Starting phenix.real_space_refine on Fri Sep 11 12:04:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pqr_20452/09_2026/6pqr_20452.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqr_20452/09_2026/6pqr_20452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pqr_20452/09_2026/6pqr_20452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqr_20452/09_2026/6pqr_20452.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pqr_20452/09_2026/6pqr_20452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqr_20452/09_2026/6pqr_20452.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6pqr_20452/09_2026/6pqr_20452.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pqr_20452/09_2026/6pqr_20452.cif" } resolution = 3.4 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= 0.004 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: 8 Type Number sf(0) Gaussians K 2 8.98 5 Zn 2 6.06 5 P 88 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 5612 2.51 5 N 1592 2.21 5 O 1934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9266 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3728 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 450} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 456 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "C" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 446 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 3728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3728 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 450} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 456 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "F" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 446 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 1, ' MG': 1, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 1, ' MG': 1, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1629 SG CYS A 240 77.598 110.856 39.273 1.00166.71 S ATOM 1655 SG CYS A 243 80.541 111.292 41.321 1.00170.90 S ATOM 6259 SG CYS D 240 25.377 15.136 39.255 1.00167.58 S ATOM 6285 SG CYS D 243 22.435 14.693 41.303 1.00171.67 S Time building chain proxies: 2.16, per 1000 atoms: 0.23 Number of scatterers: 9266 At special positions: 0 Unit cell: (103.95, 127.05, 91.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 K 2 19.00 S 34 16.00 P 88 15.00 Mg 2 11.99 O 1934 8.00 N 1592 7.00 C 5612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 413 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 408 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 243 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 240 " pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" NE2 HIS D 413 " pdb="ZN ZN D 602 " - pdb=" NE2 HIS D 408 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 243 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 240 " Number of angles added : 4 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 51.7% alpha, 15.8% beta 34 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.619A pdb=" N LEU A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 53 removed outlier: 3.621A pdb=" N THR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.618A pdb=" N GLN A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 105 Processing helix chain 'A' and resid 171 through 175 removed outlier: 4.069A pdb=" N TYR A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 202 removed outlier: 3.547A pdb=" N VAL A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 231 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 276 through 289 removed outlier: 3.885A pdb=" N MET A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 321 Processing helix chain 'A' and resid 337 through 347 removed outlier: 4.507A pdb=" N ARG A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 358 through 373 removed outlier: 3.621A pdb=" N ILE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 396 removed outlier: 3.522A pdb=" N GLU A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.585A pdb=" N LEU A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.868A pdb=" N ILE A 417 " --> pdb=" O HIS A 413 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 447 Processing helix chain 'A' and resid 453 through 468 removed outlier: 3.735A pdb=" N ILE A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 494 removed outlier: 3.797A pdb=" N VAL A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 489 through 494' Processing helix chain 'D' and resid 25 through 36 removed outlier: 3.619A pdb=" N LEU D 30 " --> pdb=" O PRO D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 53 removed outlier: 3.623A pdb=" N THR D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 71 removed outlier: 3.612A pdb=" N GLN D 71 " --> pdb=" O LYS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 105 Processing helix chain 'D' and resid 171 through 175 removed outlier: 4.070A pdb=" N TYR D 174 " --> pdb=" O SER D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.547A pdb=" N VAL D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 196 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 231 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 276 through 289 removed outlier: 3.884A pdb=" N MET D 280 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS D 282 " --> pdb=" O ASN D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 321 Processing helix chain 'D' and resid 337 through 347 removed outlier: 4.507A pdb=" N ARG D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE D 347 " --> pdb=" O ARG D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 356 Processing helix chain 'D' and resid 358 through 373 removed outlier: 3.620A pdb=" N ILE D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 396 removed outlier: 3.522A pdb=" N GLU D 385 " --> pdb=" O PRO D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 413 removed outlier: 3.585A pdb=" N LEU D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 421 removed outlier: 3.868A pdb=" N ILE D 417 " --> pdb=" O HIS D 413 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE D 418 " --> pdb=" O GLY D 414 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA D 419 " --> pdb=" O GLY D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 447 Processing helix chain 'D' and resid 453 through 468 removed outlier: 3.734A pdb=" N ILE D 467 " --> pdb=" O ASN D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 494 removed outlier: 3.796A pdb=" N VAL D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU D 494 " --> pdb=" O LYS D 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 489 through 494' Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.228A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU A 151 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 179 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU A 154 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL A 165 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 156 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.228A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU A 151 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 179 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE A 147 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA A 127 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR A 149 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP A 125 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU A 151 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLY A 123 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS A 121 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N LEU A 116 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 11.105A pdb=" N LEU A 218 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N LEU A 118 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 11.154A pdb=" N MET A 220 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 10.749A pdb=" N SER A 120 " --> pdb=" O MET A 220 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N MET A 222 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP A 122 " --> pdb=" O MET A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 378 removed outlier: 4.261A pdb=" N ILE A 377 " --> pdb=" O GLN A 497 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 79 through 81 removed outlier: 6.228A pdb=" N VAL D 178 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU D 151 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 179 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU D 154 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL D 165 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU D 156 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 79 through 81 removed outlier: 6.228A pdb=" N VAL D 178 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU D 151 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 179 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE D 147 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ALA D 127 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR D 149 " --> pdb=" O ASP D 125 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP D 125 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU D 151 " --> pdb=" O GLY D 123 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY D 123 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LYS D 121 " --> pdb=" O PRO D 153 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N LEU D 116 " --> pdb=" O HIS D 216 " (cutoff:3.500A) removed outlier: 11.105A pdb=" N LEU D 218 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N LEU D 118 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N MET D 220 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 10.751A pdb=" N SER D 120 " --> pdb=" O MET D 220 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N MET D 222 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP D 122 " --> pdb=" O MET D 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 377 through 378 removed outlier: 4.261A pdb=" N ILE D 377 " --> pdb=" O GLN D 497 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 86 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2078 1.33 - 1.45: 2347 1.45 - 1.57: 4965 1.57 - 1.69: 172 1.69 - 1.81: 52 Bond restraints: 9614 Sorted by residual: bond pdb=" C3' DG F 16 " pdb=" O3' DG F 16 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.40e+01 bond pdb=" C3' DG C 16 " pdb=" O3' DG C 16 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.39e+01 bond pdb=" C3' DG B 24 " pdb=" O3' DG B 24 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.30e+01 bond pdb=" C3' DG E 23 " pdb=" O3' DG E 23 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.30e+01 bond pdb=" C3' DG E 24 " pdb=" O3' DG E 24 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.27e+01 ... (remaining 9609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 11896 1.37 - 2.74: 1273 2.74 - 4.11: 137 4.11 - 5.48: 40 5.48 - 6.84: 8 Bond angle restraints: 13354 Sorted by residual: angle pdb=" O4' DA B 25 " pdb=" C4' DA B 25 " pdb=" C3' DA B 25 " ideal model delta sigma weight residual 106.00 102.62 3.38 6.00e-01 2.78e+00 3.18e+01 angle pdb=" O4' DA E 25 " pdb=" C4' DA E 25 " pdb=" C3' DA E 25 " ideal model delta sigma weight residual 106.00 102.62 3.38 6.00e-01 2.78e+00 3.17e+01 angle pdb=" N3 DT F 4 " pdb=" C4 DT F 4 " pdb=" O4 DT F 4 " ideal model delta sigma weight residual 119.90 122.77 -2.87 6.00e-01 2.78e+00 2.28e+01 angle pdb=" N3 DT C 4 " pdb=" C4 DT C 4 " pdb=" O4 DT C 4 " ideal model delta sigma weight residual 119.90 122.73 -2.83 6.00e-01 2.78e+00 2.23e+01 angle pdb=" O4 DT C 4 " pdb=" C4 DT C 4 " pdb=" C5 DT C 4 " ideal model delta sigma weight residual 124.90 121.80 3.10 7.00e-01 2.04e+00 1.96e+01 ... (remaining 13349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 4336 16.84 - 33.68: 716 33.68 - 50.52: 394 50.52 - 67.37: 154 67.37 - 84.21: 14 Dihedral angle restraints: 5614 sinusoidal: 2862 harmonic: 2752 Sorted by residual: dihedral pdb=" CA ASP D 326 " pdb=" C ASP D 326 " pdb=" N ILE D 327 " pdb=" CA ILE D 327 " ideal model delta harmonic sigma weight residual -180.00 -150.80 -29.20 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA ASP A 326 " pdb=" C ASP A 326 " pdb=" N ILE A 327 " pdb=" CA ILE A 327 " ideal model delta harmonic sigma weight residual -180.00 -150.83 -29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ALA A 234 " pdb=" C ALA A 234 " pdb=" N LYS A 235 " pdb=" CA LYS A 235 " ideal model delta harmonic sigma weight residual -180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 5611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 831 0.037 - 0.075: 470 0.075 - 0.112: 158 0.112 - 0.149: 46 0.149 - 0.186: 17 Chirality restraints: 1522 Sorted by residual: chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CB ILE D 105 " pdb=" CA ILE D 105 " pdb=" CG1 ILE D 105 " pdb=" CG2 ILE D 105 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" C3' DG E 23 " pdb=" C4' DG E 23 " pdb=" O3' DG E 23 " pdb=" C2' DG E 23 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.15e-01 ... (remaining 1519 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 450 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C ARG D 450 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG D 450 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS D 451 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 450 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C ARG A 450 " 0.033 2.00e-02 2.50e+03 pdb=" O ARG A 450 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 451 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA B 31 " -0.019 2.00e-02 2.50e+03 8.23e-03 1.86e+00 pdb=" N9 DA B 31 " 0.016 2.00e-02 2.50e+03 pdb=" C8 DA B 31 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA B 31 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA B 31 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA B 31 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA B 31 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA B 31 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA B 31 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA B 31 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA B 31 " 0.007 2.00e-02 2.50e+03 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.69: 462 2.69 - 3.30: 10606 3.30 - 3.92: 18688 3.92 - 4.53: 24093 4.53 - 5.14: 36038 Nonbonded interactions: 89887 Sorted by model distance: nonbonded pdb=" OD1 ASP A 125 " pdb="MG MG A 601 " model vdw 2.081 2.170 nonbonded pdb=" OD1 ASP D 125 " pdb="MG MG D 601 " model vdw 2.081 2.170 nonbonded pdb=" OD2 ASP A 224 " pdb="MG MG A 601 " model vdw 2.098 2.170 nonbonded pdb=" OD2 ASP D 224 " pdb="MG MG D 601 " model vdw 2.098 2.170 nonbonded pdb=" OG1 THR D 186 " pdb=" OD1 ASP D 188 " model vdw 2.201 3.040 ... (remaining 89882 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.240 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 9622 Z= 0.627 Angle : 0.916 13.236 13358 Z= 0.647 Chirality : 0.053 0.186 1522 Planarity : 0.004 0.033 1380 Dihedral : 22.102 84.207 3822 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.24 % Allowed : 11.59 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -3.38 (0.23), residues: 920 helix: -2.20 (0.19), residues: 452 sheet: -0.96 (0.57), residues: 60 loop : -2.38 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 450 TYR 0.011 0.002 TYR A 394 PHE 0.023 0.002 PHE A 102 TRP 0.016 0.003 TRP A 400 HIS 0.008 0.002 HIS A 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00933 / 0.63 ( 9614) covalent geometry : angle 0.89871 / 0.65 (13354) hydrogen bonds : bond 0.14442 / 9.01 ( 420) hydrogen bonds : angle 6.83112 / 4.91 ( 1198) metal coordination : bond 0.03271 / 1.87 ( 8) metal coordination : angle 10.25246 / 5.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 HIS cc_start: 0.7547 (m90) cc_final: 0.7150 (m170) REVERT: A 344 PHE cc_start: 0.7881 (t80) cc_final: 0.7552 (t80) REVERT: A 417 ILE cc_start: 0.7852 (mm) cc_final: 0.7600 (mt) REVERT: D 285 HIS cc_start: 0.7553 (m90) cc_final: 0.7164 (m170) REVERT: D 344 PHE cc_start: 0.7873 (t80) cc_final: 0.7467 (t80) outliers start: 2 outliers final: 2 residues processed: 115 average time/residue: 0.1070 time to fit residues: 17.0359 Evaluate side-chains 80 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain D residue 79 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN A 91 GLN A 314 GLN A 421 ASN A 448 HIS D 66 GLN D 91 GLN D 314 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 ASN D 448 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.183555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.128125 restraints weight = 14122.528| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.92 r_work: 0.3601 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9622 Z= 0.151 Angle : 0.660 9.323 13358 Z= 0.368 Chirality : 0.047 0.226 1522 Planarity : 0.004 0.035 1380 Dihedral : 25.152 71.249 1972 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.93 % Allowed : 16.91 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.13 (0.25), residues: 920 helix: -1.05 (0.22), residues: 444 sheet: -0.32 (0.61), residues: 60 loop : -1.91 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 106 TYR 0.016 0.002 TYR A 241 PHE 0.017 0.002 PHE D 268 TRP 0.009 0.002 TRP D 400 HIS 0.005 0.001 HIS A 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 ( 9614) covalent geometry : angle 0.65993 / 0.37 (13354) hydrogen bonds : bond 0.04556 / 3.05 ( 420) hydrogen bonds : angle 4.73395 / 3.42 ( 1198) metal coordination : bond 0.01499 / 0.95 ( 8) metal coordination : angle 1.50752 / 0.74 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7798 (ttp) cc_final: 0.7286 (ttp) REVERT: A 281 GLU cc_start: 0.7797 (pp20) cc_final: 0.7571 (pp20) REVERT: A 285 HIS cc_start: 0.7885 (m90) cc_final: 0.7491 (m-70) REVERT: A 485 ARG cc_start: 0.7174 (ttt90) cc_final: 0.6839 (mtp180) REVERT: D 285 HIS cc_start: 0.7820 (m90) cc_final: 0.7444 (m-70) REVERT: D 344 PHE cc_start: 0.7833 (t80) cc_final: 0.7589 (t80) outliers start: 16 outliers final: 6 residues processed: 112 average time/residue: 0.0931 time to fit residues: 15.1280 Evaluate side-chains 98 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 314 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 94 optimal weight: 0.0050 chunk 16 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 29 optimal weight: 0.0470 chunk 54 optimal weight: 1.9990 overall best weight: 0.3892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.186148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.131166 restraints weight = 14153.068| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.87 r_work: 0.3646 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9622 Z= 0.133 Angle : 0.613 8.754 13358 Z= 0.342 Chirality : 0.044 0.197 1522 Planarity : 0.004 0.035 1380 Dihedral : 24.799 70.286 1972 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.45 % Allowed : 16.79 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.79 (0.25), residues: 920 helix: -0.75 (0.22), residues: 444 sheet: -0.09 (0.63), residues: 60 loop : -1.78 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 106 TYR 0.017 0.001 TYR A 488 PHE 0.012 0.001 PHE A 268 TRP 0.008 0.002 TRP D 122 HIS 0.005 0.001 HIS D 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 9614) covalent geometry : angle 0.61178 / 0.34 (13354) hydrogen bonds : bond 0.04066 / 2.74 ( 420) hydrogen bonds : angle 4.31285 / 3.11 ( 1198) metal coordination : bond 0.01973 / 1.25 ( 8) metal coordination : angle 2.19549 / 1.11 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8728 (ttp) cc_final: 0.8527 (ttp) REVERT: A 280 MET cc_start: 0.7693 (ttp) cc_final: 0.7075 (ttp) REVERT: A 285 HIS cc_start: 0.7929 (m90) cc_final: 0.7726 (m170) REVERT: A 344 PHE cc_start: 0.8143 (t80) cc_final: 0.7511 (t80) REVERT: A 364 ARG cc_start: 0.7464 (mtt90) cc_final: 0.7264 (ptm160) REVERT: D 220 MET cc_start: 0.8729 (ttp) cc_final: 0.8502 (ttp) REVERT: D 285 HIS cc_start: 0.7949 (m90) cc_final: 0.7554 (m-70) REVERT: D 403 MET cc_start: 0.6120 (mtm) cc_final: 0.5807 (mtp) outliers start: 12 outliers final: 6 residues processed: 117 average time/residue: 0.0882 time to fit residues: 15.0013 Evaluate side-chains 101 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 0.0970 chunk 23 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.190063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.137249 restraints weight = 14323.712| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.75 r_work: 0.3643 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9622 Z= 0.147 Angle : 0.596 7.486 13358 Z= 0.329 Chirality : 0.043 0.189 1522 Planarity : 0.004 0.030 1380 Dihedral : 24.762 68.997 1972 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.93 % Allowed : 18.96 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.41 (0.26), residues: 920 helix: -0.30 (0.23), residues: 444 sheet: 0.08 (0.64), residues: 60 loop : -1.77 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 106 TYR 0.019 0.001 TYR A 488 PHE 0.022 0.002 PHE D 345 TRP 0.008 0.002 TRP A 164 HIS 0.004 0.001 HIS A 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 9614) covalent geometry : angle 0.59494 / 0.33 (13354) hydrogen bonds : bond 0.03897 / 2.60 ( 420) hydrogen bonds : angle 4.04546 / 2.94 ( 1198) metal coordination : bond 0.01571 / 1.00 ( 8) metal coordination : angle 2.04544 / 1.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7752 (ttp) cc_final: 0.7387 (ttp) REVERT: A 344 PHE cc_start: 0.7908 (t80) cc_final: 0.7657 (t80) REVERT: D 344 PHE cc_start: 0.8073 (t80) cc_final: 0.7826 (t80) REVERT: D 403 MET cc_start: 0.6208 (mtm) cc_final: 0.5955 (mtp) outliers start: 16 outliers final: 10 residues processed: 106 average time/residue: 0.0793 time to fit residues: 12.8536 Evaluate side-chains 103 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 327 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 13 optimal weight: 0.0470 chunk 31 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.186204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.131144 restraints weight = 14394.786| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.90 r_work: 0.3644 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9622 Z= 0.134 Angle : 0.576 7.821 13358 Z= 0.318 Chirality : 0.043 0.202 1522 Planarity : 0.003 0.029 1380 Dihedral : 24.749 69.300 1972 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.57 % Allowed : 19.81 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.19 (0.26), residues: 920 helix: -0.08 (0.23), residues: 446 sheet: 0.19 (0.65), residues: 60 loop : -1.71 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 106 TYR 0.018 0.001 TYR D 488 PHE 0.012 0.002 PHE D 345 TRP 0.007 0.001 TRP A 400 HIS 0.002 0.001 HIS D 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9614) covalent geometry : angle 0.57620 / 0.32 (13354) hydrogen bonds : bond 0.03748 / 2.50 ( 420) hydrogen bonds : angle 3.93791 / 2.87 ( 1198) metal coordination : bond 0.00851 / 0.52 ( 8) metal coordination : angle 1.21392 / 0.63 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7690 (ttp) cc_final: 0.7338 (ttp) REVERT: A 344 PHE cc_start: 0.7999 (t80) cc_final: 0.7741 (t80) REVERT: D 280 MET cc_start: 0.7121 (ttp) cc_final: 0.6763 (ttp) REVERT: D 344 PHE cc_start: 0.8146 (t80) cc_final: 0.7890 (t80) REVERT: D 403 MET cc_start: 0.6168 (mtm) cc_final: 0.5943 (mtp) outliers start: 13 outliers final: 7 residues processed: 102 average time/residue: 0.0899 time to fit residues: 13.2321 Evaluate side-chains 98 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 369 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 chunk 93 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 483 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.191988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.139470 restraints weight = 14375.739| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.74 r_work: 0.3684 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9622 Z= 0.117 Angle : 0.558 8.288 13358 Z= 0.308 Chirality : 0.042 0.198 1522 Planarity : 0.003 0.028 1380 Dihedral : 24.656 69.189 1972 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.54 % Allowed : 19.81 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.01 (0.26), residues: 920 helix: 0.13 (0.23), residues: 446 sheet: 0.38 (0.66), residues: 60 loop : -1.71 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 106 TYR 0.012 0.001 TYR D 488 PHE 0.015 0.001 PHE A 489 TRP 0.006 0.001 TRP D 400 HIS 0.003 0.001 HIS D 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 ( 9614) covalent geometry : angle 0.55716 / 0.31 (13354) hydrogen bonds : bond 0.03641 / 2.44 ( 420) hydrogen bonds : angle 3.82892 / 2.80 ( 1198) metal coordination : bond 0.01016 / 0.65 ( 8) metal coordination : angle 1.43883 / 0.73 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8295 (ptpt) cc_final: 0.8002 (mttm) REVERT: A 280 MET cc_start: 0.7706 (ttp) cc_final: 0.7375 (ttp) REVERT: A 344 PHE cc_start: 0.7976 (t80) cc_final: 0.7771 (t80) REVERT: D 226 LYS cc_start: 0.8292 (ptpt) cc_final: 0.8025 (mttm) REVERT: D 344 PHE cc_start: 0.8119 (t80) cc_final: 0.7831 (t80) outliers start: 21 outliers final: 8 residues processed: 110 average time/residue: 0.0842 time to fit residues: 13.7731 Evaluate side-chains 103 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 ARG Chi-restraints excluded: chain D residue 171 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.191650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.138750 restraints weight = 14445.851| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.74 r_work: 0.3666 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9622 Z= 0.138 Angle : 0.570 7.095 13358 Z= 0.314 Chirality : 0.042 0.175 1522 Planarity : 0.003 0.029 1380 Dihedral : 24.655 67.823 1972 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.33 % Allowed : 20.77 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.90 (0.26), residues: 920 helix: 0.23 (0.23), residues: 448 sheet: 0.49 (0.66), residues: 60 loop : -1.70 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 106 TYR 0.016 0.001 TYR D 488 PHE 0.012 0.001 PHE D 489 TRP 0.006 0.001 TRP A 400 HIS 0.003 0.001 HIS A 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 9614) covalent geometry : angle 0.57027 / 0.31 (13354) hydrogen bonds : bond 0.03674 / 2.44 ( 420) hydrogen bonds : angle 3.83491 / 2.80 ( 1198) metal coordination : bond 0.00284 / 0.17 ( 8) metal coordination : angle 0.96059 / 0.51 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8281 (ptpt) cc_final: 0.8008 (mttm) REVERT: A 280 MET cc_start: 0.7701 (ttp) cc_final: 0.7390 (ttp) REVERT: A 344 PHE cc_start: 0.7963 (t80) cc_final: 0.7722 (t80) REVERT: A 402 TYR cc_start: 0.6288 (m-80) cc_final: 0.5472 (p90) REVERT: D 226 LYS cc_start: 0.8291 (ptpt) cc_final: 0.8030 (mttm) REVERT: D 364 ARG cc_start: 0.6733 (ptm160) cc_final: 0.6529 (ptm160) REVERT: D 392 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7375 (mt-10) outliers start: 11 outliers final: 8 residues processed: 100 average time/residue: 0.0889 time to fit residues: 13.0559 Evaluate side-chains 102 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 ARG Chi-restraints excluded: chain D residue 171 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 63 optimal weight: 0.0670 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 0.0030 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 overall best weight: 0.5530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 483 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.188797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.133837 restraints weight = 14335.510| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.90 r_work: 0.3683 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9622 Z= 0.116 Angle : 0.550 6.104 13358 Z= 0.305 Chirality : 0.041 0.160 1522 Planarity : 0.003 0.027 1380 Dihedral : 24.532 67.285 1972 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.33 % Allowed : 21.74 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.79 (0.26), residues: 920 helix: 0.33 (0.23), residues: 448 sheet: 0.62 (0.67), residues: 60 loop : -1.67 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 106 TYR 0.023 0.001 TYR A 488 PHE 0.013 0.001 PHE D 489 TRP 0.005 0.001 TRP D 41 HIS 0.003 0.001 HIS A 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 ( 9614) covalent geometry : angle 0.54992 / 0.31 (13354) hydrogen bonds : bond 0.03605 / 2.41 ( 420) hydrogen bonds : angle 3.78683 / 2.77 ( 1198) metal coordination : bond 0.00403 / 0.20 ( 8) metal coordination : angle 1.13742 / 0.59 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8299 (ptpt) cc_final: 0.8069 (mttm) REVERT: A 280 MET cc_start: 0.7698 (ttp) cc_final: 0.6643 (tpt) REVERT: A 402 TYR cc_start: 0.6332 (m-80) cc_final: 0.5650 (p90) REVERT: A 403 MET cc_start: 0.6249 (tpp) cc_final: 0.5716 (tpp) REVERT: D 226 LYS cc_start: 0.8301 (ptpt) cc_final: 0.8063 (mttm) REVERT: D 364 ARG cc_start: 0.6809 (ptm160) cc_final: 0.6604 (ptm160) REVERT: D 392 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7315 (mt-10) REVERT: D 402 TYR cc_start: 0.6148 (m-80) cc_final: 0.5381 (p90) REVERT: D 403 MET cc_start: 0.6506 (OUTLIER) cc_final: 0.6292 (tpp) outliers start: 11 outliers final: 8 residues processed: 101 average time/residue: 0.0858 time to fit residues: 12.8641 Evaluate side-chains 102 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 403 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.187068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.131663 restraints weight = 14372.813| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.90 r_work: 0.3653 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9622 Z= 0.148 Angle : 0.584 8.929 13358 Z= 0.317 Chirality : 0.041 0.162 1522 Planarity : 0.003 0.029 1380 Dihedral : 24.545 66.355 1972 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.33 % Allowed : 21.62 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.79 (0.27), residues: 920 helix: 0.38 (0.23), residues: 446 sheet: 0.61 (0.68), residues: 60 loop : -1.72 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 106 TYR 0.030 0.001 TYR A 73 PHE 0.012 0.002 PHE D 345 TRP 0.007 0.001 TRP A 400 HIS 0.003 0.001 HIS D 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 9614) covalent geometry : angle 0.58409 / 0.32 (13354) hydrogen bonds : bond 0.03661 / 2.42 ( 420) hydrogen bonds : angle 3.79780 / 2.78 ( 1198) metal coordination : bond 0.00500 / 0.32 ( 8) metal coordination : angle 1.06995 / 0.55 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8278 (ptpt) cc_final: 0.8072 (mttm) REVERT: A 280 MET cc_start: 0.7714 (ttp) cc_final: 0.6763 (tpt) REVERT: A 402 TYR cc_start: 0.6421 (m-80) cc_final: 0.5714 (p90) REVERT: A 403 MET cc_start: 0.6379 (tpp) cc_final: 0.5901 (tpp) REVERT: D 226 LYS cc_start: 0.8315 (ptpt) cc_final: 0.8095 (mttm) REVERT: D 403 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.6063 (mmt) outliers start: 11 outliers final: 6 residues processed: 96 average time/residue: 0.0865 time to fit residues: 12.2312 Evaluate side-chains 94 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 403 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 63 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.188263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.132949 restraints weight = 14393.719| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.92 r_work: 0.3670 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9622 Z= 0.130 Angle : 0.574 10.599 13358 Z= 0.314 Chirality : 0.041 0.160 1522 Planarity : 0.003 0.028 1380 Dihedral : 24.442 67.435 1972 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.85 % Allowed : 22.34 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.69 (0.27), residues: 920 helix: 0.43 (0.23), residues: 446 sheet: 0.63 (0.68), residues: 60 loop : -1.64 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 364 TYR 0.018 0.001 TYR A 73 PHE 0.014 0.001 PHE D 489 TRP 0.011 0.002 TRP A 164 HIS 0.003 0.001 HIS D 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 9614) covalent geometry : angle 0.57383 / 0.31 (13354) hydrogen bonds : bond 0.03660 / 2.44 ( 420) hydrogen bonds : angle 3.78467 / 2.77 ( 1198) metal coordination : bond 0.00207 / 0.13 ( 8) metal coordination : angle 0.94038 / 0.48 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8301 (ptpt) cc_final: 0.8067 (mttm) REVERT: A 280 MET cc_start: 0.7490 (ttp) cc_final: 0.7108 (tpt) REVERT: A 402 TYR cc_start: 0.6449 (m-80) cc_final: 0.5709 (p90) REVERT: D 226 LYS cc_start: 0.8297 (ptpt) cc_final: 0.7952 (mttm) outliers start: 7 outliers final: 6 residues processed: 93 average time/residue: 0.0807 time to fit residues: 11.2688 Evaluate side-chains 94 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 37 optimal weight: 0.2980 chunk 46 optimal weight: 20.0000 chunk 20 optimal weight: 0.0670 chunk 96 optimal weight: 20.0000 chunk 66 optimal weight: 0.0370 chunk 13 optimal weight: 0.3980 chunk 79 optimal weight: 0.0770 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 overall best weight: 0.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.192121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.137636 restraints weight = 14384.802| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.91 r_work: 0.3731 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9622 Z= 0.112 Angle : 0.545 6.125 13358 Z= 0.301 Chirality : 0.040 0.158 1522 Planarity : 0.003 0.028 1380 Dihedral : 24.206 69.258 1972 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.60 % Allowed : 22.95 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.65 (0.27), residues: 920 helix: 0.45 (0.23), residues: 452 sheet: 0.96 (0.68), residues: 64 loop : -1.71 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 364 TYR 0.015 0.001 TYR A 488 PHE 0.021 0.002 PHE A 345 TRP 0.011 0.001 TRP A 164 HIS 0.003 0.001 HIS A 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 9614) covalent geometry : angle 0.54479 / 0.30 (13354) hydrogen bonds : bond 0.03533 / 2.36 ( 420) hydrogen bonds : angle 3.67088 / 2.72 ( 1198) metal coordination : bond 0.00433 / 0.31 ( 8) metal coordination : angle 1.32042 / 0.68 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2380.99 seconds wall clock time: 42 minutes 2.93 seconds (2522.93 seconds total)