad_42060/12_2024/8uad_42060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uad_42060/12_2024/8uad_42060.map" model { file = "/net/cci-nas-00/data/ceres_data/8uad_42060/12_2024/8uad_42060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uad_42060/12_2024/8uad_42060.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 7722 2.51 5 N 2073 2.21 5 O 2460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12318 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2617 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 319} Chain: "B" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1277 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain: "C" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2617 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 319} Chain: "D" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1277 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain: "E" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2617 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 319} Chain: "F" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1277 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.02, per 1000 atoms: 0.65 Number of scatterers: 12318 At special positions: 0 Unit cell: (95.55, 93.73, 144.69, 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 63 16.00 O 2460 8.00 N 2073 7.00 C 7722 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 57 " distance=2.05 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 143 " distance=2.02 Simple disulfide: pdb=" SG CYS A 178 " - pdb=" SG CYS A 272 " distance=2.04 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 318 " distance=2.04 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 57 " distance=2.05 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 143 " distance=2.02 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 272 " distance=2.04 Simple disulfide: pdb=" SG CYS C 292 " - pdb=" SG CYS C 318 " distance=2.04 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.04 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 57 " distance=2.05 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 143 " distance=2.02 Simple disulfide: pdb=" SG CYS E 178 " - pdb=" SG CYS E 272 " distance=2.04 Simple disulfide: pdb=" SG CYS E 292 " - pdb=" SG CYS E 318 " distance=2.04 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 401 " - " ASN A 59 " " NAG A 402 " - " ASN A 230 " " NAG C 401 " - " ASN C 59 " " NAG C 402 " - " ASN C 230 " " NAG E 401 " - " ASN E 59 " " NAG E 402 " - " ASN E 230 " " NAG G 1 " - " ASN A 330 " " NAG H 1 " - " ASN A 301 " " NAG I 1 " - " ASN A 25 " " NAG J 1 " - " ASN A 194 " " NAG K 1 " - " ASN A 145 " " NAG L 1 " - " ASN C 330 " " NAG M 1 " - " ASN C 301 " " NAG N 1 " - " ASN C 25 " " NAG O 1 " - " ASN C 194 " " NAG P 1 " - " ASN C 145 " " NAG Q 1 " - " ASN E 330 " " NAG R 1 " - " ASN E 301 " " NAG S 1 " - " ASN E 25 " " NAG T 1 " - " ASN E 194 " " NAG U 1 " - " ASN E 145 " Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 1.6 seconds 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 30 sheets defined 27.4% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.549A pdb=" N ARG A 101 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR A 102 " --> pdb=" O HIS A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 98 through 102' Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.527A pdb=" N GLY A 129 " --> pdb=" O ASN A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.535A pdb=" N LYS A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 removed outlier: 3.873A pdb=" N ILE B 6 " --> pdb=" O PHE B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 57 removed outlier: 3.999A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 110 Processing helix chain 'B' and resid 112 through 127 removed outlier: 3.532A pdb=" N LEU B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.518A pdb=" N GLU B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.550A pdb=" N ARG C 101 " --> pdb=" O MET C 98 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR C 102 " --> pdb=" O HIS C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 102' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.528A pdb=" N GLY C 129 " --> pdb=" O ASN C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 202 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.536A pdb=" N LYS C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 8 removed outlier: 3.873A pdb=" N ILE D 6 " --> pdb=" O PHE D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 57 removed outlier: 3.999A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 110 Processing helix chain 'D' and resid 112 through 127 removed outlier: 3.532A pdb=" N LEU D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.518A pdb=" N GLU D 161 " --> pdb=" O ASP D 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 68 Processing helix chain 'E' and resid 98 through 102 removed outlier: 3.549A pdb=" N ARG E 101 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR E 102 " --> pdb=" O HIS E 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 98 through 102' Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 126 through 130 removed outlier: 3.527A pdb=" N GLY E 129 " --> pdb=" O ASN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 202 Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.536A pdb=" N LYS E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 removed outlier: 3.873A pdb=" N ILE F 6 " --> pdb=" O PHE F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 57 removed outlier: 4.000A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 110 Processing helix chain 'F' and resid 112 through 127 removed outlier: 3.532A pdb=" N LEU F 118 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 Processing helix chain 'F' and resid 158 through 163 removed outlier: 3.518A pdb=" N GLU F 161 " --> pdb=" O ASP F 158 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 removed outlier: 3.554A pdb=" N VAL B 131 " --> pdb=" O GLU B 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.102A pdb=" N ASN A 43 " --> pdb=" O ALA A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.527A pdb=" N ILE A 280 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 119 removed outlier: 7.494A pdb=" N VAL A 187 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE A 264 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 116 through 119 Processing sheet with id=AA8, first strand: chain 'A' and resid 170 through 174 Processing sheet with id=AA9, first strand: chain 'A' and resid 298 through 300 Processing sheet with id=AB1, first strand: chain 'A' and resid 306 through 307 Processing sheet with id=AB2, first strand: chain 'D' and resid 31 through 36 removed outlier: 3.555A pdb=" N VAL D 131 " --> pdb=" O GLU D 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AB5, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.102A pdb=" N ASN C 43 " --> pdb=" O ALA C 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 49 through 50 removed outlier: 3.527A pdb=" N ILE C 280 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 116 through 119 removed outlier: 7.494A pdb=" N VAL C 187 " --> pdb=" O PRO C 267 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE C 264 " --> pdb=" O ALA C 159 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 116 through 119 Processing sheet with id=AB9, first strand: chain 'C' and resid 170 through 174 Processing sheet with id=AC1, first strand: chain 'C' and resid 298 through 300 Processing sheet with id=AC2, first strand: chain 'C' and resid 306 through 307 Processing sheet with id=AC3, first strand: chain 'F' and resid 31 through 36 removed outlier: 3.556A pdb=" N VAL F 131 " --> pdb=" O GLU F 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 14 through 17 Processing sheet with id=AC5, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AC6, first strand: chain 'E' and resid 43 through 44 removed outlier: 6.102A pdb=" N ASN E 43 " --> pdb=" O ALA E 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 49 through 50 removed outlier: 3.527A pdb=" N ILE E 280 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 116 through 119 removed outlier: 7.493A pdb=" N VAL E 187 " --> pdb=" O PRO E 267 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE E 264 " --> pdb=" O ALA E 159 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 116 through 119 Processing sheet with id=AD1, first strand: chain 'E' and resid 170 through 174 Processing sheet with id=AD2, first strand: chain 'E' and resid 298 through 300 Processing sheet with id=AD3, first strand: chain 'E' and resid 306 through 307 492 hydrogen bonds defined for protein. 1314 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: 3.93 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3825 1.34 - 1.46: 2773 1.46 - 1.58: 5882 1.58 - 1.71: 0 1.71 - 1.83: 84 Bond restraints: 12564 Sorted by residual: bond pdb=" C1 BMA Q 3 " pdb=" C2 BMA Q 3 " ideal model delta sigma weight residual 1.519 1.562 -0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" C1 BMA L 3 " pdb=" C2 BMA L 3 " ideal model delta sigma weight residual 1.519 1.562 -0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.562 -0.043 2.00e-02 2.50e+03 4.53e+00 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.79e+00 bond pdb=" C1 BMA S 3 " pdb=" C2 BMA S 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.78e+00 ... (remaining 12559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 16108 1.95 - 3.90: 724 3.90 - 5.85: 142 5.85 - 7.80: 45 7.80 - 9.75: 12 Bond angle restraints: 17031 Sorted by residual: angle pdb=" CA CYS C 94 " pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " ideal model delta sigma weight residual 114.40 124.15 -9.75 2.30e+00 1.89e-01 1.80e+01 angle pdb=" CA CYS A 94 " pdb=" CB CYS A 94 " pdb=" SG CYS A 94 " ideal model delta sigma weight residual 114.40 124.14 -9.74 2.30e+00 1.89e-01 1.79e+01 angle pdb=" CA CYS E 94 " pdb=" CB CYS E 94 " pdb=" SG CYS E 94 " ideal model delta sigma weight residual 114.40 124.12 -9.72 2.30e+00 1.89e-01 1.79e+01 angle pdb=" C GLY C 93 " pdb=" N CYS C 94 " pdb=" CA CYS C 94 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C GLY A 93 " pdb=" N CYS A 94 " pdb=" CA CYS A 94 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 ... (remaining 17026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.32: 7495 22.32 - 44.63: 449 44.63 - 66.95: 90 66.95 - 89.27: 81 89.27 - 111.59: 72 Dihedral angle restraints: 8187 sinusoidal: 3864 harmonic: 4323 Sorted by residual: dihedral pdb=" CA THR C 179 " pdb=" C THR C 179 " pdb=" N GLU C 180 " pdb=" CA GLU C 180 " ideal model delta harmonic sigma weight residual -180.00 -158.13 -21.87 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA THR E 179 " pdb=" C THR E 179 " pdb=" N GLU E 180 " pdb=" CA GLU E 180 " ideal model delta harmonic sigma weight residual 180.00 -158.14 -21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA THR A 179 " pdb=" C THR A 179 " pdb=" N GLU A 180 " pdb=" CA GLU A 180 " ideal model delta harmonic sigma weight residual -180.00 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 8184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1547 0.062 - 0.123: 426 0.123 - 0.185: 61 0.185 - 0.246: 12 0.246 - 0.308: 18 Chirality restraints: 2064 Sorted by residual: chirality pdb=" CG LEU E 170 " pdb=" CB LEU E 170 " pdb=" CD1 LEU E 170 " pdb=" CD2 LEU E 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CG LEU A 170 " pdb=" CB LEU A 170 " pdb=" CD1 LEU A 170 " pdb=" CD2 LEU A 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CG LEU C 170 " pdb=" CB LEU C 170 " pdb=" CD1 LEU C 170 " pdb=" CD2 LEU C 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 2061 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 114 " 0.015 2.00e-02 2.50e+03 1.40e-02 3.41e+00 pdb=" CG PHE F 114 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE F 114 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE F 114 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 114 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 114 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 114 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 114 " 0.015 2.00e-02 2.50e+03 1.38e-02 3.35e+00 pdb=" CG PHE D 114 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE D 114 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D 114 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE D 114 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 114 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 114 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 114 " -0.015 2.00e-02 2.50e+03 1.38e-02 3.33e+00 pdb=" CG PHE B 114 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 114 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 114 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 114 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 114 " -0.003 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1647 2.75 - 3.29: 10387 3.29 - 3.83: 18809 3.83 - 4.36: 22964 4.36 - 4.90: 41350 Nonbonded interactions: 95157 Sorted by model distance: nonbonded pdb=" OH TYR C 176 " pdb=" O GLU C 182 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR E 176 " pdb=" O GLU E 182 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR A 176 " pdb=" O GLU A 182 " model vdw 2.217 3.040 nonbonded pdb=" NZ LYS E 38 " pdb=" O SER E 39 " model vdw 2.221 3.120 nonbonded pdb=" NZ LYS C 38 " pdb=" O SER C 39 " model vdw 2.221 3.120 ... (remaining 95152 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'K' selection = chain 'P' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.420 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 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:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 : 0.009 0.057 12564 Z= 0.596 Angle : 1.027 9.749 17031 Z= 0.506 Chirality : 0.062 0.308 2064 Planarity : 0.006 0.042 2121 Dihedral : 20.425 111.586 5370 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.71 % Allowed : 0.94 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.82 (0.21), residues: 1521 helix: 0.35 (0.29), residues: 363 sheet: 0.45 (0.29), residues: 294 loop : -1.34 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 188 HIS 0.007 0.002 HIS C 294 PHE 0.033 0.003 PHE F 114 TYR 0.014 0.003 TYR A 307 ARG 0.008 0.001 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 181 time to evaluate : 1.405 Fit side-chains REVERT: C 198 MET cc_start: 0.8819 (mmm) cc_final: 0.8521 (mmm) outliers start: 9 outliers final: 1 residues processed: 181 average time/residue: 1.5461 time to fit residues: 299.8583 Evaluate side-chains 111 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 323 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12564 Z= 0.179 Angle : 0.683 9.261 17031 Z= 0.329 Chirality : 0.046 0.246 2064 Planarity : 0.005 0.037 2121 Dihedral : 15.607 87.895 2611 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.02 % Allowed : 7.70 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.06 (0.21), residues: 1521 helix: 1.50 (0.30), residues: 342 sheet: 0.57 (0.29), residues: 309 loop : -0.93 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 21 HIS 0.003 0.001 HIS E 99 PHE 0.014 0.002 PHE D 114 TYR 0.010 0.001 TYR A 307 ARG 0.003 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7194 (mt-10) outliers start: 13 outliers final: 3 residues processed: 149 average time/residue: 1.4177 time to fit residues: 228.6891 Evaluate side-chains 135 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12564 Z= 0.345 Angle : 0.781 9.754 17031 Z= 0.376 Chirality : 0.051 0.262 2064 Planarity : 0.005 0.038 2121 Dihedral : 12.157 78.791 2607 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.18 % Allowed : 11.24 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1521 helix: 1.46 (0.30), residues: 339 sheet: 0.53 (0.29), residues: 309 loop : -1.03 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 188 HIS 0.007 0.001 HIS E 99 PHE 0.016 0.002 PHE C 190 TYR 0.015 0.002 TYR E 307 ARG 0.003 0.001 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ARG cc_start: 0.7553 (mtp-110) cc_final: 0.7196 (ptt180) REVERT: D 59 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7239 (mt-10) outliers start: 15 outliers final: 6 residues processed: 159 average time/residue: 1.4895 time to fit residues: 254.6743 Evaluate side-chains 137 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.0070 chunk 102 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 144 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN D 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12564 Z= 0.174 Angle : 0.622 9.559 17031 Z= 0.300 Chirality : 0.044 0.261 2064 Planarity : 0.004 0.033 2121 Dihedral : 9.929 68.035 2607 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.57 % Allowed : 12.50 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.14 (0.21), residues: 1521 helix: 1.87 (0.30), residues: 342 sheet: 0.57 (0.29), residues: 309 loop : -0.84 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 271 HIS 0.003 0.001 HIS E 99 PHE 0.012 0.001 PHE C 190 TYR 0.008 0.001 TYR A 307 ARG 0.009 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ARG cc_start: 0.7494 (mtp-110) cc_final: 0.7139 (ptt180) outliers start: 20 outliers final: 6 residues processed: 170 average time/residue: 1.3448 time to fit residues: 247.7001 Evaluate side-chains 143 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 107 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 100 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12564 Z= 0.198 Angle : 0.642 9.658 17031 Z= 0.306 Chirality : 0.044 0.256 2064 Planarity : 0.004 0.032 2121 Dihedral : 9.007 58.675 2607 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.34 % Allowed : 13.36 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1521 helix: 1.63 (0.30), residues: 360 sheet: 0.61 (0.30), residues: 309 loop : -0.82 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 188 HIS 0.004 0.001 HIS E 99 PHE 0.014 0.001 PHE C 190 TYR 0.011 0.001 TYR E 307 ARG 0.005 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ARG cc_start: 0.7589 (mtp-110) cc_final: 0.7274 (ptt180) REVERT: D 47 LYS cc_start: 0.8317 (mtpp) cc_final: 0.8072 (mtmt) REVERT: F 59 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7121 (mt-10) outliers start: 17 outliers final: 8 residues processed: 152 average time/residue: 1.3690 time to fit residues: 226.3334 Evaluate side-chains 141 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 120 optimal weight: 0.0570 chunk 67 optimal weight: 5.9990 chunk 12 optimal weight: 0.0370 chunk 76 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12564 Z= 0.278 Angle : 0.707 9.769 17031 Z= 0.339 Chirality : 0.047 0.262 2064 Planarity : 0.005 0.033 2121 Dihedral : 8.517 59.559 2607 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.89 % Allowed : 13.92 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.00 (0.21), residues: 1521 helix: 1.51 (0.30), residues: 357 sheet: 0.33 (0.29), residues: 324 loop : -0.81 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 188 HIS 0.005 0.001 HIS E 99 PHE 0.017 0.002 PHE C 190 TYR 0.012 0.002 TYR A 307 ARG 0.006 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8572 (mt) REVERT: C 88 ARG cc_start: 0.7593 (mtp-110) cc_final: 0.7288 (ptt180) REVERT: F 59 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7248 (mt-10) outliers start: 24 outliers final: 12 residues processed: 151 average time/residue: 1.2733 time to fit residues: 209.9537 Evaluate side-chains 148 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12564 Z= 0.339 Angle : 0.756 9.891 17031 Z= 0.364 Chirality : 0.049 0.268 2064 Planarity : 0.005 0.036 2121 Dihedral : 8.149 59.497 2607 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.44 % Allowed : 13.52 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.21), residues: 1521 helix: 1.31 (0.30), residues: 357 sheet: 0.29 (0.29), residues: 324 loop : -0.90 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 188 HIS 0.006 0.001 HIS E 99 PHE 0.017 0.002 PHE C 190 TYR 0.013 0.002 TYR E 307 ARG 0.004 0.001 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8596 (mt) REVERT: B 59 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: C 88 ARG cc_start: 0.7591 (mtp-110) cc_final: 0.7320 (ptt180) REVERT: F 59 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7325 (mt-10) outliers start: 31 outliers final: 20 residues processed: 163 average time/residue: 1.3489 time to fit residues: 238.8882 Evaluate side-chains 158 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 0.0770 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12564 Z= 0.185 Angle : 0.627 9.614 17031 Z= 0.301 Chirality : 0.043 0.258 2064 Planarity : 0.004 0.032 2121 Dihedral : 7.443 57.675 2607 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.57 % Allowed : 14.70 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1521 helix: 1.58 (0.30), residues: 360 sheet: 0.56 (0.29), residues: 309 loop : -0.77 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 188 HIS 0.004 0.001 HIS E 99 PHE 0.014 0.001 PHE C 190 TYR 0.010 0.001 TYR A 307 ARG 0.004 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ARG cc_start: 0.7543 (mtp-110) cc_final: 0.7246 (ptt180) REVERT: E 88 ARG cc_start: 0.7458 (mtp-110) cc_final: 0.7191 (ptt180) REVERT: F 59 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7252 (mt-10) outliers start: 20 outliers final: 11 residues processed: 157 average time/residue: 1.2629 time to fit residues: 215.8686 Evaluate side-chains 148 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.1980 chunk 138 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12564 Z= 0.163 Angle : 0.592 9.625 17031 Z= 0.285 Chirality : 0.042 0.254 2064 Planarity : 0.004 0.031 2121 Dihedral : 6.887 57.859 2607 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.42 % Allowed : 15.41 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.22), residues: 1521 helix: 1.88 (0.30), residues: 357 sheet: 0.66 (0.30), residues: 309 loop : -0.59 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 14 HIS 0.004 0.001 HIS E 40 PHE 0.013 0.001 PHE C 190 TYR 0.009 0.001 TYR A 307 ARG 0.007 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ARG cc_start: 0.7523 (mtp-110) cc_final: 0.7226 (ptt180) REVERT: E 88 ARG cc_start: 0.7405 (mtp-110) cc_final: 0.7138 (ptt180) outliers start: 18 outliers final: 12 residues processed: 152 average time/residue: 1.1927 time to fit residues: 198.5727 Evaluate side-chains 145 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 149 optimal weight: 0.0980 chunk 137 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 12 optimal weight: 0.0770 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 overall best weight: 1.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 GLN E 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12564 Z= 0.179 Angle : 0.601 9.646 17031 Z= 0.289 Chirality : 0.043 0.254 2064 Planarity : 0.004 0.031 2121 Dihedral : 6.754 58.039 2607 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.10 % Allowed : 16.04 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.44 (0.22), residues: 1521 helix: 1.92 (0.30), residues: 357 sheet: 0.68 (0.30), residues: 309 loop : -0.57 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 271 HIS 0.004 0.001 HIS E 99 PHE 0.014 0.001 PHE C 190 TYR 0.011 0.001 TYR A 307 ARG 0.006 0.000 ARG A 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ARG cc_start: 0.7522 (mtp-110) cc_final: 0.7216 (ptt180) outliers start: 14 outliers final: 12 residues processed: 143 average time/residue: 1.1644 time to fit residues: 182.7603 Evaluate side-chains 142 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 119 optimal weight: 0.6980 chunk 49 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 21 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.164274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.121873 restraints weight = 12425.783| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.77 r_work: 0.3125 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12564 Z= 0.212 Angle : 0.626 9.698 17031 Z= 0.302 Chirality : 0.044 0.257 2064 Planarity : 0.004 0.031 2121 Dihedral : 6.747 58.777 2607 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.34 % Allowed : 15.72 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.38 (0.22), residues: 1521 helix: 1.86 (0.30), residues: 357 sheet: 0.65 (0.30), residues: 309 loop : -0.59 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 14 HIS 0.004 0.001 HIS E 99 PHE 0.014 0.001 PHE C 190 TYR 0.011 0.001 TYR A 307 ARG 0.007 0.001 ARG E 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4158.71 seconds wall clock time: 75 minutes 52.86 seconds (4552.86 seconds total)