Starting phenix.real_space_refine on Sun May 25 12:44:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jmi_36422/05_2025/8jmi_36422_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jmi_36422/05_2025/8jmi_36422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jmi_36422/05_2025/8jmi_36422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jmi_36422/05_2025/8jmi_36422.map" model { file = "/net/cci-nas-00/data/ceres_data/8jmi_36422/05_2025/8jmi_36422_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jmi_36422/05_2025/8jmi_36422_neut_trim.cif" } resolution = 2.6 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= 0.007 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 S 96 5.16 5 C 8872 2.51 5 N 2212 2.21 5 O 2264 1.98 5 H 13812 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27256 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "B" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "C" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "D" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.00, per 1000 atoms: 0.48 Number of scatterers: 27256 At special positions: 0 Unit cell: (116.25, 116.25, 103.23, 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 96 16.00 O 2264 8.00 N 2212 7.00 C 8872 6.00 H 13812 1.00 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 Links applied ALPHA1-4 " BGC E 1 " - " GLC E 2 " " BGC F 1 " - " GLC F 2 " " BGC G 1 " - " GLC G 2 " " BGC H 1 " - " GLC H 2 " Time building additional restraints: 7.70 Conformation dependent library (CDL) restraints added in 2.1 seconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3136 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 79.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 58 through 73 Proline residue: A 65 - end of helix removed outlier: 3.703A pdb=" N VAL A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 95 through 123 Processing helix chain 'A' and resid 125 through 164 removed outlier: 4.015A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLY A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 177 through 214 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 242 through 287 removed outlier: 4.479A pdb=" N ASP A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 339 removed outlier: 3.570A pdb=" N PHE A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 387 removed outlier: 3.901A pdb=" N ILE A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 443 through 450 removed outlier: 3.822A pdb=" N GLY A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 73 Proline residue: B 65 - end of helix removed outlier: 3.704A pdb=" N VAL B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'B' and resid 95 through 123 Processing helix chain 'B' and resid 125 through 164 removed outlier: 4.030A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLY B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 177 through 214 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 242 through 287 removed outlier: 4.479A pdb=" N ASP B 264 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 339 removed outlier: 3.570A pdb=" N PHE B 298 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N SER B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 387 removed outlier: 3.900A pdb=" N ILE B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 443 through 450 removed outlier: 3.821A pdb=" N GLY B 450 " --> pdb=" O ASN B 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 73 Proline residue: C 65 - end of helix removed outlier: 3.703A pdb=" N VAL C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 95 through 123 Processing helix chain 'C' and resid 125 through 164 removed outlier: 4.016A pdb=" N VAL C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY C 131 " --> pdb=" O LYS C 127 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Proline residue: C 153 - end of helix Processing helix chain 'C' and resid 165 through 168 Processing helix chain 'C' and resid 177 through 214 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 242 through 287 removed outlier: 4.478A pdb=" N ASP C 264 " --> pdb=" O TRP C 260 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 339 removed outlier: 3.573A pdb=" N PHE C 298 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N SER C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 387 removed outlier: 3.893A pdb=" N ILE C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C 385 " --> pdb=" O ARG C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'C' and resid 421 through 440 Processing helix chain 'C' and resid 443 through 450 removed outlier: 3.822A pdb=" N GLY C 450 " --> pdb=" O ASN C 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 73 Proline residue: D 65 - end of helix removed outlier: 3.704A pdb=" N VAL D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 95 through 123 Processing helix chain 'D' and resid 125 through 164 removed outlier: 4.030A pdb=" N VAL D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLY D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 132 " --> pdb=" O ASN D 128 " (cutoff:3.500A) Proline residue: D 153 - end of helix Processing helix chain 'D' and resid 165 through 168 Processing helix chain 'D' and resid 177 through 214 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 242 through 287 removed outlier: 4.478A pdb=" N ASP D 264 " --> pdb=" O TRP D 260 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 339 removed outlier: 3.568A pdb=" N PHE D 298 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 387 removed outlier: 3.895A pdb=" N ILE D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL D 385 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'D' and resid 421 through 440 Processing helix chain 'D' and resid 443 through 450 removed outlier: 3.822A pdb=" N GLY D 450 " --> pdb=" O ASN D 446 " (cutoff:3.500A) 988 hydrogen bonds defined for protein. 2928 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: 10.09 Time building geometry restraints manager: 9.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13772 1.03 - 1.23: 41 1.23 - 1.42: 5787 1.42 - 1.61: 7840 1.61 - 1.81: 152 Bond restraints: 27592 Sorted by residual: bond pdb=" C3 BGC H 1 " pdb=" O3 BGC H 1 " ideal model delta sigma weight residual 1.408 1.492 -0.084 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C3 BGC E 1 " pdb=" O3 BGC E 1 " ideal model delta sigma weight residual 1.408 1.491 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C3 BGC F 1 " pdb=" O3 BGC F 1 " ideal model delta sigma weight residual 1.408 1.491 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C3 BGC G 1 " pdb=" O3 BGC G 1 " ideal model delta sigma weight residual 1.408 1.490 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C1 GLC G 2 " pdb=" O5 GLC G 2 " ideal model delta sigma weight residual 1.402 1.474 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 27587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 46800 1.10 - 2.20: 2780 2.20 - 3.30: 159 3.30 - 4.40: 65 4.40 - 5.50: 20 Bond angle restraints: 49824 Sorted by residual: angle pdb=" C TYR D 262 " pdb=" N MET D 263 " pdb=" CA MET D 263 " ideal model delta sigma weight residual 120.44 118.00 2.44 1.30e+00 5.92e-01 3.51e+00 angle pdb=" C TRP C 152 " pdb=" CA TRP C 152 " pdb=" CB TRP C 152 " ideal model delta sigma weight residual 112.76 109.33 3.43 1.86e+00 2.89e-01 3.40e+00 angle pdb=" C TYR B 262 " pdb=" N MET B 263 " pdb=" CA MET B 263 " ideal model delta sigma weight residual 120.44 118.05 2.39 1.30e+00 5.92e-01 3.39e+00 angle pdb=" C TRP B 152 " pdb=" CA TRP B 152 " pdb=" CB TRP B 152 " ideal model delta sigma weight residual 112.76 109.34 3.42 1.86e+00 2.89e-01 3.39e+00 angle pdb=" C TRP A 152 " pdb=" CA TRP A 152 " pdb=" CB TRP A 152 " ideal model delta sigma weight residual 112.76 109.34 3.42 1.86e+00 2.89e-01 3.38e+00 ... (remaining 49819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 11648 17.55 - 35.11: 1021 35.11 - 52.66: 322 52.66 - 70.21: 80 70.21 - 87.76: 9 Dihedral angle restraints: 13080 sinusoidal: 7076 harmonic: 6004 Sorted by residual: dihedral pdb=" CB MET D 98 " pdb=" CG MET D 98 " pdb=" SD MET D 98 " pdb=" CE MET D 98 " ideal model delta sinusoidal sigma weight residual -180.00 -120.50 -59.50 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET B 98 " pdb=" CG MET B 98 " pdb=" SD MET B 98 " pdb=" CE MET B 98 " ideal model delta sinusoidal sigma weight residual -180.00 -120.54 -59.46 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB ARG A 286 " pdb=" CG ARG A 286 " pdb=" CD ARG A 286 " pdb=" NE ARG A 286 " ideal model delta sinusoidal sigma weight residual -60.00 -119.46 59.46 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 13077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1508 0.027 - 0.055: 381 0.055 - 0.082: 214 0.082 - 0.109: 62 0.109 - 0.137: 15 Chirality restraints: 2180 Sorted by residual: chirality pdb=" C1 GLC E 2 " pdb=" O4 BGC E 1 " pdb=" C2 GLC E 2 " pdb=" O5 GLC E 2 " both_signs ideal model delta sigma weight residual False 2.40 2.38 0.02 2.00e-02 2.50e+03 1.21e+00 chirality pdb=" C1 GLC G 2 " pdb=" O4 BGC G 1 " pdb=" C2 GLC G 2 " pdb=" O5 GLC G 2 " both_signs ideal model delta sigma weight residual False 2.40 2.38 0.02 2.00e-02 2.50e+03 1.11e+00 chirality pdb=" CA ILE B 218 " pdb=" N ILE B 218 " pdb=" C ILE B 218 " pdb=" CB ILE B 218 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 2177 not shown) Planarity restraints: 3836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 142 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.08e+00 pdb=" C TYR B 142 " 0.030 2.00e-02 2.50e+03 pdb=" O TYR B 142 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL B 143 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 142 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C TYR C 142 " -0.030 2.00e-02 2.50e+03 pdb=" O TYR C 142 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 143 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 142 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C TYR D 142 " 0.030 2.00e-02 2.50e+03 pdb=" O TYR D 142 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL D 143 " -0.010 2.00e-02 2.50e+03 ... (remaining 3833 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 2173 2.21 - 2.81: 58534 2.81 - 3.41: 80688 3.41 - 4.00: 104783 4.00 - 4.60: 161104 Nonbonded interactions: 407282 Sorted by model distance: nonbonded pdb="HH22 ARG B 346 " pdb=" O GLN B 452 " model vdw 1.616 2.450 nonbonded pdb="HH22 ARG D 346 " pdb=" O GLN D 452 " model vdw 1.617 2.450 nonbonded pdb="HH22 ARG A 346 " pdb=" O GLN A 452 " model vdw 1.617 2.450 nonbonded pdb="HH22 ARG C 346 " pdb=" O GLN C 452 " model vdw 1.617 2.450 nonbonded pdb=" HH TYR A 208 " pdb=" OD1 ASN A 226 " model vdw 1.648 2.450 ... (remaining 407277 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: 0.12 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.470 Extract box with map and model: 1.140 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 57.870 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.090 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:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.004 0.084 13784 Z= 0.219 Angle : 0.546 5.497 18712 Z= 0.286 Chirality : 0.035 0.137 2180 Planarity : 0.004 0.033 2276 Dihedral : 15.877 87.765 5160 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.88 % Allowed : 16.64 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.54 (0.21), residues: 1620 helix: 2.29 (0.15), residues: 1192 sheet: None (None), residues: 0 loop : -0.03 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 152 HIS 0.001 0.000 HIS D 118 PHE 0.010 0.001 PHE B 66 TYR 0.011 0.001 TYR D 241 ARG 0.002 0.000 ARG B 82 Details of bonding type rmsd link_ALPHA1-4 : bond 0.05675 ( 4) link_ALPHA1-4 : angle 3.68477 ( 12) hydrogen bonds : bond 0.10592 ( 988) hydrogen bonds : angle 5.46274 ( 2928) covalent geometry : bond 0.00417 (13780) covalent geometry : angle 0.53804 (18700) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 211 time to evaluate : 1.981 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 224 average time/residue: 3.2201 time to fit residues: 778.9304 Evaluate side-chains 215 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 398 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 ASN B 441 GLN C 441 GLN D 253 ASN D 441 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.136342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.101551 restraints weight = 38443.171| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.34 r_work: 0.2847 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 13784 Z= 0.176 Angle : 0.515 5.090 18712 Z= 0.280 Chirality : 0.037 0.132 2180 Planarity : 0.004 0.034 2276 Dihedral : 5.152 47.181 2017 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.68 % Allowed : 16.51 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.99 (0.20), residues: 1620 helix: 2.75 (0.14), residues: 1172 sheet: None (None), residues: 0 loop : -0.16 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 355 HIS 0.003 0.001 HIS A 60 PHE 0.013 0.002 PHE D 66 TYR 0.013 0.002 TYR C 241 ARG 0.002 0.000 ARG A 180 Details of bonding type rmsd link_ALPHA1-4 : bond 0.00095 ( 4) link_ALPHA1-4 : angle 1.20959 ( 12) hydrogen bonds : bond 0.05245 ( 988) hydrogen bonds : angle 4.16093 ( 2928) covalent geometry : bond 0.00368 (13780) covalent geometry : angle 0.51431 (18700) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 199 time to evaluate : 2.018 Fit side-chains REVERT: A 214 MET cc_start: 0.6328 (ptp) cc_final: 0.6096 (ptp) REVERT: B 214 MET cc_start: 0.6336 (ptp) cc_final: 0.6103 (ptp) REVERT: C 214 MET cc_start: 0.6328 (ptp) cc_final: 0.6099 (ptp) REVERT: D 214 MET cc_start: 0.6233 (ptp) cc_final: 0.6015 (ptp) outliers start: 10 outliers final: 7 residues processed: 208 average time/residue: 3.2818 time to fit residues: 736.3624 Evaluate side-chains 200 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 193 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 123 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN B 253 ASN B 441 GLN C 441 GLN D 229 GLN D 253 ASN D 441 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.135308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.100668 restraints weight = 38601.299| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.34 r_work: 0.2835 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13784 Z= 0.173 Angle : 0.508 5.392 18712 Z= 0.276 Chirality : 0.037 0.135 2180 Planarity : 0.004 0.034 2276 Dihedral : 3.764 15.795 1988 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.68 % Allowed : 16.51 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.95 (0.20), residues: 1620 helix: 2.78 (0.14), residues: 1172 sheet: None (None), residues: 0 loop : -0.37 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 355 HIS 0.004 0.001 HIS B 60 PHE 0.014 0.002 PHE C 66 TYR 0.013 0.002 TYR D 241 ARG 0.004 0.000 ARG C 346 Details of bonding type rmsd link_ALPHA1-4 : bond 0.00107 ( 4) link_ALPHA1-4 : angle 1.34863 ( 12) hydrogen bonds : bond 0.05137 ( 988) hydrogen bonds : angle 4.10528 ( 2928) covalent geometry : bond 0.00366 (13780) covalent geometry : angle 0.50735 (18700) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 205 time to evaluate : 1.994 Fit side-chains REVERT: A 172 GLU cc_start: 0.8049 (pt0) cc_final: 0.7798 (pt0) REVERT: B 172 GLU cc_start: 0.8020 (pt0) cc_final: 0.7799 (pt0) REVERT: D 172 GLU cc_start: 0.8004 (pt0) cc_final: 0.7768 (pt0) outliers start: 10 outliers final: 8 residues processed: 211 average time/residue: 3.2019 time to fit residues: 730.1378 Evaluate side-chains 207 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 153 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 229 GLN B 253 ASN B 329 ASN B 441 GLN C 229 GLN C 329 ASN C 441 GLN D 229 GLN D 253 ASN D 329 ASN D 441 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.133358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.098583 restraints weight = 38721.585| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.35 r_work: 0.2803 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13784 Z= 0.245 Angle : 0.562 5.145 18712 Z= 0.307 Chirality : 0.039 0.137 2180 Planarity : 0.005 0.035 2276 Dihedral : 4.085 21.018 1988 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.70 % Allowed : 15.62 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.60 (0.20), residues: 1620 helix: 2.43 (0.14), residues: 1224 sheet: None (None), residues: 0 loop : -0.59 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 355 HIS 0.004 0.001 HIS C 60 PHE 0.018 0.002 PHE A 419 TYR 0.016 0.002 TYR A 276 ARG 0.004 0.001 ARG D 346 Details of bonding type rmsd link_ALPHA1-4 : bond 0.00302 ( 4) link_ALPHA1-4 : angle 1.44216 ( 12) hydrogen bonds : bond 0.05501 ( 988) hydrogen bonds : angle 4.20542 ( 2928) covalent geometry : bond 0.00536 (13780) covalent geometry : angle 0.56067 (18700) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 2.169 Fit side-chains REVERT: A 310 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8523 (mt-10) REVERT: C 172 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7773 (pt0) REVERT: C 310 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8480 (mt-10) REVERT: D 310 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8486 (mt-10) outliers start: 25 outliers final: 16 residues processed: 220 average time/residue: 3.1537 time to fit residues: 753.3947 Evaluate side-chains 208 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 398 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 129 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 229 GLN B 253 ASN B 441 GLN C 441 GLN D 229 GLN D 441 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.134888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.100544 restraints weight = 38463.864| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.32 r_work: 0.2832 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13784 Z= 0.160 Angle : 0.510 5.746 18712 Z= 0.276 Chirality : 0.036 0.135 2180 Planarity : 0.004 0.036 2276 Dihedral : 3.862 18.246 1988 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.36 % Allowed : 15.83 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.70 (0.20), residues: 1620 helix: 2.58 (0.14), residues: 1196 sheet: None (None), residues: 0 loop : -0.60 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 355 HIS 0.003 0.001 HIS C 60 PHE 0.013 0.002 PHE D 419 TYR 0.013 0.002 TYR C 241 ARG 0.003 0.000 ARG B 346 Details of bonding type rmsd link_ALPHA1-4 : bond 0.00092 ( 4) link_ALPHA1-4 : angle 1.22312 ( 12) hydrogen bonds : bond 0.05024 ( 988) hydrogen bonds : angle 4.08941 ( 2928) covalent geometry : bond 0.00329 (13780) covalent geometry : angle 0.50904 (18700) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 2.035 Fit side-chains REVERT: A 249 ILE cc_start: 0.8300 (mm) cc_final: 0.7930 (mm) REVERT: A 253 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8128 (m-40) REVERT: C 172 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7713 (pt0) REVERT: C 249 ILE cc_start: 0.8292 (mm) cc_final: 0.7913 (mm) REVERT: C 253 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.8122 (m-40) outliers start: 20 outliers final: 9 residues processed: 217 average time/residue: 3.3694 time to fit residues: 791.5990 Evaluate side-chains 208 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 6 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 253 ASN C 229 GLN D 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.132882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.098452 restraints weight = 38660.078| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.33 r_work: 0.2801 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 13784 Z= 0.258 Angle : 0.568 5.287 18712 Z= 0.311 Chirality : 0.040 0.130 2180 Planarity : 0.005 0.037 2276 Dihedral : 4.125 20.617 1988 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.90 % Allowed : 14.88 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.59 (0.20), residues: 1620 helix: 2.48 (0.14), residues: 1196 sheet: None (None), residues: 0 loop : -0.59 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 355 HIS 0.004 0.001 HIS B 197 PHE 0.019 0.002 PHE A 419 TYR 0.015 0.002 TYR D 276 ARG 0.003 0.001 ARG D 284 Details of bonding type rmsd link_ALPHA1-4 : bond 0.00310 ( 4) link_ALPHA1-4 : angle 1.51407 ( 12) hydrogen bonds : bond 0.05509 ( 988) hydrogen bonds : angle 4.21312 ( 2928) covalent geometry : bond 0.00570 (13780) covalent geometry : angle 0.56702 (18700) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 2.056 Fit side-chains REVERT: A 172 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7710 (pt0) REVERT: A 249 ILE cc_start: 0.8324 (mm) cc_final: 0.7970 (mm) REVERT: A 253 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8247 (m-40) REVERT: A 310 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8497 (mt-10) REVERT: B 172 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7723 (pt0) REVERT: C 172 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7697 (pt0) REVERT: C 249 ILE cc_start: 0.8335 (mm) cc_final: 0.7956 (mm) REVERT: C 253 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8247 (m-40) REVERT: D 172 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7689 (pt0) REVERT: D 310 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8506 (mt-10) outliers start: 28 outliers final: 16 residues processed: 216 average time/residue: 3.2082 time to fit residues: 750.1144 Evaluate side-chains 221 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 398 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.133417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.099026 restraints weight = 38416.512| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.32 r_work: 0.2811 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 13784 Z= 0.216 Angle : 0.543 5.672 18712 Z= 0.296 Chirality : 0.038 0.130 2180 Planarity : 0.005 0.037 2276 Dihedral : 4.073 19.199 1988 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.77 % Allowed : 15.22 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.63 (0.20), residues: 1620 helix: 2.51 (0.14), residues: 1196 sheet: None (None), residues: 0 loop : -0.58 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 355 HIS 0.004 0.001 HIS D 60 PHE 0.017 0.002 PHE A 419 TYR 0.015 0.002 TYR A 276 ARG 0.003 0.000 ARG C 180 Details of bonding type rmsd link_ALPHA1-4 : bond 0.00139 ( 4) link_ALPHA1-4 : angle 1.34919 ( 12) hydrogen bonds : bond 0.05308 ( 988) hydrogen bonds : angle 4.18089 ( 2928) covalent geometry : bond 0.00466 (13780) covalent geometry : angle 0.54226 (18700) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 2.000 Fit side-chains REVERT: A 172 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7716 (pt0) REVERT: A 249 ILE cc_start: 0.8332 (mm) cc_final: 0.8072 (mm) REVERT: A 253 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8169 (m-40) REVERT: B 172 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: C 172 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: C 249 ILE cc_start: 0.8340 (mm) cc_final: 0.7961 (mm) REVERT: C 253 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8175 (m-40) REVERT: D 172 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7687 (pt0) outliers start: 26 outliers final: 16 residues processed: 220 average time/residue: 3.3713 time to fit residues: 798.7300 Evaluate side-chains 219 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 16 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 329 ASN B 229 GLN C 229 GLN D 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.133008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.098754 restraints weight = 38378.975| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.31 r_work: 0.2808 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 13784 Z= 0.231 Angle : 0.551 5.906 18712 Z= 0.301 Chirality : 0.039 0.128 2180 Planarity : 0.005 0.038 2276 Dihedral : 4.113 18.529 1988 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.04 % Allowed : 15.29 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.57 (0.20), residues: 1620 helix: 2.46 (0.14), residues: 1196 sheet: None (None), residues: 0 loop : -0.57 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 355 HIS 0.004 0.001 HIS A 60 PHE 0.018 0.002 PHE A 419 TYR 0.015 0.002 TYR D 276 ARG 0.003 0.001 ARG D 346 Details of bonding type rmsd link_ALPHA1-4 : bond 0.00155 ( 4) link_ALPHA1-4 : angle 1.37435 ( 12) hydrogen bonds : bond 0.05369 ( 988) hydrogen bonds : angle 4.20159 ( 2928) covalent geometry : bond 0.00505 (13780) covalent geometry : angle 0.55054 (18700) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 2.079 Fit side-chains REVERT: A 249 ILE cc_start: 0.8369 (mm) cc_final: 0.8103 (mm) REVERT: A 253 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8181 (m-40) REVERT: A 310 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8495 (mt-10) REVERT: C 172 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7639 (pt0) REVERT: C 249 ILE cc_start: 0.8373 (mm) cc_final: 0.8098 (mm) REVERT: C 253 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8183 (m-40) outliers start: 30 outliers final: 20 residues processed: 221 average time/residue: 3.0531 time to fit residues: 732.5672 Evaluate side-chains 219 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 398 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 150 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.134210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.099689 restraints weight = 38455.325| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.34 r_work: 0.2823 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13784 Z= 0.161 Angle : 0.518 6.292 18712 Z= 0.281 Chirality : 0.037 0.134 2180 Planarity : 0.004 0.037 2276 Dihedral : 3.950 15.746 1988 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.15 % Allowed : 16.30 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.74 (0.20), residues: 1620 helix: 2.60 (0.14), residues: 1196 sheet: None (None), residues: 0 loop : -0.55 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 355 HIS 0.003 0.001 HIS B 60 PHE 0.014 0.002 PHE A 419 TYR 0.013 0.002 TYR A 276 ARG 0.002 0.000 ARG D 180 Details of bonding type rmsd link_ALPHA1-4 : bond 0.00067 ( 4) link_ALPHA1-4 : angle 1.18735 ( 12) hydrogen bonds : bond 0.05025 ( 988) hydrogen bonds : angle 4.14118 ( 2928) covalent geometry : bond 0.00331 (13780) covalent geometry : angle 0.51755 (18700) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 2.052 Fit side-chains REVERT: A 172 GLU cc_start: 0.8114 (pm20) cc_final: 0.7711 (pt0) REVERT: A 253 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.8144 (m-40) REVERT: B 172 GLU cc_start: 0.8108 (pm20) cc_final: 0.7711 (pt0) REVERT: C 172 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7662 (pt0) REVERT: C 249 ILE cc_start: 0.8306 (mm) cc_final: 0.8016 (mm) REVERT: C 253 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8147 (m-40) REVERT: D 172 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7735 (pt0) outliers start: 17 outliers final: 12 residues processed: 209 average time/residue: 3.2155 time to fit residues: 729.0230 Evaluate side-chains 208 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 150 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 159 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN D 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.136230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.101802 restraints weight = 38327.803| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.33 r_work: 0.2978 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13784 Z= 0.123 Angle : 0.489 6.435 18712 Z= 0.262 Chirality : 0.036 0.137 2180 Planarity : 0.004 0.037 2276 Dihedral : 3.716 15.142 1988 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.68 % Allowed : 16.78 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.85 (0.20), residues: 1620 helix: 2.69 (0.14), residues: 1212 sheet: None (None), residues: 0 loop : -0.67 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 355 HIS 0.002 0.001 HIS D 118 PHE 0.010 0.001 PHE A 66 TYR 0.012 0.002 TYR A 232 ARG 0.002 0.000 ARG C 161 Details of bonding type rmsd link_ALPHA1-4 : bond 0.00080 ( 4) link_ALPHA1-4 : angle 1.03480 ( 12) hydrogen bonds : bond 0.04665 ( 988) hydrogen bonds : angle 4.05135 ( 2928) covalent geometry : bond 0.00239 (13780) covalent geometry : angle 0.48873 (18700) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 2.029 Fit side-chains REVERT: A 229 GLN cc_start: 0.7915 (mt0) cc_final: 0.7692 (mt0) REVERT: A 249 ILE cc_start: 0.8363 (mm) cc_final: 0.8018 (mm) REVERT: A 253 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8150 (m-40) REVERT: C 172 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7663 (pt0) REVERT: C 249 ILE cc_start: 0.8433 (mm) cc_final: 0.8185 (mm) REVERT: C 253 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8153 (m-40) REVERT: D 172 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7729 (pt0) outliers start: 10 outliers final: 6 residues processed: 213 average time/residue: 3.1624 time to fit residues: 729.1420 Evaluate side-chains 207 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 172 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 157 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 154 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 125 optimal weight: 0.0270 chunk 74 optimal weight: 4.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN C 71 GLN D 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.136610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.102105 restraints weight = 38379.484| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.33 r_work: 0.2998 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 13784 Z= 0.124 Angle : 0.491 6.638 18712 Z= 0.264 Chirality : 0.036 0.134 2180 Planarity : 0.004 0.036 2276 Dihedral : 3.642 15.059 1988 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.54 % Allowed : 17.60 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.91 (0.20), residues: 1620 helix: 2.77 (0.14), residues: 1188 sheet: None (None), residues: 0 loop : -0.58 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 355 HIS 0.002 0.001 HIS D 60 PHE 0.011 0.001 PHE B 66 TYR 0.013 0.001 TYR B 232 ARG 0.002 0.000 ARG C 180 Details of bonding type rmsd link_ALPHA1-4 : bond 0.00103 ( 4) link_ALPHA1-4 : angle 1.03070 ( 12) hydrogen bonds : bond 0.04646 ( 988) hydrogen bonds : angle 4.03524 ( 2928) covalent geometry : bond 0.00242 (13780) covalent geometry : angle 0.49033 (18700) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19773.17 seconds wall clock time: 338 minutes 36.11 seconds (20316.11 seconds total)