Starting phenix.real_space_refine on Thu May 15 05:35:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t50_41041/05_2025/8t50_41041.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t50_41041/05_2025/8t50_41041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t50_41041/05_2025/8t50_41041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t50_41041/05_2025/8t50_41041.map" model { file = "/net/cci-nas-00/data/ceres_data/8t50_41041/05_2025/8t50_41041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t50_41041/05_2025/8t50_41041.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 56 5.16 5 C 8016 2.51 5 N 2280 2.21 5 O 2364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12720 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3158 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 12, 'TRANS': 461} Chain breaks: 5 Unresolved non-hydrogen bonds: 754 Unresolved non-hydrogen angles: 942 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 14, 'GLU:plan': 11, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 361 Chain: "B" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3158 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 12, 'TRANS': 461} Chain breaks: 5 Unresolved non-hydrogen bonds: 754 Unresolved non-hydrogen angles: 942 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 14, 'GLU:plan': 11, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 361 Chain: "A" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3158 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 12, 'TRANS': 461} Chain breaks: 5 Unresolved non-hydrogen bonds: 754 Unresolved non-hydrogen angles: 942 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 14, 'GLU:plan': 11, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 361 Chain: "D" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3158 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 12, 'TRANS': 461} Chain breaks: 5 Unresolved non-hydrogen bonds: 754 Unresolved non-hydrogen angles: 942 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 14, 'GLU:plan': 11, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 361 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 8.08, per 1000 atoms: 0.64 Number of scatterers: 12720 At special positions: 0 Unit cell: (105.342, 105.342, 115.116, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 4 15.00 O 2364 8.00 N 2280 7.00 C 8016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 385 " distance=2.04 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 385 " distance=2.04 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 385 " distance=2.04 Simple disulfide: pdb=" SG CYS D 309 " - pdb=" SG CYS D 385 " distance=2.04 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: 3.54 Conformation dependent library (CDL) restraints added in 2.0 seconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 77.8% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'C' and resid 107 through 115 removed outlier: 4.131A pdb=" N LEU C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 130 Processing helix chain 'C' and resid 141 through 165 Proline residue: C 161 - end of helix removed outlier: 3.766A pdb=" N THR C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 195 Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 221 through 229 Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'C' and resid 253 through 259 Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 263 through 285 removed outlier: 3.895A pdb=" N ARG C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 324 removed outlier: 3.622A pdb=" N ASN C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 341 through 358 Processing helix chain 'C' and resid 368 through 422 removed outlier: 3.573A pdb=" N LEU C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYR C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 452 Processing helix chain 'C' and resid 454 through 466 Processing helix chain 'C' and resid 466 through 473 removed outlier: 3.713A pdb=" N MET C 473 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 479 removed outlier: 3.687A pdb=" N ALA C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 490 Processing helix chain 'C' and resid 539 through 546 removed outlier: 3.618A pdb=" N LEU C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 576 Processing helix chain 'C' and resid 576 through 595 removed outlier: 4.005A pdb=" N ARG C 580 " --> pdb=" O TYR C 576 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 581 " --> pdb=" O PRO C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 606 Processing helix chain 'C' and resid 617 through 634 Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 116 through 130 Processing helix chain 'B' and resid 141 through 165 Proline residue: B 161 - end of helix removed outlier: 3.766A pdb=" N THR B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 195 Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'B' and resid 231 through 242 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 263 through 285 removed outlier: 3.902A pdb=" N ARG B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 324 removed outlier: 3.641A pdb=" N ASN B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 341 through 357 Processing helix chain 'B' and resid 368 through 422 removed outlier: 3.584A pdb=" N LEU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TYR B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 439 Processing helix chain 'B' and resid 445 through 452 Processing helix chain 'B' and resid 454 through 466 Processing helix chain 'B' and resid 466 through 473 removed outlier: 3.761A pdb=" N MET B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.750A pdb=" N ALA B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 539 through 546 removed outlier: 3.515A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 576 Processing helix chain 'B' and resid 576 through 595 removed outlier: 4.040A pdb=" N ARG B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG B 581 " --> pdb=" O PRO B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 606 Processing helix chain 'B' and resid 617 through 634 Processing helix chain 'A' and resid 108 through 115 Processing helix chain 'A' and resid 116 through 130 Processing helix chain 'A' and resid 141 through 165 Proline residue: A 161 - end of helix removed outlier: 3.766A pdb=" N THR A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 195 Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 253 through 259 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 263 through 285 removed outlier: 3.894A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 324 removed outlier: 3.635A pdb=" N ASN A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 341 through 358 Processing helix chain 'A' and resid 368 through 422 removed outlier: 3.625A pdb=" N LEU A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TYR A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 454 through 466 Processing helix chain 'A' and resid 466 through 473 removed outlier: 3.676A pdb=" N MET A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.704A pdb=" N ALA A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.519A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 Processing helix chain 'A' and resid 576 through 595 removed outlier: 4.025A pdb=" N ARG A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 581 " --> pdb=" O PRO A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 606 Processing helix chain 'A' and resid 617 through 634 Processing helix chain 'D' and resid 108 through 115 Processing helix chain 'D' and resid 116 through 130 Processing helix chain 'D' and resid 141 through 165 Proline residue: D 161 - end of helix removed outlier: 3.766A pdb=" N THR D 165 " --> pdb=" O PRO D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 195 Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 242 Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.892A pdb=" N ARG D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 324 removed outlier: 3.641A pdb=" N ASN D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 341 through 358 Processing helix chain 'D' and resid 368 through 422 removed outlier: 4.417A pdb=" N ARG D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR D 407 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 454 through 466 Processing helix chain 'D' and resid 466 through 473 removed outlier: 3.551A pdb=" N MET D 473 " --> pdb=" O LEU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 479 removed outlier: 3.668A pdb=" N ALA D 477 " --> pdb=" O MET D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 490 Processing helix chain 'D' and resid 539 through 546 removed outlier: 3.553A pdb=" N LEU D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 576 Processing helix chain 'D' and resid 576 through 595 removed outlier: 4.023A pdb=" N ARG D 580 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 581 " --> pdb=" O PRO D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 606 Processing helix chain 'D' and resid 617 through 634 Processing sheet with id=AA1, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.395A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER C 536 " --> pdb=" O ILE C 515 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.147A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 503 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.391A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER B 536 " --> pdb=" O ILE B 515 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.217A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 503 " --> pdb=" O VAL B 553 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.390A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 536 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.197A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 503 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.324A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER D 536 " --> pdb=" O ILE D 515 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.189A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 503 " --> pdb=" O VAL D 553 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 3309 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: 4.51 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4362 1.35 - 1.46: 3221 1.46 - 1.58: 5293 1.58 - 1.70: 8 1.70 - 1.82: 88 Bond restraints: 12972 Sorted by residual: bond pdb=" C3' CMP D 901 " pdb=" C4' CMP D 901 " ideal model delta sigma weight residual 1.521 1.499 0.022 1.50e-02 4.44e+03 2.15e+00 bond pdb=" C3' CMP B 901 " pdb=" C4' CMP B 901 " ideal model delta sigma weight residual 1.521 1.499 0.022 1.50e-02 4.44e+03 2.15e+00 bond pdb=" C3' CMP C 901 " pdb=" C4' CMP C 901 " ideal model delta sigma weight residual 1.521 1.499 0.022 1.50e-02 4.44e+03 2.11e+00 bond pdb=" C3' CMP A 901 " pdb=" C4' CMP A 901 " ideal model delta sigma weight residual 1.521 1.499 0.022 1.50e-02 4.44e+03 2.06e+00 bond pdb=" C4 CMP D 901 " pdb=" C5 CMP D 901 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.20e+00 ... (remaining 12967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 17338 1.78 - 3.56: 340 3.56 - 5.34: 76 5.34 - 7.13: 13 7.13 - 8.91: 9 Bond angle restraints: 17776 Sorted by residual: angle pdb=" CA LYS C 422 " pdb=" CB LYS C 422 " pdb=" CG LYS C 422 " ideal model delta sigma weight residual 114.10 121.15 -7.05 2.00e+00 2.50e-01 1.24e+01 angle pdb=" CA LYS D 422 " pdb=" CB LYS D 422 " pdb=" CG LYS D 422 " ideal model delta sigma weight residual 114.10 120.82 -6.72 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CA LYS B 422 " pdb=" CB LYS B 422 " pdb=" CG LYS B 422 " ideal model delta sigma weight residual 114.10 120.74 -6.64 2.00e+00 2.50e-01 1.10e+01 angle pdb=" CA LYS A 422 " pdb=" CB LYS A 422 " pdb=" CG LYS A 422 " ideal model delta sigma weight residual 114.10 120.73 -6.63 2.00e+00 2.50e-01 1.10e+01 angle pdb=" C THR D 472 " pdb=" N MET D 473 " pdb=" CA MET D 473 " ideal model delta sigma weight residual 120.69 111.79 8.90 2.95e+00 1.15e-01 9.11e+00 ... (remaining 17771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.61: 7206 25.61 - 51.22: 339 51.22 - 76.82: 18 76.82 - 102.43: 1 102.43 - 128.04: 4 Dihedral angle restraints: 7568 sinusoidal: 2000 harmonic: 5568 Sorted by residual: dihedral pdb=" CA PHE B 285 " pdb=" C PHE B 285 " pdb=" N HIS B 286 " pdb=" CA HIS B 286 " ideal model delta harmonic sigma weight residual 180.00 -157.56 -22.44 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA LEU C 561 " pdb=" C LEU C 561 " pdb=" N TYR C 562 " pdb=" CA TYR C 562 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA LEU D 561 " pdb=" C LEU D 561 " pdb=" N TYR D 562 " pdb=" CA TYR D 562 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 7565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1695 0.053 - 0.106: 333 0.106 - 0.159: 32 0.159 - 0.212: 0 0.212 - 0.265: 4 Chirality restraints: 2064 Sorted by residual: chirality pdb=" CG LEU A 377 " pdb=" CB LEU A 377 " pdb=" CD1 LEU A 377 " pdb=" CD2 LEU A 377 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CG LEU B 377 " pdb=" CB LEU B 377 " pdb=" CD1 LEU B 377 " pdb=" CD2 LEU B 377 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CG LEU D 377 " pdb=" CB LEU D 377 " pdb=" CD1 LEU D 377 " pdb=" CD2 LEU D 377 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 2061 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 422 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C LYS C 422 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS C 422 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU C 423 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 175 " -0.009 2.00e-02 2.50e+03 9.93e-03 2.47e+00 pdb=" CG TRP C 175 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP C 175 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 175 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 175 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 175 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 175 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 175 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 175 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 175 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 175 " 0.009 2.00e-02 2.50e+03 9.93e-03 2.47e+00 pdb=" CG TRP B 175 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP B 175 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 175 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 175 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 175 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 175 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 175 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 175 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 175 " -0.000 2.00e-02 2.50e+03 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 779 2.74 - 3.28: 13663 3.28 - 3.82: 22225 3.82 - 4.36: 21370 4.36 - 4.90: 38295 Nonbonded interactions: 96332 Sorted by model distance: nonbonded pdb=" N GLU C 540 " pdb=" OE1 GLU C 540 " model vdw 2.194 3.120 nonbonded pdb=" OH TYR C 435 " pdb=" OE2 GLU D 452 " model vdw 2.202 3.040 nonbonded pdb=" OE2 GLU B 452 " pdb=" OH TYR A 435 " model vdw 2.229 3.040 nonbonded pdb=" OE2 GLU A 452 " pdb=" OH TYR D 435 " model vdw 2.251 3.040 nonbonded pdb=" OE1 GLU B 540 " pdb=" O2' CMP B 901 " model vdw 2.252 3.040 ... (remaining 96327 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.880 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: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.580 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 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 : 0.003 0.030 12976 Z= 0.155 Angle : 0.671 8.908 17784 Z= 0.371 Chirality : 0.040 0.265 2064 Planarity : 0.003 0.031 2344 Dihedral : 14.504 128.040 3932 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.47 % Allowed : 20.19 % Favored : 79.34 % 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: 2.00 (0.19), residues: 1848 helix: 2.20 (0.14), residues: 1360 sheet: 1.23 (0.48), residues: 84 loop : -1.84 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 175 HIS 0.005 0.001 HIS A 517 PHE 0.026 0.001 PHE D 420 TYR 0.014 0.001 TYR B 411 ARG 0.006 0.001 ARG A 581 Details of bonding type rmsd hydrogen bonds : bond 0.09013 ( 1119) hydrogen bonds : angle 5.02287 ( 3309) SS BOND : bond 0.00613 ( 4) SS BOND : angle 1.35853 ( 8) covalent geometry : bond 0.00303 (12972) covalent geometry : angle 0.67070 (17776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 311 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 GLN cc_start: 0.7954 (mm110) cc_final: 0.7317 (tp40) REVERT: C 419 SER cc_start: 0.9406 (t) cc_final: 0.9023 (p) REVERT: C 562 TYR cc_start: 0.8333 (m-80) cc_final: 0.6822 (m-80) REVERT: B 408 GLN cc_start: 0.7872 (mm110) cc_final: 0.7228 (tp40) REVERT: B 419 SER cc_start: 0.9481 (t) cc_final: 0.9266 (p) REVERT: B 562 TYR cc_start: 0.8399 (m-80) cc_final: 0.7041 (m-80) REVERT: A 562 TYR cc_start: 0.8236 (m-80) cc_final: 0.7009 (m-80) REVERT: D 418 MET cc_start: 0.7942 (mtm) cc_final: 0.7636 (mtp) REVERT: D 419 SER cc_start: 0.9452 (t) cc_final: 0.9054 (p) outliers start: 4 outliers final: 1 residues processed: 312 average time/residue: 0.2217 time to fit residues: 99.7118 Evaluate side-chains 288 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 287 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 79 optimal weight: 0.0170 chunk 48 optimal weight: 30.0000 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 109 optimal weight: 20.0000 chunk 170 optimal weight: 1.9990 overall best weight: 1.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 GLN C 478 ASN B 286 HIS B 413 GLN B 478 ASN A 286 HIS A 413 GLN A 478 ASN D 286 HIS D 413 GLN D 478 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.223227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.154628 restraints weight = 16737.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.157015 restraints weight = 10705.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.157195 restraints weight = 7836.993| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12976 Z= 0.195 Angle : 0.625 10.958 17784 Z= 0.323 Chirality : 0.043 0.246 2064 Planarity : 0.004 0.037 2344 Dihedral : 7.371 130.063 2042 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.40 % Allowed : 18.90 % Favored : 75.70 % 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: 2.12 (0.19), residues: 1848 helix: 2.31 (0.14), residues: 1372 sheet: 1.04 (0.50), residues: 84 loop : -1.95 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 175 HIS 0.006 0.001 HIS D 517 PHE 0.017 0.002 PHE C 166 TYR 0.015 0.001 TYR C 411 ARG 0.007 0.001 ARG C 581 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 1119) hydrogen bonds : angle 4.41185 ( 3309) SS BOND : bond 0.00336 ( 4) SS BOND : angle 0.60883 ( 8) covalent geometry : bond 0.00438 (12972) covalent geometry : angle 0.62454 (17776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 GLN cc_start: 0.8261 (mm110) cc_final: 0.7678 (tp40) REVERT: B 408 GLN cc_start: 0.8170 (mm110) cc_final: 0.7800 (tp40) REVERT: B 562 TYR cc_start: 0.8136 (m-80) cc_final: 0.7854 (m-80) REVERT: D 540 GLU cc_start: 0.7180 (pm20) cc_final: 0.6873 (pm20) outliers start: 46 outliers final: 44 residues processed: 311 average time/residue: 0.2219 time to fit residues: 101.4648 Evaluate side-chains 321 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 277 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 564 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 11 optimal weight: 60.0000 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 182 optimal weight: 0.0980 chunk 129 optimal weight: 0.9980 chunk 155 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 142 optimal weight: 50.0000 chunk 57 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 GLN C 416 GLN C 478 ASN B 413 GLN B 463 ASN B 478 ASN A 413 GLN D 413 GLN D 416 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.226123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.155833 restraints weight = 16768.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.159758 restraints weight = 10682.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.162514 restraints weight = 8012.926| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12976 Z= 0.134 Angle : 0.568 8.779 17784 Z= 0.294 Chirality : 0.040 0.229 2064 Planarity : 0.003 0.037 2344 Dihedral : 7.381 131.862 2042 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.16 % Allowed : 19.25 % Favored : 75.59 % 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: 2.14 (0.19), residues: 1848 helix: 2.35 (0.14), residues: 1376 sheet: 0.97 (0.48), residues: 84 loop : -2.07 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 175 HIS 0.004 0.001 HIS A 517 PHE 0.014 0.001 PHE B 166 TYR 0.023 0.001 TYR D 439 ARG 0.008 0.000 ARG C 581 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 1119) hydrogen bonds : angle 4.19378 ( 3309) SS BOND : bond 0.00321 ( 4) SS BOND : angle 0.65106 ( 8) covalent geometry : bond 0.00275 (12972) covalent geometry : angle 0.56767 (17776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 290 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9263 (t80) cc_final: 0.8937 (t80) REVERT: C 408 GLN cc_start: 0.8225 (mm110) cc_final: 0.7529 (tp40) REVERT: C 581 ARG cc_start: 0.8047 (ttm110) cc_final: 0.7664 (mtm110) REVERT: B 408 GLN cc_start: 0.8187 (mm110) cc_final: 0.7572 (tp40) REVERT: A 540 GLU cc_start: 0.6948 (pm20) cc_final: 0.6729 (pm20) REVERT: A 562 TYR cc_start: 0.8302 (m-80) cc_final: 0.7443 (m-80) REVERT: D 562 TYR cc_start: 0.8253 (m-80) cc_final: 0.7435 (m-80) outliers start: 44 outliers final: 39 residues processed: 313 average time/residue: 0.2143 time to fit residues: 98.8345 Evaluate side-chains 313 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 274 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 564 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 6 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 94 optimal weight: 50.0000 chunk 76 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 121 optimal weight: 0.0170 chunk 185 optimal weight: 20.0000 chunk 99 optimal weight: 40.0000 chunk 152 optimal weight: 60.0000 overall best weight: 1.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 GLN C 463 ASN C 478 ASN B 413 GLN A 413 GLN A 463 ASN D 413 GLN D 463 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.222138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.150471 restraints weight = 16893.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.153404 restraints weight = 11646.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.154458 restraints weight = 8658.777| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12976 Z= 0.227 Angle : 0.634 9.881 17784 Z= 0.329 Chirality : 0.043 0.221 2064 Planarity : 0.004 0.032 2344 Dihedral : 7.332 129.178 2042 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 7.39 % Allowed : 19.95 % Favored : 72.65 % 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: 2.12 (0.20), residues: 1848 helix: 2.35 (0.14), residues: 1376 sheet: 0.93 (0.49), residues: 84 loop : -2.17 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 175 HIS 0.007 0.001 HIS B 517 PHE 0.018 0.002 PHE C 538 TYR 0.018 0.002 TYR B 411 ARG 0.004 0.000 ARG C 581 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 1119) hydrogen bonds : angle 4.27276 ( 3309) SS BOND : bond 0.00428 ( 4) SS BOND : angle 0.57909 ( 8) covalent geometry : bond 0.00522 (12972) covalent geometry : angle 0.63396 (17776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 276 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9179 (t80) cc_final: 0.8845 (t80) REVERT: C 408 GLN cc_start: 0.8258 (mm110) cc_final: 0.7622 (tp40) REVERT: C 581 ARG cc_start: 0.8211 (ttm110) cc_final: 0.7745 (mtm110) REVERT: B 408 GLN cc_start: 0.8185 (mm110) cc_final: 0.7628 (tp40) REVERT: A 540 GLU cc_start: 0.7151 (pm20) cc_final: 0.6843 (pm20) REVERT: D 540 GLU cc_start: 0.7167 (pm20) cc_final: 0.6962 (pm20) outliers start: 63 outliers final: 52 residues processed: 315 average time/residue: 0.2243 time to fit residues: 103.9866 Evaluate side-chains 314 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 564 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 101 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 168 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 76 optimal weight: 0.0570 chunk 4 optimal weight: 8.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 GLN A 413 GLN A 463 ASN D 413 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.224607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.157468 restraints weight = 16848.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.156895 restraints weight = 12446.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.158414 restraints weight = 9492.397| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12976 Z= 0.147 Angle : 0.583 8.556 17784 Z= 0.301 Chirality : 0.041 0.208 2064 Planarity : 0.003 0.030 2344 Dihedral : 7.373 131.376 2042 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 6.34 % Allowed : 22.54 % Favored : 71.13 % 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: 2.20 (0.20), residues: 1848 helix: 2.40 (0.14), residues: 1376 sheet: 1.02 (0.45), residues: 84 loop : -2.12 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 175 HIS 0.004 0.001 HIS A 517 PHE 0.016 0.002 PHE D 317 TYR 0.017 0.001 TYR B 411 ARG 0.003 0.000 ARG C 581 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 1119) hydrogen bonds : angle 4.11824 ( 3309) SS BOND : bond 0.00351 ( 4) SS BOND : angle 0.63365 ( 8) covalent geometry : bond 0.00320 (12972) covalent geometry : angle 0.58340 (17776) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 287 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9206 (t80) cc_final: 0.8932 (t80) REVERT: C 408 GLN cc_start: 0.8203 (mm110) cc_final: 0.7546 (tp40) REVERT: C 581 ARG cc_start: 0.8139 (ttm110) cc_final: 0.7792 (mtm110) REVERT: B 284 ILE cc_start: 0.7032 (tt) cc_final: 0.6791 (tp) REVERT: B 408 GLN cc_start: 0.8185 (mm110) cc_final: 0.7516 (tp40) REVERT: B 540 GLU cc_start: 0.7058 (pm20) cc_final: 0.6823 (pm20) REVERT: D 284 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6706 (tp) REVERT: D 540 GLU cc_start: 0.7027 (pm20) cc_final: 0.6795 (pm20) outliers start: 54 outliers final: 53 residues processed: 318 average time/residue: 0.2234 time to fit residues: 104.4940 Evaluate side-chains 323 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 269 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 554 ARG Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 564 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 74 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 53 optimal weight: 40.0000 chunk 99 optimal weight: 30.0000 chunk 115 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 86 optimal weight: 0.6980 chunk 76 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 478 ASN B 413 GLN A 413 GLN D 413 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.224191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.152461 restraints weight = 17070.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.156349 restraints weight = 10910.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.159036 restraints weight = 8244.165| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12976 Z= 0.161 Angle : 0.599 8.824 17784 Z= 0.309 Chirality : 0.041 0.192 2064 Planarity : 0.003 0.030 2344 Dihedral : 7.318 130.460 2042 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 7.86 % Allowed : 22.54 % Favored : 69.60 % 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: 2.22 (0.20), residues: 1848 helix: 2.43 (0.14), residues: 1376 sheet: 1.03 (0.43), residues: 84 loop : -2.16 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 175 HIS 0.004 0.001 HIS D 517 PHE 0.013 0.002 PHE C 538 TYR 0.015 0.001 TYR B 411 ARG 0.003 0.000 ARG A 590 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 1119) hydrogen bonds : angle 4.09285 ( 3309) SS BOND : bond 0.00348 ( 4) SS BOND : angle 0.69271 ( 8) covalent geometry : bond 0.00359 (12972) covalent geometry : angle 0.59865 (17776) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 275 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9278 (t80) cc_final: 0.8989 (t80) REVERT: C 408 GLN cc_start: 0.8220 (mm110) cc_final: 0.7580 (tp40) REVERT: C 581 ARG cc_start: 0.8065 (ttm110) cc_final: 0.7849 (mtm110) REVERT: B 284 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.7017 (tp) REVERT: B 408 GLN cc_start: 0.8113 (mm110) cc_final: 0.7488 (tp40) REVERT: A 540 GLU cc_start: 0.6819 (pm20) cc_final: 0.6520 (pm20) REVERT: D 280 GLN cc_start: 0.8083 (tp40) cc_final: 0.7869 (tp40) REVERT: D 284 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6909 (tp) outliers start: 67 outliers final: 62 residues processed: 314 average time/residue: 0.2108 time to fit residues: 98.8345 Evaluate side-chains 330 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 266 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 564 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 102 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 45 optimal weight: 30.0000 chunk 74 optimal weight: 0.0170 chunk 147 optimal weight: 40.0000 chunk 107 optimal weight: 50.0000 chunk 106 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 9 optimal weight: 10.0000 overall best weight: 5.0028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 463 ASN B 413 GLN A 413 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.215291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.145942 restraints weight = 17044.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.147978 restraints weight = 12866.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.146688 restraints weight = 9258.974| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.092 12976 Z= 0.495 Angle : 0.858 12.414 17784 Z= 0.448 Chirality : 0.049 0.188 2064 Planarity : 0.005 0.050 2344 Dihedral : 7.440 124.852 2042 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 8.45 % Allowed : 22.65 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.81 (0.20), residues: 1848 helix: 2.10 (0.14), residues: 1408 sheet: 0.93 (0.46), residues: 84 loop : -2.59 (0.27), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 175 HIS 0.016 0.002 HIS B 517 PHE 0.033 0.004 PHE A 538 TYR 0.019 0.003 TYR D 434 ARG 0.006 0.001 ARG A 438 Details of bonding type rmsd hydrogen bonds : bond 0.04922 ( 1119) hydrogen bonds : angle 4.70178 ( 3309) SS BOND : bond 0.00715 ( 4) SS BOND : angle 0.81223 ( 8) covalent geometry : bond 0.01164 (12972) covalent geometry : angle 0.85756 (17776) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 268 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9270 (t80) cc_final: 0.9006 (t80) REVERT: C 408 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7873 (tp40) REVERT: C 573 LEU cc_start: 0.8115 (tp) cc_final: 0.7912 (tp) REVERT: B 286 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.6663 (m-70) REVERT: B 408 GLN cc_start: 0.8276 (mm110) cc_final: 0.7953 (tp40) REVERT: B 554 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7298 (ptt90) REVERT: A 554 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7329 (ptt90) outliers start: 72 outliers final: 59 residues processed: 309 average time/residue: 0.2068 time to fit residues: 96.2043 Evaluate side-chains 326 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 263 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 109 optimal weight: 0.3980 chunk 112 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 92 optimal weight: 40.0000 chunk 145 optimal weight: 7.9990 chunk 45 optimal weight: 50.0000 chunk 43 optimal weight: 0.8980 chunk 160 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 482 ASN B 413 GLN B 478 ASN B 482 ASN A 413 GLN A 478 ASN D 478 ASN D 482 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.221204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.150342 restraints weight = 17055.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.153679 restraints weight = 13081.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.154697 restraints weight = 9135.793| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12976 Z= 0.193 Angle : 0.637 10.203 17784 Z= 0.331 Chirality : 0.042 0.181 2064 Planarity : 0.004 0.035 2344 Dihedral : 7.499 131.235 2042 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 7.98 % Allowed : 24.06 % Favored : 67.96 % 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: 1.94 (0.19), residues: 1848 helix: 2.28 (0.14), residues: 1384 sheet: 1.03 (0.43), residues: 84 loop : -2.63 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 175 HIS 0.006 0.001 HIS A 517 PHE 0.014 0.002 PHE A 538 TYR 0.018 0.001 TYR A 411 ARG 0.006 0.000 ARG D 581 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 1119) hydrogen bonds : angle 4.28465 ( 3309) SS BOND : bond 0.00407 ( 4) SS BOND : angle 0.60105 ( 8) covalent geometry : bond 0.00441 (12972) covalent geometry : angle 0.63695 (17776) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 275 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9166 (t80) cc_final: 0.8897 (t80) REVERT: C 408 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7510 (tp40) REVERT: C 540 GLU cc_start: 0.7162 (pm20) cc_final: 0.6924 (pm20) REVERT: B 408 GLN cc_start: 0.8203 (mm110) cc_final: 0.7493 (tp40) REVERT: A 540 GLU cc_start: 0.7175 (pm20) cc_final: 0.6806 (pm20) REVERT: A 554 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7103 (ptt90) REVERT: D 280 GLN cc_start: 0.8067 (tp40) cc_final: 0.7820 (tp40) REVERT: D 284 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6605 (tp) REVERT: D 473 MET cc_start: 0.7962 (ptp) cc_final: 0.7723 (ptp) outliers start: 68 outliers final: 61 residues processed: 316 average time/residue: 0.2003 time to fit residues: 95.3320 Evaluate side-chains 333 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 269 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 564 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 169 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 GLN A 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.222312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.150168 restraints weight = 17040.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.153906 restraints weight = 10982.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.156500 restraints weight = 8317.422| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12976 Z= 0.175 Angle : 0.624 11.458 17784 Z= 0.323 Chirality : 0.042 0.175 2064 Planarity : 0.003 0.032 2344 Dihedral : 7.431 131.481 2042 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 7.51 % Allowed : 24.77 % Favored : 67.72 % 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: 2.11 (0.20), residues: 1848 helix: 2.39 (0.14), residues: 1368 sheet: 1.12 (0.41), residues: 84 loop : -2.33 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 175 HIS 0.006 0.001 HIS A 517 PHE 0.013 0.002 PHE C 166 TYR 0.017 0.001 TYR B 411 ARG 0.006 0.000 ARG D 581 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 1119) hydrogen bonds : angle 4.16049 ( 3309) SS BOND : bond 0.00336 ( 4) SS BOND : angle 0.71470 ( 8) covalent geometry : bond 0.00395 (12972) covalent geometry : angle 0.62365 (17776) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 275 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9262 (t80) cc_final: 0.8979 (t80) REVERT: C 408 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7507 (tp40) REVERT: B 280 GLN cc_start: 0.8135 (tp40) cc_final: 0.7903 (tp40) REVERT: B 408 GLN cc_start: 0.8132 (mm110) cc_final: 0.7434 (tp40) REVERT: B 573 LEU cc_start: 0.7926 (tp) cc_final: 0.7715 (tp) REVERT: A 540 GLU cc_start: 0.7137 (pm20) cc_final: 0.6767 (pm20) REVERT: A 554 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7078 (ptt90) REVERT: D 280 GLN cc_start: 0.8171 (tp40) cc_final: 0.7919 (tp40) REVERT: D 284 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6971 (tp) REVERT: D 410 LYS cc_start: 0.8354 (ttpt) cc_final: 0.8052 (ttpp) outliers start: 64 outliers final: 61 residues processed: 313 average time/residue: 0.1997 time to fit residues: 94.3483 Evaluate side-chains 333 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 269 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 564 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 55 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 98 optimal weight: 0.0870 chunk 145 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 GLN A 413 GLN D 568 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.220047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.159128 restraints weight = 16973.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.154653 restraints weight = 11640.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.154093 restraints weight = 8838.666| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12976 Z= 0.251 Angle : 0.687 11.624 17784 Z= 0.356 Chirality : 0.044 0.171 2064 Planarity : 0.004 0.035 2344 Dihedral : 7.421 129.460 2042 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 7.63 % Allowed : 24.41 % Favored : 67.96 % 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: 2.06 (0.20), residues: 1848 helix: 2.37 (0.14), residues: 1368 sheet: 1.21 (0.41), residues: 84 loop : -2.44 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 175 HIS 0.008 0.001 HIS C 517 PHE 0.019 0.002 PHE A 538 TYR 0.015 0.002 TYR C 411 ARG 0.006 0.000 ARG D 581 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 1119) hydrogen bonds : angle 4.24233 ( 3309) SS BOND : bond 0.00474 ( 4) SS BOND : angle 0.61126 ( 8) covalent geometry : bond 0.00588 (12972) covalent geometry : angle 0.68711 (17776) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 272 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9301 (t80) cc_final: 0.9031 (t80) REVERT: C 408 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7543 (tp40) REVERT: B 280 GLN cc_start: 0.8131 (tp40) cc_final: 0.7893 (tp40) REVERT: B 408 GLN cc_start: 0.8184 (mm110) cc_final: 0.7511 (tp40) REVERT: A 540 GLU cc_start: 0.7227 (pm20) cc_final: 0.6894 (pm20) REVERT: A 554 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7139 (ptt90) REVERT: D 280 GLN cc_start: 0.8163 (tp40) cc_final: 0.7907 (tp40) REVERT: D 284 ILE cc_start: 0.7239 (OUTLIER) cc_final: 0.6936 (tp) REVERT: D 410 LYS cc_start: 0.8428 (ttpt) cc_final: 0.8131 (ttpp) outliers start: 65 outliers final: 61 residues processed: 312 average time/residue: 0.2008 time to fit residues: 94.9999 Evaluate side-chains 333 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 269 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 564 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 145 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 47 optimal weight: 60.0000 chunk 36 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 125 optimal weight: 0.7980 chunk 21 optimal weight: 20.0000 chunk 179 optimal weight: 1.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 GLN A 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.219744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.151166 restraints weight = 17041.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.153429 restraints weight = 12944.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.153644 restraints weight = 8271.241| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12976 Z= 0.255 Angle : 0.686 11.422 17784 Z= 0.356 Chirality : 0.043 0.171 2064 Planarity : 0.004 0.036 2344 Dihedral : 7.437 129.751 2042 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 7.75 % Allowed : 24.88 % Favored : 67.37 % 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: 2.01 (0.20), residues: 1848 helix: 2.35 (0.14), residues: 1376 sheet: 1.24 (0.40), residues: 84 loop : -2.63 (0.26), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 175 HIS 0.008 0.001 HIS B 517 PHE 0.019 0.002 PHE A 538 TYR 0.016 0.002 TYR A 411 ARG 0.009 0.001 ARG A 581 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 1119) hydrogen bonds : angle 4.24945 ( 3309) SS BOND : bond 0.00426 ( 4) SS BOND : angle 0.64924 ( 8) covalent geometry : bond 0.00596 (12972) covalent geometry : angle 0.68608 (17776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4339.30 seconds wall clock time: 76 minutes 12.69 seconds (4572.69 seconds total)