Starting phenix.real_space_refine on Sat Aug 23 14:41:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t50_41041/08_2025/8t50_41041.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t50_41041/08_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_41041/08_2025/8t50_41041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t50_41041/08_2025/8t50_41041.map" model { file = "/net/cci-nas-00/data/ceres_data/8t50_41041/08_2025/8t50_41041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t50_41041/08_2025/8t50_41041.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASN:plan1': 9, 'PHE:plan': 14, 'ARG:plan': 16, 'GLN:plan1': 13, 'GLU:plan': 11, 'ASP:plan': 13, 'TYR:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'ASN:plan1': 9, 'PHE:plan': 14, 'ARG:plan': 16, 'GLN:plan1': 13, 'GLU:plan': 11, 'ASP:plan': 13, 'TYR:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'ASN:plan1': 9, 'PHE:plan': 14, 'ARG:plan': 16, 'GLN:plan1': 13, 'GLU:plan': 11, 'ASP:plan': 13, 'TYR:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'ASN:plan1': 9, 'PHE:plan': 14, 'ARG:plan': 16, 'GLN:plan1': 13, 'GLU:plan': 11, 'ASP:plan': 13, 'TYR:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1} 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: 2.80, per 1000 atoms: 0.22 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: 0.87 Conformation dependent library (CDL) restraints added in 492.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.29 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: 1.56 Time building geometry restraints manager: 1.07 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: 0.03 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: 0.920 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.150 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.930 ------------------------------------------------------------------------------- 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 : 7.61 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (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 ARG 0.006 0.001 ARG A 581 TYR 0.014 0.001 TYR B 411 PHE 0.026 0.001 PHE D 420 TRP 0.027 0.002 TRP C 175 HIS 0.005 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00303 (12972) covalent geometry : angle 0.67070 (17776) SS BOND : bond 0.00613 ( 4) SS BOND : angle 1.35853 ( 8) hydrogen bonds : bond 0.09013 ( 1119) hydrogen bonds : angle 5.02287 ( 3309) *********************** 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 : 0.357 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: 0.0927 time to fit residues: 42.2126 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 : 0.388 ------------------------------------------------------------------------------- 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 98 optimal weight: 6.9990 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 286 HIS B 413 GLN B 463 ASN B 478 ASN A 286 HIS A 413 GLN A 463 ASN A 478 ASN D 286 HIS D 413 GLN D 463 ASN D 478 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.223395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.162721 restraints weight = 16814.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.160999 restraints weight = 10844.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.158290 restraints weight = 8585.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.159387 restraints weight = 9371.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.159416 restraints weight = 8298.884| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12976 Z= 0.191 Angle : 0.622 10.815 17784 Z= 0.322 Chirality : 0.043 0.242 2064 Planarity : 0.004 0.037 2344 Dihedral : 7.370 130.132 2042 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.87 % Allowed : 18.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.19), residues: 1848 helix: 2.31 (0.14), residues: 1372 sheet: 1.04 (0.50), residues: 84 loop : -1.94 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 581 TYR 0.015 0.001 TYR C 411 PHE 0.018 0.002 PHE B 166 TRP 0.015 0.001 TRP D 175 HIS 0.006 0.001 HIS D 517 Details of bonding type rmsd covalent geometry : bond 0.00431 (12972) covalent geometry : angle 0.62152 (17776) SS BOND : bond 0.00376 ( 4) SS BOND : angle 0.58329 ( 8) hydrogen bonds : bond 0.04049 ( 1119) hydrogen bonds : angle 4.40701 ( 3309) *********************** 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 339 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 289 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 GLN cc_start: 0.8272 (mm110) cc_final: 0.7668 (tp40) REVERT: B 408 GLN cc_start: 0.8182 (mm110) cc_final: 0.7797 (tp40) REVERT: B 562 TYR cc_start: 0.8139 (m-80) cc_final: 0.7858 (m-80) REVERT: D 540 GLU cc_start: 0.7152 (pm20) cc_final: 0.6851 (pm20) outliers start: 50 outliers final: 45 residues processed: 315 average time/residue: 0.0822 time to fit residues: 38.7216 Evaluate side-chains 321 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 276 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 418 MET 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 110 optimal weight: 6.9990 chunk 141 optimal weight: 50.0000 chunk 186 optimal weight: 40.0000 chunk 65 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 32 optimal weight: 0.0370 chunk 39 optimal weight: 0.5980 chunk 166 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 162 optimal weight: 0.0670 overall best weight: 1.6798 ------------------------------------------------------------------------------- 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 478 ASN A 413 GLN 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 = 0.4698 r_free = 0.4698 target = 0.222585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.151383 restraints weight = 17036.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.154105 restraints weight = 11228.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.155233 restraints weight = 8647.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.155496 restraints weight = 8002.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.155794 restraints weight = 7622.329| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12976 Z= 0.201 Angle : 0.614 9.265 17784 Z= 0.320 Chirality : 0.042 0.230 2064 Planarity : 0.004 0.039 2344 Dihedral : 7.367 130.173 2042 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 6.81 % Allowed : 18.54 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.20), residues: 1848 helix: 2.32 (0.14), residues: 1376 sheet: 0.97 (0.51), residues: 84 loop : -2.15 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 581 TYR 0.023 0.002 TYR D 439 PHE 0.016 0.002 PHE A 538 TRP 0.013 0.001 TRP B 175 HIS 0.006 0.001 HIS C 517 Details of bonding type rmsd covalent geometry : bond 0.00458 (12972) covalent geometry : angle 0.61448 (17776) SS BOND : bond 0.00407 ( 4) SS BOND : angle 0.58794 ( 8) hydrogen bonds : bond 0.04021 ( 1119) hydrogen bonds : angle 4.32575 ( 3309) *********************** 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 338 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 280 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9154 (t80) cc_final: 0.8841 (t80) REVERT: C 408 GLN cc_start: 0.8264 (mm110) cc_final: 0.7646 (tp40) REVERT: C 579 MET cc_start: 0.7400 (mmp) cc_final: 0.7162 (mmt) REVERT: C 581 ARG cc_start: 0.8185 (ttm110) cc_final: 0.7748 (mtm110) REVERT: B 408 GLN cc_start: 0.8265 (mm110) cc_final: 0.7781 (tp40) REVERT: A 540 GLU cc_start: 0.7101 (pm20) cc_final: 0.6721 (pm20) REVERT: D 540 GLU cc_start: 0.7282 (pm20) cc_final: 0.6880 (pm20) outliers start: 58 outliers final: 51 residues processed: 314 average time/residue: 0.0845 time to fit residues: 40.1536 Evaluate side-chains 318 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 267 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 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 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 396 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 166 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 141 optimal weight: 50.0000 chunk 142 optimal weight: 30.0000 chunk 125 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 GLN 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 = 0.4659 r_free = 0.4659 target = 0.218445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.149229 restraints weight = 17054.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.150455 restraints weight = 14240.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151263 restraints weight = 10159.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.151263 restraints weight = 8718.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151376 restraints weight = 8165.171| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 12976 Z= 0.330 Angle : 0.717 11.275 17784 Z= 0.375 Chirality : 0.046 0.220 2064 Planarity : 0.004 0.041 2344 Dihedral : 7.440 128.051 2042 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 7.98 % Allowed : 20.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.19), residues: 1848 helix: 2.25 (0.14), residues: 1380 sheet: 0.79 (0.49), residues: 84 loop : -2.41 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 581 TYR 0.018 0.002 TYR B 411 PHE 0.023 0.003 PHE A 538 TRP 0.011 0.001 TRP D 175 HIS 0.010 0.001 HIS C 517 Details of bonding type rmsd covalent geometry : bond 0.00770 (12972) covalent geometry : angle 0.71726 (17776) SS BOND : bond 0.00520 ( 4) SS BOND : angle 0.57842 ( 8) hydrogen bonds : bond 0.04483 ( 1119) hydrogen bonds : angle 4.52176 ( 3309) *********************** 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 349 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 281 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7783 (tp40) REVERT: C 581 ARG cc_start: 0.8182 (ttm110) cc_final: 0.7836 (mtm110) REVERT: B 408 GLN cc_start: 0.8337 (mm110) cc_final: 0.8003 (tp40) REVERT: A 540 GLU cc_start: 0.7293 (pm20) cc_final: 0.6935 (pm20) REVERT: D 540 GLU cc_start: 0.7271 (pm20) cc_final: 0.6911 (pm20) outliers start: 68 outliers final: 62 residues processed: 320 average time/residue: 0.0848 time to fit residues: 40.3764 Evaluate side-chains 325 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 262 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 408 GLN Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 419 SER 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 512 MET Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 541 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 541 ILE 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 396 LEU 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 444 PHE 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 357 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 397 ILE 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 470 VAL 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 541 ILE Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 557 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 129 optimal weight: 0.8980 chunk 105 optimal weight: 60.0000 chunk 104 optimal weight: 8.9990 chunk 182 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 165 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 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 413 GLN C 482 ASN B 413 GLN A 413 GLN D 413 GLN D 463 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.222597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.154225 restraints weight = 17008.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.157292 restraints weight = 12166.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.156946 restraints weight = 8048.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.157303 restraints weight = 7732.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.157482 restraints weight = 7259.129| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12976 Z= 0.164 Angle : 0.603 8.595 17784 Z= 0.314 Chirality : 0.041 0.209 2064 Planarity : 0.003 0.035 2344 Dihedral : 7.473 131.347 2042 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 7.04 % Allowed : 22.54 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.19), residues: 1848 helix: 2.31 (0.14), residues: 1376 sheet: 0.99 (0.46), residues: 84 loop : -2.27 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 581 TYR 0.018 0.001 TYR B 411 PHE 0.012 0.002 PHE B 166 TRP 0.011 0.001 TRP A 175 HIS 0.006 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00367 (12972) covalent geometry : angle 0.60313 (17776) SS BOND : bond 0.00357 ( 4) SS BOND : angle 0.60931 ( 8) hydrogen bonds : bond 0.03873 ( 1119) hydrogen bonds : angle 4.24022 ( 3309) *********************** 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 346 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 286 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9213 (t80) cc_final: 0.8914 (t80) REVERT: C 408 GLN cc_start: 0.8244 (mm110) cc_final: 0.7546 (tp40) REVERT: C 581 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7790 (mtm110) REVERT: B 408 GLN cc_start: 0.8254 (mm110) cc_final: 0.7604 (tp40) REVERT: B 562 TYR cc_start: 0.8520 (m-80) cc_final: 0.8149 (m-80) REVERT: D 562 TYR cc_start: 0.8385 (m-80) cc_final: 0.8022 (m-80) outliers start: 60 outliers final: 58 residues processed: 323 average time/residue: 0.0847 time to fit residues: 41.2827 Evaluate side-chains 327 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 269 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 396 LEU 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 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 396 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 512 MET 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 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 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 541 ILE Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 554 ARG 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 23 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 GLN 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 = 0.4709 r_free = 0.4709 target = 0.223745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.153091 restraints weight = 16829.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.157129 restraints weight = 10578.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.159833 restraints weight = 7910.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.161721 restraints weight = 6577.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.162436 restraints weight = 5884.592| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12976 Z= 0.152 Angle : 0.605 8.614 17784 Z= 0.313 Chirality : 0.041 0.192 2064 Planarity : 0.003 0.033 2344 Dihedral : 7.414 131.456 2042 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 7.39 % Allowed : 23.24 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.20), residues: 1848 helix: 2.38 (0.14), residues: 1376 sheet: 0.96 (0.44), residues: 84 loop : -2.26 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 581 TYR 0.018 0.001 TYR B 411 PHE 0.017 0.002 PHE D 317 TRP 0.011 0.001 TRP B 175 HIS 0.005 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00334 (12972) covalent geometry : angle 0.60466 (17776) SS BOND : bond 0.00312 ( 4) SS BOND : angle 0.72019 ( 8) hydrogen bonds : bond 0.03735 ( 1119) hydrogen bonds : angle 4.16031 ( 3309) *********************** 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 340 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 277 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9307 (t80) cc_final: 0.8994 (t80) REVERT: C 408 GLN cc_start: 0.8160 (mm110) cc_final: 0.7554 (tp40) REVERT: C 418 MET cc_start: 0.8006 (mtm) cc_final: 0.7715 (mtp) REVERT: C 581 ARG cc_start: 0.8028 (ttm110) cc_final: 0.7774 (mtm110) REVERT: B 408 GLN cc_start: 0.8205 (mm110) cc_final: 0.7502 (tp40) REVERT: B 562 TYR cc_start: 0.8373 (m-80) cc_final: 0.7957 (m-80) REVERT: A 540 GLU cc_start: 0.6812 (pm20) cc_final: 0.6520 (pm20) REVERT: D 540 GLU cc_start: 0.6790 (pm20) cc_final: 0.6522 (pm20) REVERT: D 562 TYR cc_start: 0.8385 (m-80) cc_final: 0.7979 (m-80) outliers start: 63 outliers final: 58 residues processed: 316 average time/residue: 0.0830 time to fit residues: 39.7881 Evaluate side-chains 328 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 270 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 396 LEU Chi-restraints excluded: chain C residue 413 GLN 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 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 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 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 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 485 THR 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 554 ARG Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 19 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 156 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 126 optimal weight: 0.0170 chunk 82 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 GLN 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 = 0.4705 r_free = 0.4705 target = 0.222982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.151364 restraints weight = 16963.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.155208 restraints weight = 10927.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.157528 restraints weight = 8264.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.159480 restraints weight = 6970.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.160219 restraints weight = 6247.261| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12976 Z= 0.175 Angle : 0.614 8.808 17784 Z= 0.318 Chirality : 0.042 0.184 2064 Planarity : 0.003 0.033 2344 Dihedral : 7.375 130.583 2042 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 7.51 % Allowed : 22.77 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.20), residues: 1848 helix: 2.40 (0.14), residues: 1376 sheet: 1.01 (0.43), residues: 84 loop : -2.29 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 581 TYR 0.017 0.001 TYR D 411 PHE 0.014 0.002 PHE B 538 TRP 0.013 0.001 TRP B 175 HIS 0.005 0.001 HIS D 517 Details of bonding type rmsd covalent geometry : bond 0.00396 (12972) covalent geometry : angle 0.61414 (17776) SS BOND : bond 0.00387 ( 4) SS BOND : angle 0.65177 ( 8) hydrogen bonds : bond 0.03749 ( 1119) hydrogen bonds : angle 4.14726 ( 3309) *********************** 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 339 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 275 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9291 (t80) cc_final: 0.8988 (t80) REVERT: C 408 GLN cc_start: 0.8156 (mm110) cc_final: 0.7537 (tp40) REVERT: C 418 MET cc_start: 0.8028 (mtm) cc_final: 0.7745 (mtp) REVERT: C 581 ARG cc_start: 0.8069 (ttm110) cc_final: 0.7856 (mtm110) REVERT: B 408 GLN cc_start: 0.8197 (mm110) cc_final: 0.7533 (tp40) REVERT: B 562 TYR cc_start: 0.8410 (m-80) cc_final: 0.7971 (m-80) REVERT: A 540 GLU cc_start: 0.7031 (pm20) cc_final: 0.6798 (pm20) REVERT: D 554 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.7115 (ptt90) REVERT: D 562 TYR cc_start: 0.8408 (m-80) cc_final: 0.7979 (m-80) outliers start: 64 outliers final: 58 residues processed: 315 average time/residue: 0.0842 time to fit residues: 40.3128 Evaluate side-chains 327 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 268 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 396 LEU 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 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 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 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 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 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 554 ARG Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 10 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 187 optimal weight: 40.0000 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 GLN 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 = 0.4712 r_free = 0.4712 target = 0.223819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.153286 restraints weight = 16899.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.157100 restraints weight = 11674.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.158017 restraints weight = 8104.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.158132 restraints weight = 7453.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.158271 restraints weight = 7187.084| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12976 Z= 0.161 Angle : 0.604 8.626 17784 Z= 0.313 Chirality : 0.041 0.177 2064 Planarity : 0.003 0.033 2344 Dihedral : 7.374 131.293 2042 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 7.16 % Allowed : 23.59 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.20), residues: 1848 helix: 2.44 (0.14), residues: 1376 sheet: 1.01 (0.42), residues: 84 loop : -2.29 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 581 TYR 0.017 0.001 TYR B 411 PHE 0.013 0.002 PHE C 538 TRP 0.012 0.001 TRP B 175 HIS 0.005 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00360 (12972) covalent geometry : angle 0.60365 (17776) SS BOND : bond 0.00309 ( 4) SS BOND : angle 0.74164 ( 8) hydrogen bonds : bond 0.03668 ( 1119) hydrogen bonds : angle 4.08122 ( 3309) *********************** 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 332 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 271 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9221 (t80) cc_final: 0.8911 (t80) REVERT: C 408 GLN cc_start: 0.8123 (mm110) cc_final: 0.7543 (tp40) REVERT: C 418 MET cc_start: 0.8034 (mtm) cc_final: 0.7717 (mtp) REVERT: C 581 ARG cc_start: 0.8101 (ttm110) cc_final: 0.7849 (mtm110) REVERT: B 408 GLN cc_start: 0.8143 (mm110) cc_final: 0.7513 (tp40) REVERT: B 562 TYR cc_start: 0.8377 (m-80) cc_final: 0.7935 (m-80) REVERT: A 540 GLU cc_start: 0.7022 (pm20) cc_final: 0.6807 (pm20) REVERT: D 280 GLN cc_start: 0.8044 (tp40) cc_final: 0.7821 (tp40) REVERT: D 562 TYR cc_start: 0.8380 (m-80) cc_final: 0.7949 (m-80) outliers start: 61 outliers final: 60 residues processed: 308 average time/residue: 0.0925 time to fit residues: 42.9612 Evaluate side-chains 322 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 262 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 396 LEU Chi-restraints excluded: chain C residue 413 GLN 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 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 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 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 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 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 554 ARG Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 139 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 27 optimal weight: 0.0470 chunk 176 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 164 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 140 optimal weight: 50.0000 chunk 11 optimal weight: 60.0000 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 GLN B 413 GLN A 413 GLN D 413 GLN D 568 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.223705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.154137 restraints weight = 16904.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.156507 restraints weight = 12725.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.157790 restraints weight = 8763.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.157464 restraints weight = 7088.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.157724 restraints weight = 7591.368| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12976 Z= 0.163 Angle : 0.615 8.765 17784 Z= 0.317 Chirality : 0.041 0.174 2064 Planarity : 0.003 0.033 2344 Dihedral : 7.365 131.159 2042 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 7.28 % Allowed : 23.24 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.20), residues: 1848 helix: 2.46 (0.14), residues: 1376 sheet: 0.98 (0.42), residues: 84 loop : -2.31 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 581 TYR 0.017 0.001 TYR B 411 PHE 0.013 0.002 PHE C 538 TRP 0.013 0.001 TRP B 175 HIS 0.005 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00366 (12972) covalent geometry : angle 0.61482 (17776) SS BOND : bond 0.00362 ( 4) SS BOND : angle 0.68944 ( 8) hydrogen bonds : bond 0.03633 ( 1119) hydrogen bonds : angle 4.06060 ( 3309) *********************** 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 328 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 266 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9136 (t80) cc_final: 0.8893 (t80) REVERT: C 408 GLN cc_start: 0.8089 (mm110) cc_final: 0.7523 (tp40) REVERT: C 418 MET cc_start: 0.8030 (mtm) cc_final: 0.7739 (mtp) REVERT: C 581 ARG cc_start: 0.8105 (ttm110) cc_final: 0.7860 (mtm110) REVERT: B 408 GLN cc_start: 0.8125 (mm110) cc_final: 0.7545 (tp40) REVERT: B 562 TYR cc_start: 0.8549 (m-80) cc_final: 0.8083 (m-80) REVERT: A 540 GLU cc_start: 0.7012 (pm20) cc_final: 0.6657 (pm20) REVERT: D 554 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.7047 (ptt90) REVERT: D 562 TYR cc_start: 0.8383 (m-80) cc_final: 0.7933 (m-80) outliers start: 62 outliers final: 61 residues processed: 305 average time/residue: 0.0865 time to fit residues: 40.3186 Evaluate side-chains 324 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 262 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 396 LEU 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 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 385 CYS 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 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 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 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 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 554 ARG Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 2 optimal weight: 50.0000 chunk 75 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 GLN 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 = 0.4694 r_free = 0.4694 target = 0.222316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.150867 restraints weight = 17070.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.154721 restraints weight = 10821.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.157557 restraints weight = 8073.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.159371 restraints weight = 6724.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.159853 restraints weight = 6012.376| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2005 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= 0.193 Angle : 0.637 10.122 17784 Z= 0.330 Chirality : 0.042 0.171 2064 Planarity : 0.004 0.034 2344 Dihedral : 7.368 130.644 2042 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 7.63 % Allowed : 23.59 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.20), residues: 1848 helix: 2.46 (0.14), residues: 1376 sheet: 1.02 (0.42), residues: 84 loop : -2.35 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 581 TYR 0.019 0.001 TYR C 411 PHE 0.015 0.002 PHE C 538 TRP 0.013 0.001 TRP A 175 HIS 0.005 0.001 HIS D 517 Details of bonding type rmsd covalent geometry : bond 0.00445 (12972) covalent geometry : angle 0.63706 (17776) SS BOND : bond 0.00332 ( 4) SS BOND : angle 0.74604 ( 8) hydrogen bonds : bond 0.03747 ( 1119) hydrogen bonds : angle 4.09315 ( 3309) ********************** 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 : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9300 (t80) cc_final: 0.8984 (t80) REVERT: C 408 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7555 (tp40) REVERT: B 408 GLN cc_start: 0.8120 (mm110) cc_final: 0.7521 (tp40) REVERT: A 540 GLU cc_start: 0.7012 (pm20) cc_final: 0.6689 (pm20) REVERT: A 554 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.7030 (ptt90) outliers start: 65 outliers final: 62 residues processed: 314 average time/residue: 0.0793 time to fit residues: 37.2056 Evaluate side-chains 335 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 271 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 396 LEU Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 484 VAL 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 385 CYS 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 385 CYS 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 512 MET 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 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 385 CYS 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 541 ILE Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 50.0000 chunk 48 optimal weight: 30.0000 chunk 185 optimal weight: 20.0000 chunk 163 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 170 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 172 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 GLN 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 = 0.4716 r_free = 0.4716 target = 0.224534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.157773 restraints weight = 16961.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.161910 restraints weight = 11441.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.159732 restraints weight = 7659.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.160403 restraints weight = 8033.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.160317 restraints weight = 7597.122| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2057 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= 0.148 Angle : 0.612 11.256 17784 Z= 0.314 Chirality : 0.041 0.170 2064 Planarity : 0.003 0.032 2344 Dihedral : 7.386 131.930 2042 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 6.81 % Allowed : 24.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.20), residues: 1848 helix: 2.49 (0.14), residues: 1376 sheet: 1.09 (0.42), residues: 84 loop : -2.32 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 581 TYR 0.017 0.001 TYR C 411 PHE 0.013 0.001 PHE B 166 TRP 0.013 0.001 TRP A 175 HIS 0.005 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00324 (12972) covalent geometry : angle 0.61228 (17776) SS BOND : bond 0.00327 ( 4) SS BOND : angle 0.73514 ( 8) hydrogen bonds : bond 0.03533 ( 1119) hydrogen bonds : angle 4.00188 ( 3309) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2056.16 seconds wall clock time: 36 minutes 3.12 seconds (2163.12 seconds total)