Starting phenix.real_space_refine on Sat Sep 28 00:43:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/09_2024/7onj_12996.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/09_2024/7onj_12996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/09_2024/7onj_12996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/09_2024/7onj_12996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/09_2024/7onj_12996.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onj_12996/09_2024/7onj_12996.cif" } resolution = 2.3 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= 0.009 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 42 5.16 5 C 10955 2.51 5 N 2450 2.21 5 O 3493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16947 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "G" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "B" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "C" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "D" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "E" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "F" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "A" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 50 Chain: "G" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 50 Chain: "B" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 50 Chain: "C" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 50 Chain: "D" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 50 Chain: "E" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 50 Chain: "F" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 387 Unusual residues: {'AV0': 5, 'LMT': 3, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 50 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "F" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Time building chain proxies: 10.87, per 1000 atoms: 0.64 Number of scatterers: 16947 At special positions: 0 Unit cell: (98.9055, 98.9055, 137.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 7 15.00 O 3493 8.00 N 2450 7.00 C 10955 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.47 Conformation dependent library (CDL) restraints added in 2.0 seconds 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3388 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 56.5% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 20 through 59 removed outlier: 4.518A pdb=" N LEU A 24 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 89 Processing helix chain 'A' and resid 92 through 128 removed outlier: 5.306A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 245 through 265 Processing helix chain 'G' and resid 20 through 59 removed outlier: 4.518A pdb=" N LEU G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER G 26 " --> pdb=" O ALA G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 89 Processing helix chain 'G' and resid 92 through 128 removed outlier: 5.306A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 172 Processing helix chain 'G' and resid 197 through 212 Processing helix chain 'G' and resid 245 through 265 Processing helix chain 'B' and resid 20 through 59 removed outlier: 4.518A pdb=" N LEU B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 89 Processing helix chain 'B' and resid 92 through 128 removed outlier: 5.305A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 245 through 265 Processing helix chain 'C' and resid 20 through 59 removed outlier: 4.518A pdb=" N LEU C 24 " --> pdb=" O ASN C 20 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 89 Processing helix chain 'C' and resid 92 through 128 removed outlier: 5.306A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 245 through 265 Processing helix chain 'D' and resid 20 through 59 removed outlier: 4.518A pdb=" N LEU D 24 " --> pdb=" O ASN D 20 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 89 Processing helix chain 'D' and resid 92 through 128 removed outlier: 5.306A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 245 through 265 Processing helix chain 'E' and resid 20 through 59 removed outlier: 4.518A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER E 26 " --> pdb=" O ALA E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 89 Processing helix chain 'E' and resid 92 through 128 removed outlier: 5.305A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 172 Processing helix chain 'E' and resid 197 through 212 Processing helix chain 'E' and resid 245 through 265 Processing helix chain 'F' and resid 20 through 59 removed outlier: 4.518A pdb=" N LEU F 24 " --> pdb=" O ASN F 20 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 89 Processing helix chain 'F' and resid 92 through 128 removed outlier: 5.305A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 245 through 265 Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138 removed outlier: 3.536A pdb=" N VAL A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL G 141 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 6.610A pdb=" N ASN A 234 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 279 removed outlier: 6.680A pdb=" N MET A 273 " --> pdb=" O ASN G 276 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LYS G 278 " --> pdb=" O MET A 273 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL A 275 " --> pdb=" O LYS G 278 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N MET E 273 " --> pdb=" O GLN D 272 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP D 274 " --> pdb=" O MET E 273 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL E 275 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN D 276 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE E 277 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS D 278 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ARG E 279 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.611A pdb=" N ASN G 234 " --> pdb=" O ASN G 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.611A pdb=" N ASN B 234 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 183 through 192 removed outlier: 6.611A pdb=" N ASN C 234 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.610A pdb=" N ASN D 234 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.610A pdb=" N ASN E 234 " --> pdb=" O ASN E 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 183 through 192 removed outlier: 6.611A pdb=" N ASN F 234 " --> pdb=" O ASN F 226 " (cutoff:3.500A) 1082 hydrogen bonds defined for protein. 3183 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: 5.26 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2384 1.32 - 1.44: 4260 1.44 - 1.56: 10163 1.56 - 1.68: 14 1.68 - 1.80: 84 Bond restraints: 16905 Sorted by residual: bond pdb=" O3P PEE C 303 " pdb=" P PEE C 303 " ideal model delta sigma weight residual 1.636 1.588 0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" O3P PEE D 303 " pdb=" P PEE D 303 " ideal model delta sigma weight residual 1.636 1.588 0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" O3P PEE E 303 " pdb=" P PEE E 303 " ideal model delta sigma weight residual 1.636 1.588 0.048 2.00e-02 2.50e+03 5.69e+00 bond pdb=" O3P PEE A 301 " pdb=" P PEE A 301 " ideal model delta sigma weight residual 1.636 1.588 0.048 2.00e-02 2.50e+03 5.68e+00 bond pdb=" O3P PEE G 403 " pdb=" P PEE G 403 " ideal model delta sigma weight residual 1.636 1.589 0.047 2.00e-02 2.50e+03 5.60e+00 ... (remaining 16900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 21916 2.20 - 4.41: 742 4.41 - 6.61: 36 6.61 - 8.81: 0 8.81 - 11.02: 7 Bond angle restraints: 22701 Sorted by residual: angle pdb=" O3P PEE E 303 " pdb=" P PEE E 303 " pdb=" O4P PEE E 303 " ideal model delta sigma weight residual 92.91 103.93 -11.02 3.00e+00 1.11e-01 1.35e+01 angle pdb=" O3P PEE G 403 " pdb=" P PEE G 403 " pdb=" O4P PEE G 403 " ideal model delta sigma weight residual 92.91 103.90 -10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" O3P PEE A 301 " pdb=" P PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 92.91 103.90 -10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" O3P PEE B 303 " pdb=" P PEE B 303 " pdb=" O4P PEE B 303 " ideal model delta sigma weight residual 92.91 103.89 -10.98 3.00e+00 1.11e-01 1.34e+01 angle pdb=" O3P PEE F 405 " pdb=" P PEE F 405 " pdb=" O4P PEE F 405 " ideal model delta sigma weight residual 92.91 103.89 -10.98 3.00e+00 1.11e-01 1.34e+01 ... (remaining 22696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.71: 11543 28.71 - 57.42: 609 57.42 - 86.14: 175 86.14 - 114.85: 238 114.85 - 143.56: 126 Dihedral angle restraints: 12691 sinusoidal: 7434 harmonic: 5257 Sorted by residual: dihedral pdb=" C3 PEE B 303 " pdb=" C1 PEE B 303 " pdb=" C2 PEE B 303 " pdb=" O3P PEE B 303 " ideal model delta sinusoidal sigma weight residual 62.73 -80.83 143.56 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C3 PEE E 303 " pdb=" C1 PEE E 303 " pdb=" C2 PEE E 303 " pdb=" O3P PEE E 303 " ideal model delta sinusoidal sigma weight residual 62.73 -80.76 143.49 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C3 PEE A 301 " pdb=" C1 PEE A 301 " pdb=" C2 PEE A 301 " pdb=" O3P PEE A 301 " ideal model delta sinusoidal sigma weight residual 62.73 -80.75 143.48 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 12688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2286 0.054 - 0.108: 512 0.108 - 0.163: 83 0.163 - 0.217: 38 0.217 - 0.271: 7 Chirality restraints: 2926 Sorted by residual: chirality pdb=" C2 PEE B 303 " pdb=" C1 PEE B 303 " pdb=" C3 PEE B 303 " pdb=" O2 PEE B 303 " both_signs ideal model delta sigma weight residual False -2.33 -2.60 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C2 PEE D 303 " pdb=" C1 PEE D 303 " pdb=" C3 PEE D 303 " pdb=" O2 PEE D 303 " both_signs ideal model delta sigma weight residual False -2.33 -2.60 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C2 PEE E 303 " pdb=" C1 PEE E 303 " pdb=" C3 PEE E 303 " pdb=" O2 PEE E 303 " both_signs ideal model delta sigma weight residual False -2.33 -2.60 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2923 not shown) Planarity restraints: 2450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 83 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.54e+00 pdb=" C ILE B 83 " -0.021 2.00e-02 2.50e+03 pdb=" O ILE B 83 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA B 84 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 83 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" C ILE E 83 " -0.021 2.00e-02 2.50e+03 pdb=" O ILE E 83 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA E 84 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 83 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C ILE G 83 " 0.021 2.00e-02 2.50e+03 pdb=" O ILE G 83 " -0.008 2.00e-02 2.50e+03 pdb=" N ALA G 84 " -0.007 2.00e-02 2.50e+03 ... (remaining 2447 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 610 2.70 - 3.25: 16477 3.25 - 3.80: 28506 3.80 - 4.35: 36414 4.35 - 4.90: 61031 Nonbonded interactions: 143038 Sorted by model distance: nonbonded pdb=" OAR AV0 A 307 " pdb=" OAN AV0 G 405 " model vdw 2.155 3.040 nonbonded pdb=" OAN AV0 B 305 " pdb=" OAR AV0 C 302 " model vdw 2.155 3.040 nonbonded pdb=" OAN AV0 A 303 " pdb=" OAR AV0 B 302 " model vdw 2.155 3.040 nonbonded pdb=" OAN AV0 E 305 " pdb=" OAR AV0 F 404 " model vdw 2.155 3.040 nonbonded pdb=" OAR AV0 G 409 " pdb=" OAN AV0 F 407 " model vdw 2.155 3.040 ... (remaining 143033 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' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'B' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'C' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'D' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'E' and (resid 19 through 280 or (resid 307 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or resid 309)) selection = (chain 'F' and (resid 19 through 280 or resid 407 or (resid 409 and (name CAA or \ name CAB or name CAW or name CAX or name CAY or name CAZ or name CBA or name CB \ B or name CBC or name CBD or name CBE or name CBF or name CBG or name CBH or nam \ e CBI or name CBJ or name CBK or name CBL or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCF or name CCH or name CCJ or name CCL or name CC \ M or name CCQ or name O1 or name OAL or name OAN or name OAP or name OBV or name \ OBX or name OCB)))) selection = (chain 'G' and (resid 19 through 280 or (resid 407 and (name CAA or name CAB or \ name CAW or name CAX or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ CBJ or name CBK or name CBL or name CBN or name CBP or name CBQ or name CBR or \ name CBS or name CBT or name CCD or name CCF or name CCH or name CCJ or name CCL \ or name CCM or name CCO or name CCQ or name CCS or name CCU or name CCW or name \ O1 or name OAJ or name OAL or name OAN or name OAP or name OAR or name OAT or n \ ame OAV or name OBV or name OBX or name OBZ or name OCB)) or (resid 409 and (nam \ e CAA or name CAB or name CAW or name CAX or name CAY or name CAZ or name CBA or \ name CBB or name CBC or name CBD or name CBE or name CBF or name CBG or name CB \ H or name CBI or name CBJ or name CBK or name CBL or name CBP or name CBQ or nam \ e CBR or name CBS or name CBT or name CCF or name CCH or name CCJ or name CCL or \ name CCM or name CCQ or name O1 or name OAL or name OAN or name OAP or name OBV \ or name OBX or name OCB)))) } 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: 1.030 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 39.890 Find NCS groups from input model: 0.980 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: 0.010 Load rotamer database and sin/cos tables:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 0.048 16905 Z= 0.590 Angle : 0.857 11.017 22701 Z= 0.378 Chirality : 0.052 0.271 2926 Planarity : 0.004 0.021 2450 Dihedral : 27.956 143.559 9303 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.47 % Allowed : 3.77 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.16), residues: 1820 helix: -0.33 (0.11), residues: 1043 sheet: 0.31 (0.29), residues: 294 loop : 0.43 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 240 PHE 0.013 0.002 PHE E 127 TYR 0.010 0.002 TYR G 75 ARG 0.004 0.001 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 308 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7672 (ttp-170) cc_final: 0.7397 (ttm170) REVERT: A 47 MET cc_start: 0.7933 (mtt) cc_final: 0.7720 (mtm) REVERT: G 197 ASP cc_start: 0.8513 (t0) cc_final: 0.8266 (t70) REVERT: G 247 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8762 (tp-100) REVERT: G 278 LYS cc_start: 0.8230 (mttt) cc_final: 0.7831 (mttt) REVERT: B 46 ARG cc_start: 0.7686 (ttp-170) cc_final: 0.7478 (ttp80) REVERT: B 54 ARG cc_start: 0.8111 (mtm110) cc_final: 0.7793 (mtm-85) REVERT: C 278 LYS cc_start: 0.8112 (mttt) cc_final: 0.7857 (mttt) REVERT: D 46 ARG cc_start: 0.7571 (ttp-170) cc_final: 0.7321 (ttp-170) REVERT: D 59 ARG cc_start: 0.8014 (mmt90) cc_final: 0.7755 (mmt90) REVERT: D 220 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8459 (pt0) REVERT: D 221 MET cc_start: 0.9153 (mtp) cc_final: 0.8904 (mtp) REVERT: F 54 ARG cc_start: 0.8026 (mtm110) cc_final: 0.7817 (mtm-85) REVERT: F 221 MET cc_start: 0.9128 (mtp) cc_final: 0.8807 (mtp) outliers start: 7 outliers final: 1 residues processed: 310 average time/residue: 1.6277 time to fit residues: 550.3176 Evaluate side-chains 248 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 246 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain D residue 220 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 73 optimal weight: 0.2980 chunk 142 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 210 GLN G 92 GLN G 112 GLN B 112 GLN B 210 GLN C 92 GLN C 210 GLN D 210 GLN E 210 GLN F 92 GLN F 203 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16905 Z= 0.171 Angle : 0.677 8.053 22701 Z= 0.295 Chirality : 0.051 0.376 2926 Planarity : 0.003 0.030 2450 Dihedral : 24.656 147.364 6180 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.68 % Allowed : 8.49 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.86 (0.17), residues: 1820 helix: 2.16 (0.14), residues: 1043 sheet: 0.31 (0.28), residues: 245 loop : -0.13 (0.22), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 251 PHE 0.014 0.001 PHE B 178 TYR 0.006 0.001 TYR C 27 ARG 0.005 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 269 time to evaluate : 1.697 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7950 (mtt) cc_final: 0.7728 (mtm) REVERT: A 59 ARG cc_start: 0.7695 (mmt90) cc_final: 0.7390 (mmt90) REVERT: A 149 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8473 (mp10) REVERT: G 88 ARG cc_start: 0.8329 (mmm160) cc_final: 0.7894 (mmt-90) REVERT: G 278 LYS cc_start: 0.8191 (mttt) cc_final: 0.7985 (mttt) REVERT: B 46 ARG cc_start: 0.7645 (ttp-170) cc_final: 0.7439 (ttp80) REVERT: B 59 ARG cc_start: 0.7691 (mmt90) cc_final: 0.7400 (mpt-90) REVERT: B 62 ASP cc_start: 0.8329 (t70) cc_final: 0.8072 (t70) REVERT: C 54 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.7968 (mtp180) REVERT: C 88 ARG cc_start: 0.8256 (mmm160) cc_final: 0.7864 (mmt-90) REVERT: D 59 ARG cc_start: 0.7805 (mmt90) cc_final: 0.7547 (mmt90) REVERT: D 88 ARG cc_start: 0.8301 (mmm160) cc_final: 0.7892 (tpt170) REVERT: E 47 MET cc_start: 0.7897 (mtm) cc_final: 0.7681 (mtm) REVERT: F 59 ARG cc_start: 0.7586 (mmt90) cc_final: 0.7323 (mmt90) outliers start: 25 outliers final: 2 residues processed: 274 average time/residue: 1.8194 time to fit residues: 538.8913 Evaluate side-chains 255 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 252 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain F residue 35 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 178 optimal weight: 0.8980 chunk 147 optimal weight: 0.0050 chunk 164 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 112 GLN A 210 GLN G 92 GLN G 112 GLN G 276 ASN B 112 GLN B 210 GLN C 92 GLN C 112 GLN D 112 GLN E 112 GLN F 92 GLN F 112 GLN F 203 GLN F 207 ASN F 210 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16905 Z= 0.192 Angle : 0.660 8.586 22701 Z= 0.285 Chirality : 0.044 0.287 2926 Planarity : 0.003 0.033 2450 Dihedral : 21.035 137.369 6174 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.95 % Allowed : 9.70 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.46 (0.18), residues: 1820 helix: 2.80 (0.15), residues: 1043 sheet: 0.32 (0.26), residues: 294 loop : -0.15 (0.23), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 251 PHE 0.013 0.001 PHE E 277 TYR 0.005 0.001 TYR B 75 ARG 0.003 0.000 ARG G 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 261 time to evaluate : 1.701 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.7970 (mtt) cc_final: 0.7752 (mtm) REVERT: A 59 ARG cc_start: 0.7853 (mmt90) cc_final: 0.7356 (mmt90) REVERT: A 88 ARG cc_start: 0.8484 (mmm160) cc_final: 0.8170 (mmt-90) REVERT: A 149 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8487 (mp10) REVERT: G 88 ARG cc_start: 0.8277 (mmm160) cc_final: 0.7880 (mmt-90) REVERT: B 88 ARG cc_start: 0.8335 (mmm160) cc_final: 0.7922 (mmt-90) REVERT: B 149 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8237 (mt0) REVERT: C 88 ARG cc_start: 0.8224 (mmm160) cc_final: 0.7914 (tpp-160) REVERT: D 59 ARG cc_start: 0.7748 (mmt90) cc_final: 0.7469 (mmt90) REVERT: F 59 ARG cc_start: 0.7800 (mmt90) cc_final: 0.7423 (mmt90) outliers start: 29 outliers final: 7 residues processed: 267 average time/residue: 1.8068 time to fit residues: 521.5353 Evaluate side-chains 251 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 242 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain F residue 35 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 210 GLN G 30 ASN G 92 GLN G 112 GLN B 30 ASN B 112 GLN B 210 GLN C 30 ASN C 92 GLN C 112 GLN C 210 GLN D 30 ASN D 112 GLN E 30 ASN E 112 GLN F 30 ASN F 92 GLN F 112 GLN F 203 GLN F 210 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16905 Z= 0.178 Angle : 0.635 7.228 22701 Z= 0.276 Chirality : 0.046 0.340 2926 Planarity : 0.003 0.030 2450 Dihedral : 20.067 136.695 6174 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.09 % Allowed : 10.31 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.71 (0.18), residues: 1820 helix: 3.07 (0.15), residues: 1043 sheet: 0.31 (0.27), residues: 280 loop : -0.15 (0.22), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 251 PHE 0.014 0.001 PHE B 277 TYR 0.005 0.001 TYR B 75 ARG 0.006 0.000 ARG E 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 247 time to evaluate : 1.775 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.7871 (mmt90) cc_final: 0.7347 (mmt90) REVERT: A 88 ARG cc_start: 0.8460 (mmm160) cc_final: 0.8135 (mmt-90) REVERT: A 149 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8507 (mp10) REVERT: G 46 ARG cc_start: 0.7567 (ttp-110) cc_final: 0.7263 (ttp80) REVERT: G 88 ARG cc_start: 0.8337 (mmm160) cc_final: 0.7930 (mmt-90) REVERT: G 278 LYS cc_start: 0.8305 (mttt) cc_final: 0.7987 (mttt) REVERT: B 88 ARG cc_start: 0.8323 (mmm160) cc_final: 0.7882 (mmt-90) REVERT: B 149 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8250 (mt0) REVERT: C 88 ARG cc_start: 0.8261 (mmm160) cc_final: 0.7945 (tpp-160) REVERT: D 59 ARG cc_start: 0.7734 (mmt90) cc_final: 0.7443 (mmt90) REVERT: D 210 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8366 (mt0) REVERT: F 59 ARG cc_start: 0.7796 (mmt90) cc_final: 0.7407 (mmt90) outliers start: 31 outliers final: 9 residues processed: 256 average time/residue: 1.8457 time to fit residues: 509.6672 Evaluate side-chains 253 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 242 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 35 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN G 30 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN C 92 GLN E 30 ASN E 112 GLN F 30 ASN F 92 GLN F 112 GLN F 203 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16905 Z= 0.229 Angle : 0.628 7.348 22701 Z= 0.281 Chirality : 0.046 0.341 2926 Planarity : 0.003 0.019 2450 Dihedral : 19.368 132.925 6174 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.16 % Allowed : 10.85 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.65 (0.18), residues: 1820 helix: 3.07 (0.15), residues: 1043 sheet: 0.66 (0.35), residues: 175 loop : -0.32 (0.21), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 240 PHE 0.012 0.001 PHE E 277 TYR 0.006 0.001 TYR B 75 ARG 0.005 0.000 ARG E 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 251 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8480 (mp10) REVERT: G 46 ARG cc_start: 0.7562 (ttp-110) cc_final: 0.7255 (ttp80) REVERT: G 88 ARG cc_start: 0.8407 (mmm160) cc_final: 0.7950 (mmt-90) REVERT: G 149 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.7905 (mp10) REVERT: G 278 LYS cc_start: 0.8355 (mttt) cc_final: 0.7981 (mttt) REVERT: B 88 ARG cc_start: 0.8396 (mmm160) cc_final: 0.7910 (mmt-90) REVERT: B 149 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: C 149 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8486 (mt0) REVERT: E 46 ARG cc_start: 0.7655 (ttm110) cc_final: 0.7395 (ttp80) REVERT: E 88 ARG cc_start: 0.8428 (mmm160) cc_final: 0.8023 (mmt-90) REVERT: F 149 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8118 (mp10) outliers start: 32 outliers final: 10 residues processed: 260 average time/residue: 1.8394 time to fit residues: 517.2520 Evaluate side-chains 257 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 242 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 149 GLN Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 149 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN G 30 ASN G 112 GLN G 210 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN C 92 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN E 112 GLN F 30 ASN F 92 GLN F 112 GLN F 203 GLN F 210 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16905 Z= 0.182 Angle : 0.597 7.368 22701 Z= 0.265 Chirality : 0.046 0.356 2926 Planarity : 0.002 0.017 2450 Dihedral : 18.864 131.663 6174 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.09 % Allowed : 11.46 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.80 (0.19), residues: 1820 helix: 3.20 (0.15), residues: 1043 sheet: 0.42 (0.27), residues: 280 loop : -0.28 (0.23), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 240 PHE 0.012 0.001 PHE E 277 TYR 0.006 0.001 TYR A 75 ARG 0.005 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 251 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.8394 (mmm160) cc_final: 0.8084 (mmt-90) REVERT: A 149 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8517 (mp10) REVERT: G 46 ARG cc_start: 0.7556 (ttp-110) cc_final: 0.7252 (ttp80) REVERT: G 88 ARG cc_start: 0.8412 (mmm160) cc_final: 0.8092 (mmt-90) REVERT: G 278 LYS cc_start: 0.8390 (mttt) cc_final: 0.8055 (mttt) REVERT: B 88 ARG cc_start: 0.8383 (mmm160) cc_final: 0.7941 (mmt-90) REVERT: B 149 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8303 (mt0) REVERT: C 88 ARG cc_start: 0.8262 (mmm160) cc_final: 0.7754 (tpp-160) REVERT: C 149 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8458 (mt0) REVERT: C 161 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8746 (mttt) REVERT: E 88 ARG cc_start: 0.8389 (mmm160) cc_final: 0.8049 (mmt-90) outliers start: 31 outliers final: 11 residues processed: 258 average time/residue: 1.9582 time to fit residues: 544.9871 Evaluate side-chains 264 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 249 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 149 GLN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 35 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 5.9990 chunk 19 optimal weight: 0.0970 chunk 100 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 chunk 148 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN G 30 ASN G 210 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN C 92 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN E 112 GLN F 30 ASN F 92 GLN F 112 GLN F 203 GLN F 210 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16905 Z= 0.171 Angle : 0.583 6.917 22701 Z= 0.260 Chirality : 0.047 0.364 2926 Planarity : 0.003 0.027 2450 Dihedral : 18.217 131.555 6174 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.82 % Allowed : 11.79 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.86 (0.19), residues: 1820 helix: 3.27 (0.15), residues: 1043 sheet: 0.43 (0.27), residues: 280 loop : -0.31 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 240 PHE 0.013 0.001 PHE B 277 TYR 0.006 0.001 TYR A 75 ARG 0.009 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 256 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.8314 (mmm160) cc_final: 0.8021 (mmt-90) REVERT: G 46 ARG cc_start: 0.7558 (ttp-110) cc_final: 0.7260 (ttp80) REVERT: G 88 ARG cc_start: 0.8420 (mmm160) cc_final: 0.8117 (mmt-90) REVERT: G 278 LYS cc_start: 0.8417 (mttt) cc_final: 0.8071 (mttt) REVERT: B 88 ARG cc_start: 0.8354 (mmm160) cc_final: 0.8047 (mmt-90) REVERT: B 149 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8236 (mt0) REVERT: C 88 ARG cc_start: 0.8216 (mmm160) cc_final: 0.7744 (tpp-160) REVERT: C 149 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8434 (mt0) REVERT: C 161 LYS cc_start: 0.9108 (mtmm) cc_final: 0.8767 (mttt) REVERT: D 88 ARG cc_start: 0.8270 (mmm160) cc_final: 0.7803 (tpt-90) REVERT: E 30 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7644 (m110) REVERT: E 88 ARG cc_start: 0.8284 (mmm160) cc_final: 0.8026 (mmt-90) outliers start: 27 outliers final: 10 residues processed: 262 average time/residue: 1.8896 time to fit residues: 534.3350 Evaluate side-chains 262 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 249 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 35 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN A 210 GLN G 30 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN C 92 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN F 92 GLN F 112 GLN F 203 GLN F 210 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16905 Z= 0.230 Angle : 0.598 7.132 22701 Z= 0.272 Chirality : 0.047 0.391 2926 Planarity : 0.003 0.033 2450 Dihedral : 17.949 132.170 6174 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.95 % Allowed : 11.86 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.75 (0.19), residues: 1820 helix: 3.18 (0.15), residues: 1043 sheet: 0.67 (0.35), residues: 175 loop : -0.35 (0.21), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 240 PHE 0.010 0.002 PHE G 277 TYR 0.008 0.001 TYR A 75 ARG 0.004 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 251 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.8372 (mmm160) cc_final: 0.8058 (mmt-90) REVERT: G 46 ARG cc_start: 0.7521 (ttp-110) cc_final: 0.7223 (ttp80) REVERT: G 88 ARG cc_start: 0.8444 (mmm160) cc_final: 0.8111 (mmt-90) REVERT: G 278 LYS cc_start: 0.8418 (mttt) cc_final: 0.8091 (mttt) REVERT: B 88 ARG cc_start: 0.8405 (mmm160) cc_final: 0.8067 (mmt-90) REVERT: B 149 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8416 (mt0) REVERT: C 88 ARG cc_start: 0.8270 (mmm160) cc_final: 0.7767 (tpp-160) REVERT: C 149 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8451 (mt0) REVERT: C 161 LYS cc_start: 0.9152 (mtmm) cc_final: 0.8811 (mttt) REVERT: E 88 ARG cc_start: 0.8354 (mmm160) cc_final: 0.7909 (mmt-90) outliers start: 29 outliers final: 12 residues processed: 256 average time/residue: 1.8879 time to fit residues: 520.8481 Evaluate side-chains 263 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 249 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain F residue 35 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 154 optimal weight: 0.0970 chunk 162 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: A 210 GLN G 30 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN C 92 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN E 112 GLN F 30 ASN F 92 GLN F 112 GLN F 203 GLN F 210 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16905 Z= 0.157 Angle : 0.559 7.170 22701 Z= 0.252 Chirality : 0.046 0.444 2926 Planarity : 0.002 0.043 2450 Dihedral : 17.380 132.409 6174 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.35 % Allowed : 12.40 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.97 (0.19), residues: 1820 helix: 3.38 (0.15), residues: 1043 sheet: 0.47 (0.27), residues: 280 loop : -0.33 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 240 PHE 0.013 0.001 PHE E 277 TYR 0.006 0.001 TYR A 75 ARG 0.007 0.000 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 256 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.8281 (mmm160) cc_final: 0.8016 (mmt-90) REVERT: G 88 ARG cc_start: 0.8423 (mmm160) cc_final: 0.8115 (mmt-90) REVERT: G 278 LYS cc_start: 0.8505 (mttt) cc_final: 0.8241 (mttt) REVERT: B 88 ARG cc_start: 0.8360 (mmm160) cc_final: 0.8037 (mmt-90) REVERT: B 149 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: C 88 ARG cc_start: 0.8168 (mmm160) cc_final: 0.7853 (tpp-160) REVERT: C 149 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8406 (mt0) REVERT: C 161 LYS cc_start: 0.9087 (mtmm) cc_final: 0.8745 (mttt) REVERT: E 88 ARG cc_start: 0.8283 (mmm160) cc_final: 0.8050 (mmt-90) outliers start: 20 outliers final: 8 residues processed: 259 average time/residue: 1.8218 time to fit residues: 509.8773 Evaluate side-chains 259 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 249 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain F residue 35 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.2980 chunk 172 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN G 30 ASN G 210 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN F 30 ASN F 92 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN F 210 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16905 Z= 0.156 Angle : 0.541 7.949 22701 Z= 0.247 Chirality : 0.044 0.443 2926 Planarity : 0.002 0.022 2450 Dihedral : 16.611 132.886 6174 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.35 % Allowed : 12.74 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.01 (0.19), residues: 1820 helix: 3.44 (0.15), residues: 1043 sheet: 0.46 (0.27), residues: 280 loop : -0.36 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 240 PHE 0.014 0.001 PHE B 277 TYR 0.007 0.001 TYR G 250 ARG 0.004 0.000 ARG B 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 255 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7655 (ttp-110) cc_final: 0.7401 (ttp80) REVERT: A 88 ARG cc_start: 0.8288 (mmm160) cc_final: 0.7947 (mmt-90) REVERT: G 88 ARG cc_start: 0.8419 (mmm160) cc_final: 0.8083 (mmt-90) REVERT: G 278 LYS cc_start: 0.8505 (mttt) cc_final: 0.8246 (mttt) REVERT: B 88 ARG cc_start: 0.8365 (mmm160) cc_final: 0.8013 (mmt-90) REVERT: B 149 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: C 88 ARG cc_start: 0.8174 (mmm160) cc_final: 0.7855 (tpp-160) REVERT: C 161 LYS cc_start: 0.9062 (mtmm) cc_final: 0.8727 (mttt) REVERT: E 30 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7687 (m110) REVERT: E 88 ARG cc_start: 0.8254 (mmm160) cc_final: 0.7948 (mmt-90) outliers start: 20 outliers final: 7 residues processed: 260 average time/residue: 1.8351 time to fit residues: 515.1651 Evaluate side-chains 261 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 252 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 220 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 112 GLN G 210 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN D 276 ASN E 30 ASN F 30 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.083343 restraints weight = 19150.041| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.48 r_work: 0.2728 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 16905 Z= 0.229 Angle : 0.750 59.199 22701 Z= 0.411 Chirality : 0.045 0.442 2926 Planarity : 0.002 0.029 2450 Dihedral : 16.609 132.921 6174 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.88 % Allowed : 13.48 % Favored : 85.65 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: 3.01 (0.19), residues: 1820 helix: 3.43 (0.15), residues: 1043 sheet: 0.48 (0.27), residues: 280 loop : -0.35 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 251 PHE 0.010 0.001 PHE G 188 TYR 0.005 0.001 TYR E 75 ARG 0.004 0.000 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7632.52 seconds wall clock time: 133 minutes 42.60 seconds (8022.60 seconds total)