Starting phenix.real_space_refine on Sun Aug 24 07:04:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gk7_40180/08_2025/8gk7_40180_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gk7_40180/08_2025/8gk7_40180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gk7_40180/08_2025/8gk7_40180_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gk7_40180/08_2025/8gk7_40180_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gk7_40180/08_2025/8gk7_40180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gk7_40180/08_2025/8gk7_40180.map" } resolution = 3.32 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= 0.001 sd= 0.017 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 34 5.16 5 C 5638 2.51 5 N 1524 2.21 5 O 1628 1.98 5 H 8791 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s 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: 17621 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 8726 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 550} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLN:plan1': 4, 'ASP:plan': 3, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 8725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 8725 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 550} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLN:plan1': 4, 'ASP:plan': 3, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "A" Number of atoms: 139 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2, 85 Unusual residues: {'ANP': 1, 'ZQF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Conformer: "B" Number of residues, atoms: 2, 85 Unusual residues: {'ANP': 1, 'ZQF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} bond proxies already assigned to first conformer: 33 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AZQF A 602 " occ=0.40 ... (106 atoms not shown) pdb=" S1 BZQF A 602 " occ=0.60 Time building chain proxies: 3.38, per 1000 atoms: 0.19 Number of scatterers: 17621 At special positions: 0 Unit cell: (71.69, 84.53, 136.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 6 15.00 O 1628 8.00 N 1524 7.00 C 5638 6.00 H 8791 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 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 536.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 67.7% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 6 through 14 removed outlier: 3.570A pdb=" N SER A 13 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 14 " --> pdb=" O ARG A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 18 through 52 removed outlier: 3.534A pdb=" N LEU A 23 " --> pdb=" O TRP A 19 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A 24 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 74 removed outlier: 3.985A pdb=" N ILE A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 105 removed outlier: 4.007A pdb=" N ALA A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.661A pdb=" N TYR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 124 removed outlier: 3.917A pdb=" N ILE A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 158 removed outlier: 3.530A pdb=" N LEU A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 removed outlier: 3.597A pdb=" N THR A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 168 through 214 removed outlier: 3.834A pdb=" N ARG A 182 " --> pdb=" O LYS A 178 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ALA A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 244 Processing helix chain 'A' and resid 245 through 265 Processing helix chain 'A' and resid 274 through 318 removed outlier: 3.962A pdb=" N PHE A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 4.241A pdb=" N GLU A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 382 removed outlier: 3.542A pdb=" N LEU A 377 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASN A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N MET A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 373 through 382' Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 424 through 430 Processing helix chain 'A' and resid 440 through 449 Processing helix chain 'A' and resid 476 through 489 removed outlier: 3.984A pdb=" N ALA A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 518 Processing helix chain 'A' and resid 531 through 536 removed outlier: 4.302A pdb=" N ASN A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 561 Processing helix chain 'A' and resid 561 through 567 removed outlier: 3.957A pdb=" N GLN A 566 " --> pdb=" O GLY A 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 14 removed outlier: 3.557A pdb=" N SER B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR B 14 " --> pdb=" O ARG B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 18 through 52 removed outlier: 4.082A pdb=" N LEU B 24 " --> pdb=" O GLY B 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 25 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 39 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS B 41 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 74 removed outlier: 3.776A pdb=" N ILE B 66 " --> pdb=" O PRO B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 105 removed outlier: 3.549A pdb=" N THR B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA B 84 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 100 " --> pdb=" O GLN B 96 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 removed outlier: 3.680A pdb=" N TYR B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 124 removed outlier: 3.542A pdb=" N LYS B 121 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE B 122 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 158 removed outlier: 3.533A pdb=" N LEU B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.584A pdb=" N THR B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 168 through 214 removed outlier: 3.857A pdb=" N ARG B 182 " --> pdb=" O LYS B 178 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ALA B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL B 210 " --> pdb=" O ASN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 265 removed outlier: 3.538A pdb=" N ARG B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) Proline residue: B 247 - end of helix Processing helix chain 'B' and resid 274 through 298 removed outlier: 3.696A pdb=" N PHE B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) Proline residue: B 291 - end of helix Processing helix chain 'B' and resid 298 through 318 Processing helix chain 'B' and resid 373 through 383 removed outlier: 3.544A pdb=" N LEU B 377 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL B 378 " --> pdb=" O LYS B 374 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ASN B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 424 through 430 Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 476 through 489 removed outlier: 3.908A pdb=" N ALA B 482 " --> pdb=" O ARG B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 518 Processing helix chain 'B' and resid 531 through 536 removed outlier: 4.402A pdb=" N ASN B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 561 Processing helix chain 'B' and resid 561 through 567 removed outlier: 3.804A pdb=" N GLN B 566 " --> pdb=" O GLY B 562 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 335 through 338 removed outlier: 3.669A pdb=" N ASP A 338 " --> pdb=" O GLN A 391 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN A 391 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 413 removed outlier: 7.002A pdb=" N ALA A 412 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASP A 497 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 494 " --> pdb=" O ILE A 525 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE A 527 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU A 496 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA A 365 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N MET A 543 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL A 367 " --> pdb=" O MET A 543 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP A 544 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ILE A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 335 through 338 removed outlier: 3.678A pdb=" N ASP B 338 " --> pdb=" O GLN B 391 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN B 391 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 412 through 413 removed outlier: 7.063A pdb=" N ALA B 412 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASP B 497 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU B 494 " --> pdb=" O ILE B 525 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE B 527 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU B 496 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP B 544 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE B 548 " --> pdb=" O ASP B 544 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1521 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: 4.69 Time building geometry restraints manager: 2.36 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: 8787 1.03 - 1.23: 16 1.23 - 1.42: 3670 1.42 - 1.62: 5228 1.62 - 1.81: 68 Bond restraints: 17769 Sorted by residual: bond pdb=" O3A ANP B 601 " pdb=" PB ANP B 601 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" O3A ANP A 601 " pdb=" PB ANP A 601 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" N3B ANP B 601 " pdb=" PG ANP B 601 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" N3B ANP A 601 " pdb=" PG ANP A 601 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C15AZQF A 602 " pdb=" O7 AZQF A 602 " ideal model delta sigma weight residual 1.233 1.305 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 17764 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 32013 3.20 - 6.40: 65 6.40 - 9.59: 8 9.59 - 12.79: 2 12.79 - 15.99: 2 Bond angle restraints: 32090 Sorted by residual: angle pdb=" PB ANP B 601 " pdb=" N3B ANP B 601 " pdb=" PG ANP B 601 " ideal model delta sigma weight residual 126.95 110.96 15.99 3.00e+00 1.11e-01 2.84e+01 angle pdb=" PB ANP A 601 " pdb=" N3B ANP A 601 " pdb=" PG ANP A 601 " ideal model delta sigma weight residual 126.95 111.15 15.80 3.00e+00 1.11e-01 2.77e+01 angle pdb=" O1B ANP B 601 " pdb=" PB ANP B 601 " pdb=" O2B ANP B 601 " ideal model delta sigma weight residual 120.08 108.97 11.11 3.00e+00 1.11e-01 1.37e+01 angle pdb=" O1B ANP A 601 " pdb=" PB ANP A 601 " pdb=" O2B ANP A 601 " ideal model delta sigma weight residual 120.08 109.00 11.08 3.00e+00 1.11e-01 1.37e+01 angle pdb=" N ILE B 65 " pdb=" CA ILE B 65 " pdb=" C ILE B 65 " ideal model delta sigma weight residual 111.81 109.28 2.53 8.60e-01 1.35e+00 8.66e+00 ... (remaining 32085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.65: 7944 28.65 - 57.30: 343 57.30 - 85.95: 49 85.95 - 114.61: 3 114.61 - 143.26: 2 Dihedral angle restraints: 8341 sinusoidal: 4609 harmonic: 3732 Sorted by residual: dihedral pdb=" C10AZQF A 602 " pdb=" C8 AZQF A 602 " pdb=" C9 AZQF A 602 " pdb=" N1 AZQF A 602 " ideal model delta sinusoidal sigma weight residual 152.09 -64.65 -143.26 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C10BZQF A 602 " pdb=" C8 BZQF A 602 " pdb=" C9 BZQF A 602 " pdb=" N1 BZQF A 602 " ideal model delta sinusoidal sigma weight residual 152.09 -72.22 -135.69 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" CB GLU A 220 " pdb=" CG GLU A 220 " pdb=" CD GLU A 220 " pdb=" OE1 GLU A 220 " ideal model delta sinusoidal sigma weight residual 0.00 -89.99 89.99 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 8338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1223 0.053 - 0.105: 174 0.105 - 0.158: 31 0.158 - 0.210: 0 0.210 - 0.263: 2 Chirality restraints: 1430 Sorted by residual: chirality pdb=" C3' ANP A 601 " pdb=" C2' ANP A 601 " pdb=" C4' ANP A 601 " pdb=" O3' ANP A 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C3' ANP B 601 " pdb=" C2' ANP B 601 " pdb=" C4' ANP B 601 " pdb=" O3' ANP B 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA ILE A 493 " pdb=" N ILE A 493 " pdb=" C ILE A 493 " pdb=" CB ILE A 493 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 1427 not shown) Planarity restraints: 2637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C BZQF A 602 " 0.019 2.00e-02 2.50e+03 3.21e-02 2.06e+01 pdb=" C1 BZQF A 602 " 0.024 2.00e-02 2.50e+03 pdb=" C2 BZQF A 602 " 0.017 2.00e-02 2.50e+03 pdb=" C31BZQF A 602 " 0.024 2.00e-02 2.50e+03 pdb=" C32BZQF A 602 " 0.019 2.00e-02 2.50e+03 pdb=" C33BZQF A 602 " 0.008 2.00e-02 2.50e+03 pdb=" C34BZQF A 602 " -0.054 2.00e-02 2.50e+03 pdb=" S BZQF A 602 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17AZQF A 602 " -0.009 2.00e-02 2.50e+03 2.98e-02 1.78e+01 pdb=" C18AZQF A 602 " -0.018 2.00e-02 2.50e+03 pdb=" C19AZQF A 602 " -0.022 2.00e-02 2.50e+03 pdb=" C20AZQF A 602 " -0.013 2.00e-02 2.50e+03 pdb=" C21AZQF A 602 " 0.054 2.00e-02 2.50e+03 pdb=" C25AZQF A 602 " -0.020 2.00e-02 2.50e+03 pdb=" C26AZQF A 602 " -0.020 2.00e-02 2.50e+03 pdb=" S1 AZQF A 602 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17BZQF A 602 " 0.006 2.00e-02 2.50e+03 1.61e-02 5.22e+00 pdb=" C18BZQF A 602 " 0.010 2.00e-02 2.50e+03 pdb=" C19BZQF A 602 " 0.011 2.00e-02 2.50e+03 pdb=" C20BZQF A 602 " 0.006 2.00e-02 2.50e+03 pdb=" C21BZQF A 602 " -0.029 2.00e-02 2.50e+03 pdb=" C25BZQF A 602 " 0.011 2.00e-02 2.50e+03 pdb=" C26BZQF A 602 " 0.011 2.00e-02 2.50e+03 pdb=" S1 BZQF A 602 " -0.026 2.00e-02 2.50e+03 ... (remaining 2634 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1092 2.21 - 2.81: 37382 2.81 - 3.40: 48256 3.40 - 4.00: 61579 4.00 - 4.60: 96488 Nonbonded interactions: 244797 Sorted by model distance: nonbonded pdb=" O THR B 274 " pdb=" H GLU B 277 " model vdw 1.610 2.450 nonbonded pdb=" OG SER A 474 " pdb=" H GLN A 477 " model vdw 1.650 2.450 nonbonded pdb=" OG SER B 474 " pdb=" H GLN B 477 " model vdw 1.662 2.450 nonbonded pdb=" O VAL A 542 " pdb=" H VAL A 549 " model vdw 1.666 2.450 nonbonded pdb=" HZ1 LYS A 101 " pdb=" O LEU A 318 " model vdw 1.666 2.450 ... (remaining 244792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 451 or (resid 452 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid 453 through 601)) selection = chain 'B' } 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=0.00 max=1.00 mean=0.50 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: 1.100 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: 0.080 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.530 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 0.142 8978 Z= 0.214 Angle : 0.607 15.989 12198 Z= 0.262 Chirality : 0.037 0.263 1430 Planarity : 0.003 0.043 1540 Dihedral : 16.388 143.257 3334 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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 aren not related in a simple way. whole: 0.67 (0.27), residues: 1124 helix: 1.58 (0.21), residues: 718 sheet: -1.15 (0.89), residues: 44 loop : -1.73 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 182 TYR 0.011 0.001 TYR A 124 PHE 0.010 0.001 PHE B 61 TRP 0.010 0.001 TRP B 159 HIS 0.002 0.000 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 8978) covalent geometry : angle 0.60729 (12198) hydrogen bonds : bond 0.22684 ( 509) hydrogen bonds : angle 7.64850 ( 1521) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TYR cc_start: 0.9265 (m-80) cc_final: 0.9050 (m-80) REVERT: A 145 MET cc_start: 0.9585 (mmm) cc_final: 0.9233 (mmm) REVERT: B 8 TYR cc_start: 0.9228 (m-80) cc_final: 0.8997 (m-80) REVERT: B 35 THR cc_start: 0.9407 (m) cc_final: 0.9058 (m) REVERT: B 36 GLU cc_start: 0.9244 (tt0) cc_final: 0.9009 (tt0) REVERT: B 203 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8735 (mt-10) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1984 time to fit residues: 45.7700 Evaluate side-chains 101 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN B 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.063242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.054244 restraints weight = 122215.538| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 6.21 r_work: 0.2821 rms_B_bonded: 6.12 restraints_weight: 2.0000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8978 Z= 0.129 Angle : 0.525 5.595 12198 Z= 0.279 Chirality : 0.038 0.134 1430 Planarity : 0.003 0.036 1540 Dihedral : 9.199 116.844 1370 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.77 % Allowed : 5.62 % Favored : 93.61 % 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 aren not related in a simple way. whole: 0.77 (0.27), residues: 1124 helix: 1.83 (0.20), residues: 706 sheet: -1.32 (0.86), residues: 44 loop : -1.94 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 72 TYR 0.017 0.001 TYR B 124 PHE 0.012 0.001 PHE B 61 TRP 0.007 0.001 TRP B 19 HIS 0.003 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8978) covalent geometry : angle 0.52465 (12198) hydrogen bonds : bond 0.05098 ( 509) hydrogen bonds : angle 5.01567 ( 1521) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 TYR cc_start: 0.9350 (t80) cc_final: 0.8641 (t80) REVERT: A 128 GLN cc_start: 0.9642 (mm-40) cc_final: 0.8923 (mp10) REVERT: A 342 LEU cc_start: 0.8978 (tp) cc_final: 0.8612 (tp) REVERT: A 456 MET cc_start: 0.9041 (mpp) cc_final: 0.8647 (pmm) REVERT: A 543 MET cc_start: 0.7948 (tmm) cc_final: 0.7574 (tmm) REVERT: B 36 GLU cc_start: 0.9632 (tt0) cc_final: 0.9340 (mm-30) REVERT: B 78 MET cc_start: 0.8458 (ppp) cc_final: 0.8069 (ppp) REVERT: B 112 ASP cc_start: 0.9319 (t0) cc_final: 0.9054 (m-30) REVERT: B 145 MET cc_start: 0.9275 (ttp) cc_final: 0.8990 (ttp) REVERT: B 342 LEU cc_start: 0.9086 (tp) cc_final: 0.8663 (tp) REVERT: B 543 MET cc_start: 0.8041 (tmm) cc_final: 0.7557 (tmm) outliers start: 7 outliers final: 4 residues processed: 114 average time/residue: 0.1545 time to fit residues: 28.0403 Evaluate side-chains 98 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 255 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 4.9990 chunk 72 optimal weight: 0.0870 chunk 100 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 428 ASN B 189 GLN B 339 HIS B 529 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.058381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.049636 restraints weight = 122382.002| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 6.04 r_work: 0.2706 rms_B_bonded: 5.95 restraints_weight: 2.0000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8978 Z= 0.198 Angle : 0.542 6.330 12198 Z= 0.295 Chirality : 0.037 0.138 1430 Planarity : 0.003 0.029 1540 Dihedral : 8.243 107.465 1370 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.55 % Allowed : 6.72 % Favored : 92.73 % 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 aren not related in a simple way. whole: 0.86 (0.26), residues: 1124 helix: 1.92 (0.19), residues: 718 sheet: -1.61 (0.78), residues: 54 loop : -2.03 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.013 0.001 TYR B 124 PHE 0.007 0.001 PHE A 278 TRP 0.004 0.001 TRP B 262 HIS 0.002 0.001 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8978) covalent geometry : angle 0.54187 (12198) hydrogen bonds : bond 0.04679 ( 509) hydrogen bonds : angle 4.88879 ( 1521) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ASP cc_start: 0.8305 (m-30) cc_final: 0.8085 (m-30) REVERT: A 342 LEU cc_start: 0.9322 (tp) cc_final: 0.9094 (tt) REVERT: A 413 MET cc_start: 0.9419 (mmm) cc_final: 0.9139 (mmm) REVERT: A 543 MET cc_start: 0.8034 (tmm) cc_final: 0.7627 (tmm) REVERT: B 36 GLU cc_start: 0.9713 (tt0) cc_final: 0.9344 (mm-30) REVERT: B 78 MET cc_start: 0.8576 (ppp) cc_final: 0.8254 (ppp) REVERT: B 245 ASN cc_start: 0.9610 (t0) cc_final: 0.9157 (t0) REVERT: B 342 LEU cc_start: 0.9349 (tp) cc_final: 0.8985 (tp) REVERT: B 543 MET cc_start: 0.8085 (tmm) cc_final: 0.7599 (tmm) outliers start: 5 outliers final: 3 residues processed: 103 average time/residue: 0.1430 time to fit residues: 23.8705 Evaluate side-chains 96 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain B residue 90 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 24 optimal weight: 0.0570 chunk 30 optimal weight: 5.9990 overall best weight: 2.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 HIS A 529 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.056951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.048355 restraints weight = 121384.406| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 5.97 r_work: 0.2663 rms_B_bonded: 5.82 restraints_weight: 2.0000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| r_final: 0.2663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8978 Z= 0.201 Angle : 0.537 6.382 12198 Z= 0.293 Chirality : 0.037 0.138 1430 Planarity : 0.003 0.024 1540 Dihedral : 8.401 102.843 1370 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.66 % Allowed : 9.25 % Favored : 90.09 % 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 aren not related in a simple way. whole: 0.72 (0.26), residues: 1124 helix: 1.91 (0.19), residues: 718 sheet: -2.63 (0.74), residues: 50 loop : -2.17 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 485 TYR 0.017 0.001 TYR A 124 PHE 0.009 0.001 PHE B 61 TRP 0.003 0.001 TRP B 262 HIS 0.003 0.001 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 8978) covalent geometry : angle 0.53712 (12198) hydrogen bonds : bond 0.04286 ( 509) hydrogen bonds : angle 4.77942 ( 1521) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 TYR cc_start: 0.9287 (t80) cc_final: 0.8800 (t80) REVERT: A 128 GLN cc_start: 0.9628 (mm-40) cc_final: 0.9349 (mm-40) REVERT: A 183 MET cc_start: 0.9665 (mtm) cc_final: 0.9464 (mtm) REVERT: A 342 LEU cc_start: 0.9428 (tp) cc_final: 0.9200 (tt) REVERT: A 413 MET cc_start: 0.9425 (mmm) cc_final: 0.9106 (mmm) REVERT: A 543 MET cc_start: 0.8236 (tmm) cc_final: 0.7956 (tmm) REVERT: B 36 GLU cc_start: 0.9714 (tt0) cc_final: 0.9316 (mm-30) REVERT: B 78 MET cc_start: 0.8576 (ppp) cc_final: 0.8232 (ppp) REVERT: B 245 ASN cc_start: 0.9605 (t0) cc_final: 0.9334 (t0) REVERT: B 297 ASP cc_start: 0.9128 (m-30) cc_final: 0.8914 (m-30) REVERT: B 342 LEU cc_start: 0.9377 (tp) cc_final: 0.9029 (tp) REVERT: B 403 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8760 (mt-10) REVERT: B 543 MET cc_start: 0.8142 (tmm) cc_final: 0.7882 (tmm) outliers start: 6 outliers final: 6 residues processed: 103 average time/residue: 0.1455 time to fit residues: 23.9116 Evaluate side-chains 99 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 494 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.057429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.048871 restraints weight = 119634.429| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 5.90 r_work: 0.2693 rms_B_bonded: 5.76 restraints_weight: 2.0000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8978 Z= 0.115 Angle : 0.497 8.851 12198 Z= 0.259 Chirality : 0.037 0.141 1430 Planarity : 0.002 0.022 1540 Dihedral : 8.295 98.361 1370 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.55 % Allowed : 10.35 % Favored : 89.10 % 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 aren not related in a simple way. whole: 1.02 (0.26), residues: 1124 helix: 2.14 (0.19), residues: 718 sheet: -2.12 (0.73), residues: 54 loop : -2.08 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.013 0.001 TYR A 124 PHE 0.016 0.001 PHE B 61 TRP 0.004 0.001 TRP B 159 HIS 0.003 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8978) covalent geometry : angle 0.49707 (12198) hydrogen bonds : bond 0.04016 ( 509) hydrogen bonds : angle 4.53461 ( 1521) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.9607 (ttm) cc_final: 0.9396 (ttm) REVERT: A 342 LEU cc_start: 0.9386 (tp) cc_final: 0.9139 (tt) REVERT: A 413 MET cc_start: 0.9435 (mmm) cc_final: 0.9194 (mmm) REVERT: A 543 MET cc_start: 0.8268 (tmm) cc_final: 0.7995 (tmm) REVERT: B 36 GLU cc_start: 0.9713 (tt0) cc_final: 0.9325 (mm-30) REVERT: B 78 MET cc_start: 0.8555 (ppp) cc_final: 0.8215 (ppp) REVERT: B 245 ASN cc_start: 0.9565 (t0) cc_final: 0.9025 (t0) REVERT: B 297 ASP cc_start: 0.9112 (m-30) cc_final: 0.8898 (m-30) REVERT: B 342 LEU cc_start: 0.9378 (tp) cc_final: 0.9019 (tp) outliers start: 5 outliers final: 5 residues processed: 96 average time/residue: 0.1523 time to fit residues: 23.6421 Evaluate side-chains 95 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 90 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.055029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.046527 restraints weight = 124491.867| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 5.96 r_work: 0.2633 rms_B_bonded: 5.80 restraints_weight: 2.0000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8978 Z= 0.215 Angle : 0.545 6.750 12198 Z= 0.296 Chirality : 0.036 0.156 1430 Planarity : 0.003 0.020 1540 Dihedral : 8.434 100.970 1370 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 0.88 % Allowed : 10.79 % Favored : 88.33 % 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 aren not related in a simple way. whole: 0.78 (0.26), residues: 1124 helix: 1.95 (0.19), residues: 722 sheet: -2.49 (0.69), residues: 54 loop : -2.16 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.016 0.001 TYR A 124 PHE 0.009 0.001 PHE A 29 TRP 0.004 0.001 TRP B 262 HIS 0.004 0.001 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 8978) covalent geometry : angle 0.54519 (12198) hydrogen bonds : bond 0.04129 ( 509) hydrogen bonds : angle 4.75261 ( 1521) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 MET cc_start: 0.9438 (mmm) cc_final: 0.9104 (mmm) REVERT: A 543 MET cc_start: 0.8341 (tmm) cc_final: 0.8041 (tmm) REVERT: B 36 GLU cc_start: 0.9747 (tt0) cc_final: 0.9361 (mm-30) REVERT: B 78 MET cc_start: 0.8629 (ppp) cc_final: 0.8240 (ppp) REVERT: B 245 ASN cc_start: 0.9593 (t0) cc_final: 0.9093 (t0) REVERT: B 297 ASP cc_start: 0.9168 (m-30) cc_final: 0.8960 (m-30) REVERT: B 342 LEU cc_start: 0.9464 (tp) cc_final: 0.9169 (tt) REVERT: B 403 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8761 (mt-10) outliers start: 8 outliers final: 7 residues processed: 96 average time/residue: 0.1601 time to fit residues: 24.4460 Evaluate side-chains 92 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 494 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 47 optimal weight: 0.0270 chunk 52 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.056416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.047749 restraints weight = 121513.292| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 5.99 r_work: 0.2670 rms_B_bonded: 5.82 restraints_weight: 2.0000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8978 Z= 0.107 Angle : 0.487 5.508 12198 Z= 0.256 Chirality : 0.037 0.157 1430 Planarity : 0.002 0.019 1540 Dihedral : 8.106 95.495 1370 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.99 % Allowed : 11.45 % Favored : 87.56 % 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 aren not related in a simple way. whole: 1.06 (0.26), residues: 1124 helix: 2.19 (0.19), residues: 722 sheet: -2.36 (0.69), residues: 54 loop : -2.12 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 72 TYR 0.010 0.001 TYR A 124 PHE 0.004 0.001 PHE A 29 TRP 0.003 0.001 TRP B 60 HIS 0.004 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 8978) covalent geometry : angle 0.48692 (12198) hydrogen bonds : bond 0.03912 ( 509) hydrogen bonds : angle 4.43213 ( 1521) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.9632 (mm-40) cc_final: 0.8855 (mp10) REVERT: A 143 ASP cc_start: 0.8319 (m-30) cc_final: 0.8071 (m-30) REVERT: A 413 MET cc_start: 0.9398 (mmm) cc_final: 0.9136 (mmm) REVERT: A 543 MET cc_start: 0.8387 (tmm) cc_final: 0.8119 (tmm) REVERT: B 36 GLU cc_start: 0.9727 (tt0) cc_final: 0.9357 (mm-30) REVERT: B 78 MET cc_start: 0.8602 (ppp) cc_final: 0.8212 (ppp) REVERT: B 245 ASN cc_start: 0.9555 (t0) cc_final: 0.9009 (t0) REVERT: B 297 ASP cc_start: 0.9112 (m-30) cc_final: 0.8897 (m-30) REVERT: B 342 LEU cc_start: 0.9420 (tp) cc_final: 0.9102 (tt) outliers start: 9 outliers final: 7 residues processed: 98 average time/residue: 0.1651 time to fit residues: 25.3440 Evaluate side-chains 94 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 494 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.055326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.046963 restraints weight = 124861.100| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 5.88 r_work: 0.2625 rms_B_bonded: 5.75 restraints_weight: 2.0000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8978 Z= 0.217 Angle : 0.549 7.775 12198 Z= 0.296 Chirality : 0.036 0.138 1430 Planarity : 0.003 0.018 1540 Dihedral : 7.896 98.320 1370 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.77 % Allowed : 11.56 % Favored : 87.67 % 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 aren not related in a simple way. whole: 0.82 (0.26), residues: 1124 helix: 1.94 (0.19), residues: 728 sheet: -2.44 (0.67), residues: 54 loop : -2.14 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.012 0.001 TYR A 124 PHE 0.008 0.001 PHE A 29 TRP 0.004 0.001 TRP B 262 HIS 0.002 0.001 HIS A 509 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 8978) covalent geometry : angle 0.54920 (12198) hydrogen bonds : bond 0.04011 ( 509) hydrogen bonds : angle 4.68697 ( 1521) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ASP cc_start: 0.8456 (m-30) cc_final: 0.8184 (m-30) REVERT: A 297 ASP cc_start: 0.9149 (m-30) cc_final: 0.8916 (m-30) REVERT: A 413 MET cc_start: 0.9445 (mmm) cc_final: 0.9133 (mmm) REVERT: A 543 MET cc_start: 0.8413 (tmm) cc_final: 0.8132 (tmm) REVERT: B 36 GLU cc_start: 0.9756 (tt0) cc_final: 0.9374 (mm-30) REVERT: B 78 MET cc_start: 0.8649 (ppp) cc_final: 0.8248 (ppp) REVERT: B 245 ASN cc_start: 0.9582 (t0) cc_final: 0.9094 (t0) REVERT: B 297 ASP cc_start: 0.9166 (m-30) cc_final: 0.8955 (m-30) REVERT: B 342 LEU cc_start: 0.9513 (tp) cc_final: 0.9239 (tt) outliers start: 7 outliers final: 7 residues processed: 92 average time/residue: 0.1612 time to fit residues: 23.2939 Evaluate side-chains 95 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 494 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.055201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.046687 restraints weight = 120665.134| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 5.97 r_work: 0.2663 rms_B_bonded: 5.81 restraints_weight: 2.0000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8978 Z= 0.103 Angle : 0.490 7.311 12198 Z= 0.255 Chirality : 0.037 0.172 1430 Planarity : 0.002 0.018 1540 Dihedral : 7.661 92.614 1370 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.55 % Allowed : 11.45 % Favored : 88.00 % 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 aren not related in a simple way. whole: 1.13 (0.26), residues: 1124 helix: 2.24 (0.20), residues: 714 sheet: -2.27 (0.68), residues: 54 loop : -1.98 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 304 TYR 0.010 0.001 TYR A 124 PHE 0.005 0.001 PHE A 61 TRP 0.005 0.001 TRP B 60 HIS 0.004 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 8978) covalent geometry : angle 0.49011 (12198) hydrogen bonds : bond 0.03787 ( 509) hydrogen bonds : angle 4.36611 ( 1521) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ASP cc_start: 0.8387 (m-30) cc_final: 0.7981 (m-30) REVERT: A 238 MET cc_start: 0.9654 (ttm) cc_final: 0.9197 (tpp) REVERT: A 413 MET cc_start: 0.9393 (mmm) cc_final: 0.9189 (mmm) REVERT: A 543 MET cc_start: 0.8433 (tmm) cc_final: 0.8167 (tmm) REVERT: B 36 GLU cc_start: 0.9736 (tt0) cc_final: 0.9359 (mm-30) REVERT: B 78 MET cc_start: 0.8573 (ppp) cc_final: 0.8168 (ppp) REVERT: B 245 ASN cc_start: 0.9552 (t0) cc_final: 0.8991 (t0) REVERT: B 297 ASP cc_start: 0.9089 (m-30) cc_final: 0.8876 (m-30) REVERT: B 342 LEU cc_start: 0.9474 (tp) cc_final: 0.9176 (tt) outliers start: 5 outliers final: 5 residues processed: 97 average time/residue: 0.1557 time to fit residues: 23.8493 Evaluate side-chains 92 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 253 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 0.3980 chunk 99 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.056920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.048395 restraints weight = 121271.081| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 5.93 r_work: 0.2664 rms_B_bonded: 5.75 restraints_weight: 2.0000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| r_final: 0.2663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8978 Z= 0.122 Angle : 0.500 7.093 12198 Z= 0.261 Chirality : 0.037 0.139 1430 Planarity : 0.002 0.017 1540 Dihedral : 7.562 91.045 1370 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.55 % Allowed : 12.00 % Favored : 87.44 % 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 aren not related in a simple way. whole: 1.18 (0.26), residues: 1124 helix: 2.26 (0.19), residues: 714 sheet: -2.15 (0.69), residues: 54 loop : -1.96 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 72 TYR 0.010 0.001 TYR A 110 PHE 0.005 0.001 PHE A 29 TRP 0.003 0.001 TRP B 262 HIS 0.003 0.000 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8978) covalent geometry : angle 0.50018 (12198) hydrogen bonds : bond 0.03762 ( 509) hydrogen bonds : angle 4.35690 ( 1521) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue MET 188 is missing expected H atoms. Skipping. Residue LYS 328 is missing expected H atoms. Skipping. Residue THR 409 is missing expected H atoms. Skipping. Residue TYR 565 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ASP cc_start: 0.8404 (m-30) cc_final: 0.8196 (m-30) REVERT: A 238 MET cc_start: 0.9621 (ttm) cc_final: 0.9264 (tpp) REVERT: A 543 MET cc_start: 0.8395 (tmm) cc_final: 0.8131 (tmm) REVERT: B 72 ARG cc_start: 0.9431 (mmm-85) cc_final: 0.9094 (tpp80) REVERT: B 78 MET cc_start: 0.8650 (ppp) cc_final: 0.8243 (ppp) REVERT: B 297 ASP cc_start: 0.9125 (m-30) cc_final: 0.8899 (m-30) REVERT: B 342 LEU cc_start: 0.9488 (tp) cc_final: 0.9199 (tt) outliers start: 5 outliers final: 5 residues processed: 91 average time/residue: 0.1659 time to fit residues: 23.6910 Evaluate side-chains 91 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 253 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.056585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.048045 restraints weight = 122456.044| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 5.97 r_work: 0.2654 rms_B_bonded: 5.78 restraints_weight: 2.0000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8978 Z= 0.139 Angle : 0.503 6.730 12198 Z= 0.265 Chirality : 0.037 0.138 1430 Planarity : 0.002 0.017 1540 Dihedral : 7.575 90.556 1370 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.66 % Allowed : 12.22 % Favored : 87.11 % 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 aren not related in a simple way. whole: 1.17 (0.26), residues: 1124 helix: 2.24 (0.19), residues: 718 sheet: -2.14 (0.69), residues: 54 loop : -1.97 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 182 TYR 0.010 0.001 TYR A 124 PHE 0.006 0.001 PHE A 29 TRP 0.004 0.001 TRP B 262 HIS 0.003 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8978) covalent geometry : angle 0.50336 (12198) hydrogen bonds : bond 0.03734 ( 509) hydrogen bonds : angle 4.37649 ( 1521) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3294.50 seconds wall clock time: 57 minutes 7.93 seconds (3427.93 seconds total)