Starting phenix.real_space_refine on Mon Aug 25 09:18:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jmi_36422/08_2025/8jmi_36422_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jmi_36422/08_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_36422/08_2025/8jmi_36422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jmi_36422/08_2025/8jmi_36422.map" model { file = "/net/cci-nas-00/data/ceres_data/8jmi_36422/08_2025/8jmi_36422_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jmi_36422/08_2025/8jmi_36422_neut_trim.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.30, per 1000 atoms: 0.19 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: 2.60 Conformation dependent library (CDL) restraints added in 731.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.56 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: 5.81 Time building geometry restraints manager: 3.55 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.890 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: 0.180 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.360 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.210 ------------------------------------------------------------------------------- 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 : 5.93 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG B 82 TYR 0.011 0.001 TYR D 241 PHE 0.010 0.001 PHE B 66 TRP 0.011 0.001 TRP B 152 HIS 0.001 0.000 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00417 (13780) covalent geometry : angle 0.53804 (18700) hydrogen bonds : bond 0.10592 ( 988) hydrogen bonds : angle 5.46274 ( 2928) link_ALPHA1-4 : bond 0.05675 ( 4) link_ALPHA1-4 : angle 3.68477 ( 12) *********************** 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 : 0.625 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 224 average time/residue: 1.7798 time to fit residues: 428.8505 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 : 0.777 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.3980 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.136219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.101622 restraints weight = 38684.395| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.32 r_work: 0.2998 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.0598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 13784 Z= 0.183 Angle : 0.521 5.105 18712 Z= 0.284 Chirality : 0.037 0.130 2180 Planarity : 0.004 0.034 2276 Dihedral : 5.169 47.167 2017 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.97 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.97 (0.20), residues: 1620 helix: 2.74 (0.14), residues: 1172 sheet: None (None), residues: 0 loop : -0.17 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 61 TYR 0.013 0.002 TYR A 241 PHE 0.013 0.002 PHE D 419 TRP 0.012 0.002 TRP B 355 HIS 0.003 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00384 (13780) covalent geometry : angle 0.52031 (18700) hydrogen bonds : bond 0.05282 ( 988) hydrogen bonds : angle 4.16281 ( 2928) link_ALPHA1-4 : bond 0.00204 ( 4) link_ALPHA1-4 : angle 1.26533 ( 12) *********************** 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 : 0.716 Fit side-chains REVERT: A 214 MET cc_start: 0.6296 (ptp) cc_final: 0.6078 (ptp) REVERT: B 214 MET cc_start: 0.6298 (ptp) cc_final: 0.6077 (ptp) REVERT: C 214 MET cc_start: 0.6283 (ptp) cc_final: 0.6067 (ptp) REVERT: D 214 MET cc_start: 0.6259 (ptp) cc_final: 0.6048 (ptp) outliers start: 10 outliers final: 7 residues processed: 208 average time/residue: 1.5413 time to fit residues: 345.1447 Evaluate side-chains 198 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 191 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 130 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 157 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 96 optimal weight: 0.0170 chunk 120 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.0624 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.135254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.100797 restraints weight = 38687.853| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.32 r_work: 0.2835 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0835 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= 0.177 Angle : 0.510 5.422 18712 Z= 0.278 Chirality : 0.037 0.133 2180 Planarity : 0.004 0.033 2276 Dihedral : 3.777 15.682 1988 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.48 % Allowed : 16.92 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.20), residues: 1620 helix: 2.77 (0.14), residues: 1172 sheet: None (None), residues: 0 loop : -0.38 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.013 0.002 TYR D 241 PHE 0.014 0.002 PHE D 66 TRP 0.013 0.002 TRP D 355 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00375 (13780) covalent geometry : angle 0.50924 (18700) hydrogen bonds : bond 0.05155 ( 988) hydrogen bonds : angle 4.11964 ( 2928) link_ALPHA1-4 : bond 0.00155 ( 4) link_ALPHA1-4 : angle 1.37360 ( 12) *********************** 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 210 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 203 time to evaluate : 0.750 Fit side-chains REVERT: B 172 GLU cc_start: 0.8032 (pt0) cc_final: 0.7802 (pt0) REVERT: D 172 GLU cc_start: 0.8002 (pt0) cc_final: 0.7758 (pt0) outliers start: 7 outliers final: 7 residues processed: 207 average time/residue: 1.5410 time to fit residues: 344.3406 Evaluate side-chains 201 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 194 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 108 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 104 optimal weight: 0.0970 chunk 150 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 441 GLN C 441 GLN D 441 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.136012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.101643 restraints weight = 38516.115| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.32 r_work: 0.2849 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13784 Z= 0.143 Angle : 0.488 5.179 18712 Z= 0.264 Chirality : 0.036 0.138 2180 Planarity : 0.004 0.033 2276 Dihedral : 3.695 15.694 1988 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.34 % Allowed : 17.26 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.99 (0.20), residues: 1620 helix: 2.83 (0.14), residues: 1172 sheet: None (None), residues: 0 loop : -0.40 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 346 TYR 0.013 0.002 TYR C 241 PHE 0.012 0.001 PHE D 66 TRP 0.011 0.002 TRP B 355 HIS 0.003 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00289 (13780) covalent geometry : angle 0.48746 (18700) hydrogen bonds : bond 0.04890 ( 988) hydrogen bonds : angle 4.03609 ( 2928) link_ALPHA1-4 : bond 0.00067 ( 4) link_ALPHA1-4 : angle 1.10495 ( 12) *********************** 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 210 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 205 time to evaluate : 0.741 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 205 average time/residue: 1.5283 time to fit residues: 337.5548 Evaluate side-chains 194 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 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 71 GLN A 229 GLN B 229 GLN C 229 GLN D 71 GLN D 229 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.134054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.099545 restraints weight = 38462.464| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.32 r_work: 0.2816 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 13784 Z= 0.219 Angle : 0.540 5.133 18712 Z= 0.296 Chirality : 0.038 0.135 2180 Planarity : 0.004 0.035 2276 Dihedral : 3.942 18.494 1988 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.36 % Allowed : 16.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.20), residues: 1620 helix: 2.53 (0.14), residues: 1196 sheet: None (None), residues: 0 loop : -0.60 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 284 TYR 0.015 0.002 TYR B 276 PHE 0.015 0.002 PHE B 419 TRP 0.014 0.002 TRP D 355 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00476 (13780) covalent geometry : angle 0.53954 (18700) hydrogen bonds : bond 0.05327 ( 988) hydrogen bonds : angle 4.12829 ( 2928) link_ALPHA1-4 : bond 0.00096 ( 4) link_ALPHA1-4 : angle 1.35458 ( 12) *********************** 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 225 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 310 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8507 (mt-10) REVERT: D 310 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8495 (mt-10) outliers start: 20 outliers final: 13 residues processed: 215 average time/residue: 1.5930 time to fit residues: 367.7172 Evaluate side-chains 209 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 368 VAL Chi-restraints excluded: chain A residue 391 SER 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 C residue 75 ILE 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 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 132 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 C 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.134828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.100274 restraints weight = 38429.087| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.34 r_work: 0.2829 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1165 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= 0.164 Angle : 0.506 5.592 18712 Z= 0.274 Chirality : 0.036 0.137 2180 Planarity : 0.004 0.035 2276 Dihedral : 3.867 16.988 1988 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.49 % Allowed : 15.42 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.73 (0.20), residues: 1620 helix: 2.60 (0.14), residues: 1196 sheet: None (None), residues: 0 loop : -0.61 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 180 TYR 0.013 0.002 TYR C 241 PHE 0.013 0.002 PHE B 419 TRP 0.012 0.002 TRP B 355 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00340 (13780) covalent geometry : angle 0.50507 (18700) hydrogen bonds : bond 0.05017 ( 988) hydrogen bonds : angle 4.07004 ( 2928) link_ALPHA1-4 : bond 0.00113 ( 4) link_ALPHA1-4 : angle 1.24336 ( 12) *********************** 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 227 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.726 Fit side-chains REVERT: B 253 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8131 (m-40) REVERT: C 172 GLU cc_start: 0.8088 (pm20) cc_final: 0.7664 (pt0) outliers start: 22 outliers final: 13 residues processed: 216 average time/residue: 1.7638 time to fit residues: 410.2225 Evaluate side-chains 211 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 368 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 253 ASN 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 368 VAL Chi-restraints excluded: chain C residue 391 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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 C 229 GLN C 253 ASN D 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.135063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.100775 restraints weight = 38470.580| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.32 r_work: 0.2836 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13784 Z= 0.160 Angle : 0.501 5.598 18712 Z= 0.271 Chirality : 0.036 0.136 2180 Planarity : 0.004 0.035 2276 Dihedral : 3.827 15.726 1988 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.70 % Allowed : 15.35 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.87 (0.20), residues: 1620 helix: 2.78 (0.14), residues: 1168 sheet: None (None), residues: 0 loop : -0.56 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 346 TYR 0.013 0.002 TYR C 241 PHE 0.013 0.001 PHE B 419 TRP 0.012 0.002 TRP D 355 HIS 0.003 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00331 (13780) covalent geometry : angle 0.50015 (18700) hydrogen bonds : bond 0.04970 ( 988) hydrogen bonds : angle 4.04656 ( 2928) link_ALPHA1-4 : bond 0.00089 ( 4) link_ALPHA1-4 : angle 1.25364 ( 12) *********************** 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 227 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.890 Fit side-chains REVERT: A 172 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7683 (pm20) REVERT: B 172 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7660 (pt0) REVERT: C 172 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7703 (pm20) outliers start: 25 outliers final: 16 residues processed: 215 average time/residue: 1.7784 time to fit residues: 412.2677 Evaluate side-chains 220 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 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 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 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 159 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.134008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.099651 restraints weight = 38418.589| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.32 r_work: 0.2820 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1346 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= 0.207 Angle : 0.531 6.091 18712 Z= 0.289 Chirality : 0.038 0.133 2180 Planarity : 0.004 0.035 2276 Dihedral : 3.972 16.972 1988 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.49 % Allowed : 15.42 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.20), residues: 1620 helix: 2.52 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -0.64 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 180 TYR 0.014 0.002 TYR A 276 PHE 0.014 0.002 PHE D 419 TRP 0.013 0.002 TRP D 355 HIS 0.004 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00445 (13780) covalent geometry : angle 0.53027 (18700) hydrogen bonds : bond 0.05211 ( 988) hydrogen bonds : angle 4.11716 ( 2928) link_ALPHA1-4 : bond 0.00200 ( 4) link_ALPHA1-4 : angle 1.36639 ( 12) *********************** 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: 22 poor density : 207 time to evaluate : 0.749 Fit side-chains REVERT: B 172 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: D 172 GLU cc_start: 0.8097 (pm20) cc_final: 0.7683 (pt0) outliers start: 22 outliers final: 15 residues processed: 219 average time/residue: 1.8309 time to fit residues: 431.2778 Evaluate side-chains 215 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 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 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 368 VAL Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 15 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 253 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 = 0.3444 r_free = 0.3444 target = 0.134735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.100240 restraints weight = 38543.608| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.34 r_work: 0.2830 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1338 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= 0.162 Angle : 0.510 6.061 18712 Z= 0.276 Chirality : 0.036 0.134 2180 Planarity : 0.004 0.035 2276 Dihedral : 3.861 15.349 1988 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.36 % Allowed : 15.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.20), residues: 1620 helix: 2.70 (0.14), residues: 1196 sheet: None (None), residues: 0 loop : -0.51 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 346 TYR 0.013 0.002 TYR A 276 PHE 0.013 0.002 PHE D 419 TRP 0.012 0.002 TRP B 355 HIS 0.003 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00333 (13780) covalent geometry : angle 0.50966 (18700) hydrogen bonds : bond 0.04988 ( 988) hydrogen bonds : angle 4.08039 ( 2928) link_ALPHA1-4 : bond 0.00079 ( 4) link_ALPHA1-4 : angle 1.22178 ( 12) *********************** 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 225 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8092 (pm20) cc_final: 0.7713 (pm20) REVERT: B 172 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7628 (pm20) REVERT: D 172 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7691 (pm20) outliers start: 20 outliers final: 18 residues processed: 219 average time/residue: 1.5748 time to fit residues: 370.3429 Evaluate side-chains 222 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 161 ARG 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 161 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 70 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.136307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.101924 restraints weight = 38346.980| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.34 r_work: 0.2857 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 13784 Z= 0.123 Angle : 0.485 6.478 18712 Z= 0.261 Chirality : 0.035 0.134 2180 Planarity : 0.004 0.035 2276 Dihedral : 3.693 15.015 1988 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.82 % Allowed : 16.44 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.90 (0.20), residues: 1620 helix: 2.77 (0.14), residues: 1188 sheet: None (None), residues: 0 loop : -0.61 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.012 0.001 TYR A 232 PHE 0.010 0.001 PHE A 66 TRP 0.011 0.002 TRP B 355 HIS 0.002 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00239 (13780) covalent geometry : angle 0.48487 (18700) hydrogen bonds : bond 0.04700 ( 988) hydrogen bonds : angle 4.02408 ( 2928) link_ALPHA1-4 : bond 0.00048 ( 4) link_ALPHA1-4 : angle 1.03997 ( 12) ********************** 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 221 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 209 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8040 (pm20) cc_final: 0.7658 (pm20) REVERT: B 172 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: C 172 GLU cc_start: 0.8004 (pm20) cc_final: 0.7583 (pm20) outliers start: 12 outliers final: 10 residues processed: 219 average time/residue: 1.6457 time to fit residues: 388.4391 Evaluate side-chains 214 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 161 ARG Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 0.0870 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN B 71 GLN C 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.135383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.101100 restraints weight = 38281.408| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.32 r_work: 0.2972 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13784 Z= 0.162 Angle : 0.506 6.287 18712 Z= 0.273 Chirality : 0.036 0.133 2180 Planarity : 0.004 0.034 2276 Dihedral : 3.765 15.171 1988 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.75 % Allowed : 16.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.97 (0.20), residues: 1620 helix: 2.77 (0.14), residues: 1196 sheet: None (None), residues: 0 loop : -0.49 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 346 TYR 0.013 0.002 TYR B 232 PHE 0.013 0.002 PHE D 419 TRP 0.011 0.002 TRP D 355 HIS 0.003 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00337 (13780) covalent geometry : angle 0.50511 (18700) hydrogen bonds : bond 0.04917 ( 988) hydrogen bonds : angle 4.05708 ( 2928) link_ALPHA1-4 : bond 0.00063 ( 4) link_ALPHA1-4 : angle 1.19927 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10093.11 seconds wall clock time: 171 minutes 39.72 seconds (10299.72 seconds total)