Starting phenix.real_space_refine on Mon Nov 18 23:55:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk7_40180/11_2024/8gk7_40180_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk7_40180/11_2024/8gk7_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk7_40180/11_2024/8gk7_40180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk7_40180/11_2024/8gk7_40180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk7_40180/11_2024/8gk7_40180_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gk7_40180/11_2024/8gk7_40180_trim.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} 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: {'GLN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} 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: 8.54, per 1000 atoms: 0.48 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: 5.13 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.43 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: 6.59 Time building geometry restraints manager: 5.96 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 569 or resid 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: 0.930 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: 0.290 Extract box with map and model: 0.610 Check model and map are aligned: 0.060 Set scattering table: 0.140 Process input model: 38.740 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.120 ------------------------------------------------------------------------------- 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= 0.279 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 : 6.23 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (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 TRP 0.010 0.001 TRP B 159 HIS 0.002 0.000 HIS A 452 PHE 0.010 0.001 PHE B 61 TYR 0.011 0.001 TYR A 124 ARG 0.001 0.000 ARG B 182 *********************** 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 : 1.431 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 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: 0.9057 (m) REVERT: B 36 GLU cc_start: 0.9244 (tt0) cc_final: 0.9009 (tt0) REVERT: B 145 MET cc_start: 0.9281 (ttp) cc_final: 0.9071 (ttp) 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: 0.4232 time to fit residues: 96.8200 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 : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN B 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8978 Z= 0.171 Angle : 0.518 5.597 12198 Z= 0.276 Chirality : 0.038 0.135 1430 Planarity : 0.003 0.036 1540 Dihedral : 9.725 120.511 1370 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.77 % Allowed : 6.06 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.27), residues: 1124 helix: 1.90 (0.20), residues: 704 sheet: -1.26 (0.87), residues: 44 loop : -1.91 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 159 HIS 0.003 0.001 HIS B 199 PHE 0.011 0.001 PHE B 61 TYR 0.015 0.001 TYR B 124 ARG 0.003 0.000 ARG B 72 *********************** 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 114 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 1.435 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: A 342 LEU cc_start: 0.8911 (tp) cc_final: 0.8538 (tp) REVERT: A 456 MET cc_start: 0.8977 (mpp) cc_final: 0.8609 (pmm) REVERT: A 543 MET cc_start: 0.7935 (tmm) cc_final: 0.7560 (tmm) REVERT: B 78 MET cc_start: 0.8499 (ppp) cc_final: 0.8063 (ppp) REVERT: B 145 MET cc_start: 0.9306 (ttp) cc_final: 0.9000 (ttp) REVERT: B 342 LEU cc_start: 0.8981 (tp) cc_final: 0.8521 (tp) REVERT: B 413 MET cc_start: 0.9167 (mmm) cc_final: 0.8615 (tpp) REVERT: B 543 MET cc_start: 0.8105 (tmm) cc_final: 0.7626 (tmm) outliers start: 7 outliers final: 4 residues processed: 112 average time/residue: 0.3324 time to fit residues: 58.6853 Evaluate side-chains 96 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 56 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 339 HIS A 428 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS B 529 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8978 Z= 0.321 Angle : 0.587 7.906 12198 Z= 0.319 Chirality : 0.037 0.137 1430 Planarity : 0.003 0.027 1540 Dihedral : 8.369 107.986 1370 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.55 % Allowed : 7.38 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1124 helix: 1.77 (0.19), residues: 718 sheet: -1.79 (0.76), residues: 54 loop : -2.06 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 262 HIS 0.003 0.001 HIS A 509 PHE 0.011 0.001 PHE A 278 TYR 0.015 0.001 TYR A 124 ARG 0.003 0.000 ARG A 72 *********************** 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 104 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 1.340 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 143 ASP cc_start: 0.8327 (m-30) cc_final: 0.7974 (m-30) REVERT: A 288 LEU cc_start: 0.9679 (tp) cc_final: 0.9451 (mt) REVERT: A 342 LEU cc_start: 0.9351 (tp) cc_final: 0.9129 (tt) REVERT: A 543 MET cc_start: 0.7960 (tmm) cc_final: 0.7694 (tmm) REVERT: B 36 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8625 (mm-30) REVERT: B 78 MET cc_start: 0.8573 (ppp) cc_final: 0.8178 (ppp) REVERT: B 245 ASN cc_start: 0.9562 (t0) cc_final: 0.9135 (t0) REVERT: B 342 LEU cc_start: 0.9348 (tp) cc_final: 0.8944 (tp) REVERT: B 403 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8283 (mt-10) REVERT: B 429 ILE cc_start: 0.9903 (mt) cc_final: 0.9664 (tp) REVERT: B 543 MET cc_start: 0.8017 (tmm) cc_final: 0.7783 (tmm) outliers start: 5 outliers final: 3 residues processed: 102 average time/residue: 0.3466 time to fit residues: 55.5181 Evaluate side-chains 93 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 1.548 ------------------------------------------------------------------------------- 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 76 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 HIS A 529 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8978 Z= 0.339 Angle : 0.585 7.367 12198 Z= 0.323 Chirality : 0.037 0.140 1430 Planarity : 0.003 0.022 1540 Dihedral : 8.797 105.041 1370 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.99 % Allowed : 9.14 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1124 helix: 1.59 (0.19), residues: 720 sheet: -3.04 (0.68), residues: 50 loop : -2.20 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 262 HIS 0.004 0.001 HIS B 452 PHE 0.010 0.001 PHE B 61 TYR 0.018 0.002 TYR A 124 ARG 0.003 0.000 ARG B 485 *********************** 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 101 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 1.379 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 342 LEU cc_start: 0.9464 (tp) cc_final: 0.9238 (tt) REVERT: A 543 MET cc_start: 0.8110 (tmm) cc_final: 0.7822 (tmm) REVERT: B 78 MET cc_start: 0.8610 (ppp) cc_final: 0.8173 (ppp) REVERT: B 245 ASN cc_start: 0.9563 (t0) cc_final: 0.8990 (t0) REVERT: B 257 MET cc_start: 0.9576 (OUTLIER) cc_final: 0.9207 (tpt) REVERT: B 297 ASP cc_start: 0.8921 (m-30) cc_final: 0.8658 (m-30) REVERT: B 342 LEU cc_start: 0.9337 (tp) cc_final: 0.8954 (tp) REVERT: B 403 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8354 (mt-10) REVERT: B 429 ILE cc_start: 0.9901 (mt) cc_final: 0.9671 (tp) REVERT: B 543 MET cc_start: 0.8075 (tmm) cc_final: 0.7823 (tmm) outliers start: 9 outliers final: 6 residues processed: 97 average time/residue: 0.3163 time to fit residues: 49.3625 Evaluate side-chains 96 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 1.539 ------------------------------------------------------------------------------- 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 255 CYS Chi-restraints excluded: chain B residue 257 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN B 117 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8978 Z= 0.234 Angle : 0.527 5.897 12198 Z= 0.284 Chirality : 0.037 0.152 1430 Planarity : 0.003 0.020 1540 Dihedral : 8.133 100.210 1370 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.66 % Allowed : 10.57 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1124 helix: 1.79 (0.19), residues: 722 sheet: -3.07 (0.67), residues: 50 loop : -2.22 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 262 HIS 0.002 0.001 HIS A 117 PHE 0.008 0.001 PHE A 29 TYR 0.011 0.001 TYR A 124 ARG 0.001 0.000 ARG A 72 *********************** 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 93 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 1.418 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: A 183 MET cc_start: 0.9598 (mtm) cc_final: 0.9394 (mtm) REVERT: A 342 LEU cc_start: 0.9417 (tp) cc_final: 0.9170 (tt) REVERT: A 413 MET cc_start: 0.9209 (mmm) cc_final: 0.8854 (mmm) REVERT: A 543 MET cc_start: 0.8151 (tmm) cc_final: 0.7872 (tmm) REVERT: B 36 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8593 (mm-30) REVERT: B 78 MET cc_start: 0.8615 (ppp) cc_final: 0.8180 (ppp) REVERT: B 245 ASN cc_start: 0.9547 (t0) cc_final: 0.9292 (t0) REVERT: B 297 ASP cc_start: 0.8933 (m-30) cc_final: 0.8691 (m-30) REVERT: B 342 LEU cc_start: 0.9379 (tp) cc_final: 0.9004 (tp) outliers start: 6 outliers final: 5 residues processed: 90 average time/residue: 0.3283 time to fit residues: 47.0717 Evaluate side-chains 88 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8978 Z= 0.235 Angle : 0.522 6.355 12198 Z= 0.282 Chirality : 0.037 0.151 1430 Planarity : 0.003 0.018 1540 Dihedral : 7.704 99.244 1370 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.77 % Allowed : 11.12 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1124 helix: 1.84 (0.19), residues: 724 sheet: -2.70 (0.65), residues: 54 loop : -2.25 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 262 HIS 0.003 0.001 HIS A 117 PHE 0.013 0.001 PHE B 61 TYR 0.012 0.001 TYR A 124 ARG 0.002 0.000 ARG A 72 *********************** 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 91 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 1.320 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 183 MET cc_start: 0.9626 (mtm) cc_final: 0.9424 (mtm) REVERT: A 297 ASP cc_start: 0.8939 (m-30) cc_final: 0.8675 (m-30) REVERT: A 342 LEU cc_start: 0.9425 (tp) cc_final: 0.9193 (tt) REVERT: A 413 MET cc_start: 0.9197 (mmm) cc_final: 0.8853 (mmm) REVERT: A 543 MET cc_start: 0.8209 (tmm) cc_final: 0.7929 (tmm) REVERT: B 78 MET cc_start: 0.8625 (ppp) cc_final: 0.8188 (ppp) REVERT: B 245 ASN cc_start: 0.9547 (t0) cc_final: 0.9305 (t0) REVERT: B 257 MET cc_start: 0.9576 (tpt) cc_final: 0.9192 (tpt) REVERT: B 297 ASP cc_start: 0.8924 (m-30) cc_final: 0.8651 (m-30) REVERT: B 342 LEU cc_start: 0.9418 (tp) cc_final: 0.9068 (tp) outliers start: 7 outliers final: 7 residues processed: 88 average time/residue: 0.3246 time to fit residues: 45.5275 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 : 1.339 ------------------------------------------------------------------------------- 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 240 ILE Chi-restraints excluded: chain B residue 253 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8978 Z= 0.186 Angle : 0.500 5.620 12198 Z= 0.266 Chirality : 0.037 0.156 1430 Planarity : 0.002 0.018 1540 Dihedral : 7.542 95.803 1370 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.77 % Allowed : 11.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 1124 helix: 1.99 (0.19), residues: 726 sheet: -2.58 (0.66), residues: 54 loop : -2.20 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 159 HIS 0.003 0.001 HIS A 117 PHE 0.012 0.001 PHE B 61 TYR 0.011 0.001 TYR A 124 ARG 0.002 0.000 ARG A 72 *********************** 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 94 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 1.318 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: 0.8308 (m-30) cc_final: 0.8076 (m-30) REVERT: A 342 LEU cc_start: 0.9424 (tp) cc_final: 0.9188 (tt) REVERT: A 413 MET cc_start: 0.9170 (mmm) cc_final: 0.8838 (mmm) REVERT: A 543 MET cc_start: 0.8239 (tmm) cc_final: 0.7973 (tmm) REVERT: B 72 ARG cc_start: 0.9488 (mmm-85) cc_final: 0.9110 (tpp80) REVERT: B 78 MET cc_start: 0.8643 (ppp) cc_final: 0.8169 (ppp) REVERT: B 245 ASN cc_start: 0.9527 (t0) cc_final: 0.8989 (t0) REVERT: B 297 ASP cc_start: 0.8908 (m-30) cc_final: 0.8641 (m-30) REVERT: B 342 LEU cc_start: 0.9407 (tp) cc_final: 0.9043 (tp) outliers start: 7 outliers final: 7 residues processed: 91 average time/residue: 0.3307 time to fit residues: 46.7669 Evaluate side-chains 88 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 240 ILE Chi-restraints excluded: chain B residue 253 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 8978 Z= 0.369 Angle : 0.590 7.902 12198 Z= 0.325 Chirality : 0.037 0.172 1430 Planarity : 0.003 0.020 1540 Dihedral : 7.779 101.795 1370 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.77 % Allowed : 12.00 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1124 helix: 1.57 (0.19), residues: 728 sheet: -2.61 (0.63), residues: 58 loop : -2.42 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 262 HIS 0.003 0.001 HIS B 509 PHE 0.010 0.001 PHE A 29 TYR 0.013 0.001 TYR A 124 ARG 0.002 0.000 ARG B 485 *********************** 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 96 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 1.353 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 48 ASP cc_start: 0.9265 (m-30) cc_final: 0.8907 (m-30) REVERT: A 297 ASP cc_start: 0.9002 (m-30) cc_final: 0.8741 (m-30) REVERT: A 413 MET cc_start: 0.9207 (mmm) cc_final: 0.8852 (mmm) REVERT: A 543 MET cc_start: 0.8206 (tmm) cc_final: 0.7925 (tmm) REVERT: B 36 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8581 (mm-30) REVERT: B 48 ASP cc_start: 0.9256 (m-30) cc_final: 0.8942 (m-30) REVERT: B 78 MET cc_start: 0.8690 (ppp) cc_final: 0.8265 (ppp) REVERT: B 245 ASN cc_start: 0.9563 (t0) cc_final: 0.9070 (t0) REVERT: B 297 ASP cc_start: 0.8959 (m-30) cc_final: 0.8719 (m-30) REVERT: B 342 LEU cc_start: 0.9482 (tp) cc_final: 0.9192 (tt) outliers start: 7 outliers final: 6 residues processed: 94 average time/residue: 0.3709 time to fit residues: 53.0696 Evaluate side-chains 92 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 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 240 ILE Chi-restraints excluded: chain B residue 253 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4528 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= 0.153 Angle : 0.501 6.314 12198 Z= 0.264 Chirality : 0.037 0.144 1430 Planarity : 0.002 0.018 1540 Dihedral : 7.556 95.592 1370 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.88 % Allowed : 12.44 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1124 helix: 2.03 (0.19), residues: 714 sheet: -2.47 (0.66), residues: 54 loop : -2.11 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 60 HIS 0.003 0.001 HIS A 117 PHE 0.012 0.001 PHE B 61 TYR 0.010 0.001 TYR A 124 ARG 0.001 0.000 ARG B 304 *********************** 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 98 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 1.458 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 48 ASP cc_start: 0.9240 (m-30) cc_final: 0.8938 (m-30) REVERT: A 297 ASP cc_start: 0.8933 (m-30) cc_final: 0.8664 (m-30) REVERT: A 413 MET cc_start: 0.9141 (mmm) cc_final: 0.8829 (mmm) REVERT: A 543 MET cc_start: 0.8305 (tmm) cc_final: 0.8051 (tmm) REVERT: B 36 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8256 (mm-30) REVERT: B 72 ARG cc_start: 0.9460 (mmm-85) cc_final: 0.8869 (tpp80) REVERT: B 78 MET cc_start: 0.8668 (ppp) cc_final: 0.8224 (ppp) REVERT: B 245 ASN cc_start: 0.9521 (t0) cc_final: 0.8981 (t0) REVERT: B 297 ASP cc_start: 0.8904 (m-30) cc_final: 0.8650 (m-30) REVERT: B 342 LEU cc_start: 0.9434 (tp) cc_final: 0.9116 (tt) outliers start: 8 outliers final: 8 residues processed: 94 average time/residue: 0.3494 time to fit residues: 51.3192 Evaluate side-chains 94 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 A residue 327 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 64 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4547 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= 0.150 Angle : 0.502 6.700 12198 Z= 0.262 Chirality : 0.037 0.175 1430 Planarity : 0.002 0.018 1540 Dihedral : 7.442 91.440 1370 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.77 % Allowed : 12.78 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1124 helix: 2.20 (0.19), residues: 714 sheet: -2.27 (0.68), residues: 54 loop : -2.00 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 159 HIS 0.003 0.000 HIS A 117 PHE 0.011 0.001 PHE B 61 TYR 0.010 0.001 TYR A 124 ARG 0.001 0.000 ARG A 72 ********************** 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 95 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 1.566 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 413 MET cc_start: 0.9141 (mmm) cc_final: 0.8828 (mmm) REVERT: A 543 MET cc_start: 0.8259 (tmm) cc_final: 0.7991 (tmm) REVERT: B 36 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8267 (mm-30) REVERT: B 72 ARG cc_start: 0.9467 (mmm-85) cc_final: 0.8850 (tpp80) REVERT: B 78 MET cc_start: 0.8690 (ppp) cc_final: 0.8215 (ppp) REVERT: B 245 ASN cc_start: 0.9498 (t0) cc_final: 0.8944 (t0) REVERT: B 297 ASP cc_start: 0.8917 (m-30) cc_final: 0.8653 (m-30) REVERT: B 342 LEU cc_start: 0.9413 (tp) cc_final: 0.9083 (tt) outliers start: 7 outliers final: 7 residues processed: 92 average time/residue: 0.3633 time to fit residues: 51.8763 Evaluate side-chains 93 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 327 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 81 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.056269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.047673 restraints weight = 128589.917| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 6.12 r_work: 0.2633 rms_B_bonded: 5.90 restraints_weight: 2.0000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 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 = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8791 | |-----------------------------------------------------------------------------| r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8978 Z= 0.195 Angle : 0.508 6.649 12198 Z= 0.271 Chirality : 0.037 0.137 1430 Planarity : 0.002 0.018 1540 Dihedral : 7.447 94.637 1370 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.77 % Allowed : 13.22 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1124 helix: 2.15 (0.19), residues: 714 sheet: -2.29 (0.69), residues: 54 loop : -2.00 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 262 HIS 0.003 0.001 HIS A 117 PHE 0.013 0.001 PHE B 61 TYR 0.012 0.001 TYR B 110 ARG 0.001 0.000 ARG A 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3524.07 seconds wall clock time: 63 minutes 52.83 seconds (3832.83 seconds total)