Starting phenix.real_space_refine on Sun Nov 17 03:39:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t50_41041/11_2024/8t50_41041.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t50_41041/11_2024/8t50_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t50_41041/11_2024/8t50_41041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t50_41041/11_2024/8t50_41041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t50_41041/11_2024/8t50_41041.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t50_41041/11_2024/8t50_41041.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 56 5.16 5 C 8016 2.51 5 N 2280 2.21 5 O 2364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12720 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3158 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 12, 'TRANS': 461} Chain breaks: 5 Unresolved non-hydrogen bonds: 754 Unresolved non-hydrogen angles: 942 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 14, 'GLU:plan': 11, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 361 Chain: "B" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3158 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 12, 'TRANS': 461} Chain breaks: 5 Unresolved non-hydrogen bonds: 754 Unresolved non-hydrogen angles: 942 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 14, 'GLU:plan': 11, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 361 Chain: "A" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3158 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 12, 'TRANS': 461} Chain breaks: 5 Unresolved non-hydrogen bonds: 754 Unresolved non-hydrogen angles: 942 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 14, 'GLU:plan': 11, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 361 Chain: "D" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3158 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 12, 'TRANS': 461} Chain breaks: 5 Unresolved non-hydrogen bonds: 754 Unresolved non-hydrogen angles: 942 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 14, 'GLU:plan': 11, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 361 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 8.40, per 1000 atoms: 0.66 Number of scatterers: 12720 At special positions: 0 Unit cell: (105.342, 105.342, 115.116, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 4 15.00 O 2364 8.00 N 2280 7.00 C 8016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 385 " distance=2.04 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 385 " distance=2.04 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 385 " distance=2.04 Simple disulfide: pdb=" SG CYS D 309 " - pdb=" SG CYS D 385 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 2.0 seconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 77.8% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'C' and resid 107 through 115 removed outlier: 4.131A pdb=" N LEU C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 130 Processing helix chain 'C' and resid 141 through 165 Proline residue: C 161 - end of helix removed outlier: 3.766A pdb=" N THR C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 195 Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 221 through 229 Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'C' and resid 253 through 259 Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 263 through 285 removed outlier: 3.895A pdb=" N ARG C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 324 removed outlier: 3.622A pdb=" N ASN C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 341 through 358 Processing helix chain 'C' and resid 368 through 422 removed outlier: 3.573A pdb=" N LEU C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYR C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 452 Processing helix chain 'C' and resid 454 through 466 Processing helix chain 'C' and resid 466 through 473 removed outlier: 3.713A pdb=" N MET C 473 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 479 removed outlier: 3.687A pdb=" N ALA C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 490 Processing helix chain 'C' and resid 539 through 546 removed outlier: 3.618A pdb=" N LEU C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 576 Processing helix chain 'C' and resid 576 through 595 removed outlier: 4.005A pdb=" N ARG C 580 " --> pdb=" O TYR C 576 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 581 " --> pdb=" O PRO C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 606 Processing helix chain 'C' and resid 617 through 634 Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 116 through 130 Processing helix chain 'B' and resid 141 through 165 Proline residue: B 161 - end of helix removed outlier: 3.766A pdb=" N THR B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 195 Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'B' and resid 231 through 242 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 263 through 285 removed outlier: 3.902A pdb=" N ARG B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 324 removed outlier: 3.641A pdb=" N ASN B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 341 through 357 Processing helix chain 'B' and resid 368 through 422 removed outlier: 3.584A pdb=" N LEU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TYR B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 439 Processing helix chain 'B' and resid 445 through 452 Processing helix chain 'B' and resid 454 through 466 Processing helix chain 'B' and resid 466 through 473 removed outlier: 3.761A pdb=" N MET B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.750A pdb=" N ALA B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 539 through 546 removed outlier: 3.515A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 576 Processing helix chain 'B' and resid 576 through 595 removed outlier: 4.040A pdb=" N ARG B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG B 581 " --> pdb=" O PRO B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 606 Processing helix chain 'B' and resid 617 through 634 Processing helix chain 'A' and resid 108 through 115 Processing helix chain 'A' and resid 116 through 130 Processing helix chain 'A' and resid 141 through 165 Proline residue: A 161 - end of helix removed outlier: 3.766A pdb=" N THR A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 195 Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 253 through 259 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 263 through 285 removed outlier: 3.894A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 324 removed outlier: 3.635A pdb=" N ASN A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 341 through 358 Processing helix chain 'A' and resid 368 through 422 removed outlier: 3.625A pdb=" N LEU A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TYR A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 454 through 466 Processing helix chain 'A' and resid 466 through 473 removed outlier: 3.676A pdb=" N MET A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.704A pdb=" N ALA A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.519A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 Processing helix chain 'A' and resid 576 through 595 removed outlier: 4.025A pdb=" N ARG A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 581 " --> pdb=" O PRO A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 606 Processing helix chain 'A' and resid 617 through 634 Processing helix chain 'D' and resid 108 through 115 Processing helix chain 'D' and resid 116 through 130 Processing helix chain 'D' and resid 141 through 165 Proline residue: D 161 - end of helix removed outlier: 3.766A pdb=" N THR D 165 " --> pdb=" O PRO D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 195 Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 242 Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.892A pdb=" N ARG D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 324 removed outlier: 3.641A pdb=" N ASN D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 341 through 358 Processing helix chain 'D' and resid 368 through 422 removed outlier: 4.417A pdb=" N ARG D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR D 407 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 454 through 466 Processing helix chain 'D' and resid 466 through 473 removed outlier: 3.551A pdb=" N MET D 473 " --> pdb=" O LEU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 479 removed outlier: 3.668A pdb=" N ALA D 477 " --> pdb=" O MET D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 490 Processing helix chain 'D' and resid 539 through 546 removed outlier: 3.553A pdb=" N LEU D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 576 Processing helix chain 'D' and resid 576 through 595 removed outlier: 4.023A pdb=" N ARG D 580 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 581 " --> pdb=" O PRO D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 606 Processing helix chain 'D' and resid 617 through 634 Processing sheet with id=AA1, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.395A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER C 536 " --> pdb=" O ILE C 515 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.147A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 503 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.391A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER B 536 " --> pdb=" O ILE B 515 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.217A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 503 " --> pdb=" O VAL B 553 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.390A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 536 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.197A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 503 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.324A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER D 536 " --> pdb=" O ILE D 515 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.189A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 503 " --> pdb=" O VAL D 553 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 3309 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 3.92 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: 0.00 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: 0.710 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.440 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.450 ------------------------------------------------------------------------------- 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 12972 Z= 0.203 Angle : 0.671 8.908 17776 Z= 0.371 Chirality : 0.040 0.265 2064 Planarity : 0.003 0.031 2344 Dihedral : 14.504 128.040 3932 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.47 % Allowed : 20.19 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.19), residues: 1848 helix: 2.20 (0.14), residues: 1360 sheet: 1.23 (0.48), residues: 84 loop : -1.84 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 175 HIS 0.005 0.001 HIS A 517 PHE 0.026 0.001 PHE D 420 TYR 0.014 0.001 TYR B 411 ARG 0.006 0.001 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 311 time to evaluate : 1.504 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: 0.2425 time to fit residues: 108.6236 Evaluate side-chains 288 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 287 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 79 optimal weight: 0.0170 chunk 48 optimal weight: 30.0000 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 109 optimal weight: 20.0000 chunk 170 optimal weight: 1.9990 overall best weight: 1.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 413 GLN C 478 ASN B 286 HIS B 413 GLN B 478 ASN A 286 HIS A 413 GLN A 478 ASN D 286 HIS D 413 GLN D 478 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12972 Z= 0.291 Angle : 0.625 10.958 17776 Z= 0.323 Chirality : 0.043 0.246 2064 Planarity : 0.004 0.037 2344 Dihedral : 7.371 130.063 2042 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.40 % Allowed : 18.90 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.19), residues: 1848 helix: 2.31 (0.14), residues: 1372 sheet: 1.04 (0.50), residues: 84 loop : -1.95 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 175 HIS 0.006 0.001 HIS D 517 PHE 0.017 0.002 PHE C 166 TYR 0.015 0.001 TYR C 411 ARG 0.007 0.001 ARG C 581 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 GLN cc_start: 0.7920 (mm110) cc_final: 0.7365 (tp40) REVERT: C 419 SER cc_start: 0.9428 (t) cc_final: 0.9051 (p) REVERT: C 540 GLU cc_start: 0.7425 (pm20) cc_final: 0.7050 (pm20) REVERT: B 408 GLN cc_start: 0.7879 (mm110) cc_final: 0.7556 (tp40) REVERT: B 419 SER cc_start: 0.9482 (t) cc_final: 0.9258 (p) REVERT: B 562 TYR cc_start: 0.8157 (m-80) cc_final: 0.7756 (m-80) REVERT: D 419 SER cc_start: 0.9443 (t) cc_final: 0.9071 (p) REVERT: D 540 GLU cc_start: 0.7455 (pm20) cc_final: 0.6848 (pm20) outliers start: 46 outliers final: 44 residues processed: 311 average time/residue: 0.2317 time to fit residues: 105.6113 Evaluate side-chains 322 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 564 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 50.0000 chunk 52 optimal weight: 50.0000 chunk 142 optimal weight: 40.0000 chunk 116 optimal weight: 4.9990 chunk 47 optimal weight: 50.0000 chunk 171 optimal weight: 0.7980 chunk 184 optimal weight: 0.8980 chunk 152 optimal weight: 50.0000 chunk 169 optimal weight: 1.9990 chunk 58 optimal weight: 60.0000 chunk 137 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 463 ASN C 478 ASN B 413 GLN B 463 ASN B 478 ASN A 413 GLN A 463 ASN D 413 GLN D 416 GLN D 463 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12972 Z= 0.339 Angle : 0.631 9.583 17776 Z= 0.328 Chirality : 0.043 0.230 2064 Planarity : 0.004 0.037 2344 Dihedral : 7.380 129.768 2042 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 7.28 % Allowed : 18.54 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.20), residues: 1848 helix: 2.30 (0.14), residues: 1376 sheet: 1.02 (0.52), residues: 84 loop : -2.17 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 175 HIS 0.006 0.001 HIS C 517 PHE 0.017 0.002 PHE A 538 TYR 0.023 0.002 TYR D 439 ARG 0.008 0.000 ARG C 581 *********************** 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 343 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 281 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9268 (t80) cc_final: 0.8986 (t80) REVERT: C 408 GLN cc_start: 0.8019 (mm110) cc_final: 0.7405 (tp40) REVERT: C 419 SER cc_start: 0.9431 (t) cc_final: 0.9058 (p) REVERT: C 540 GLU cc_start: 0.7555 (pm20) cc_final: 0.7277 (pm20) REVERT: C 573 LEU cc_start: 0.7817 (tp) cc_final: 0.7614 (tp) REVERT: C 579 MET cc_start: 0.7578 (mmp) cc_final: 0.7236 (mmt) REVERT: C 581 ARG cc_start: 0.8290 (ttm110) cc_final: 0.7691 (mtm110) REVERT: B 408 GLN cc_start: 0.7989 (mm110) cc_final: 0.7568 (tp40) REVERT: B 419 SER cc_start: 0.9482 (t) cc_final: 0.9245 (p) REVERT: A 540 GLU cc_start: 0.7471 (pm20) cc_final: 0.6864 (pm20) REVERT: D 540 GLU cc_start: 0.7517 (pm20) cc_final: 0.6836 (pm20) outliers start: 62 outliers final: 52 residues processed: 321 average time/residue: 0.2315 time to fit residues: 108.7483 Evaluate side-chains 315 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 263 time to evaluate : 2.182 ------------------------------------------------------------------------------- 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 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 418 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 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 168 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 171 optimal weight: 0.5980 chunk 181 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 48 optimal weight: 30.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12972 Z= 0.235 Angle : 0.590 8.748 17776 Z= 0.307 Chirality : 0.041 0.219 2064 Planarity : 0.003 0.033 2344 Dihedral : 7.394 131.091 2042 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 6.69 % Allowed : 20.66 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.19), residues: 1848 helix: 2.36 (0.14), residues: 1376 sheet: 1.05 (0.46), residues: 84 loop : -2.16 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 175 HIS 0.004 0.001 HIS A 517 PHE 0.013 0.002 PHE B 166 TYR 0.019 0.001 TYR C 411 ARG 0.004 0.000 ARG C 581 *********************** 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 346 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 289 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9283 (t80) cc_final: 0.8981 (t80) REVERT: C 408 GLN cc_start: 0.7955 (mm110) cc_final: 0.7266 (tp40) REVERT: C 419 SER cc_start: 0.9406 (t) cc_final: 0.9033 (p) REVERT: C 540 GLU cc_start: 0.7538 (pm20) cc_final: 0.7312 (pm20) REVERT: C 573 LEU cc_start: 0.7682 (tp) cc_final: 0.7465 (tp) REVERT: C 581 ARG cc_start: 0.8217 (ttm110) cc_final: 0.7651 (mtm110) REVERT: B 408 GLN cc_start: 0.7960 (mm110) cc_final: 0.7329 (tp40) REVERT: B 419 SER cc_start: 0.9476 (t) cc_final: 0.9233 (p) REVERT: A 540 GLU cc_start: 0.7455 (pm20) cc_final: 0.6914 (pm20) REVERT: D 284 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7260 (tp) REVERT: D 540 GLU cc_start: 0.7418 (pm20) cc_final: 0.6977 (pm20) outliers start: 57 outliers final: 54 residues processed: 321 average time/residue: 0.2461 time to fit residues: 114.0528 Evaluate side-chains 330 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 275 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 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 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 457 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 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 541 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 485 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 135 optimal weight: 0.6980 chunk 74 optimal weight: 0.0570 chunk 155 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 92 optimal weight: 40.0000 chunk 163 optimal weight: 4.9990 chunk 45 optimal weight: 40.0000 overall best weight: 0.9500 ------------------------------------------------------------------------------- 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 B 463 ASN A 413 GLN D 413 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12972 Z= 0.227 Angle : 0.594 8.631 17776 Z= 0.306 Chirality : 0.041 0.209 2064 Planarity : 0.003 0.031 2344 Dihedral : 7.363 131.228 2042 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 7.16 % Allowed : 21.48 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.19), residues: 1848 helix: 2.40 (0.14), residues: 1376 sheet: 1.00 (0.44), residues: 84 loop : -2.17 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 175 HIS 0.004 0.001 HIS A 517 PHE 0.016 0.002 PHE C 317 TYR 0.018 0.001 TYR B 411 ARG 0.003 0.000 ARG C 581 *********************** 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 343 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 282 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9266 (t80) cc_final: 0.9032 (t80) REVERT: C 408 GLN cc_start: 0.7927 (mm110) cc_final: 0.7286 (tp40) REVERT: C 419 SER cc_start: 0.9416 (t) cc_final: 0.9047 (p) REVERT: C 540 GLU cc_start: 0.7513 (pm20) cc_final: 0.7287 (pm20) REVERT: C 581 ARG cc_start: 0.8226 (ttm110) cc_final: 0.7728 (mtm110) REVERT: B 408 GLN cc_start: 0.7908 (mm110) cc_final: 0.7253 (tp40) REVERT: B 419 SER cc_start: 0.9469 (t) cc_final: 0.9228 (p) REVERT: B 540 GLU cc_start: 0.7392 (pm20) cc_final: 0.7039 (pm20) REVERT: A 540 GLU cc_start: 0.7430 (pm20) cc_final: 0.6969 (pm20) REVERT: D 280 GLN cc_start: 0.8057 (tp40) cc_final: 0.7842 (tp40) REVERT: D 284 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7160 (tp) REVERT: D 540 GLU cc_start: 0.7368 (pm20) cc_final: 0.6937 (pm20) REVERT: D 554 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6814 (ptt90) outliers start: 61 outliers final: 56 residues processed: 318 average time/residue: 0.2312 time to fit residues: 108.1619 Evaluate side-chains 334 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 276 time to evaluate : 1.514 ------------------------------------------------------------------------------- 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 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 457 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 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 284 ILE Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 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 61 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 chunk 181 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 95 optimal weight: 30.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 463 ASN B 413 GLN A 413 GLN A 463 ASN D 413 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 12972 Z= 0.516 Angle : 0.718 11.044 17776 Z= 0.374 Chirality : 0.045 0.193 2064 Planarity : 0.004 0.038 2344 Dihedral : 7.387 127.966 2042 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 7.86 % Allowed : 22.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.19), residues: 1848 helix: 2.30 (0.14), residues: 1380 sheet: 1.05 (0.45), residues: 84 loop : -2.49 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 175 HIS 0.011 0.001 HIS B 517 PHE 0.025 0.003 PHE A 538 TYR 0.017 0.002 TYR B 411 ARG 0.003 0.001 ARG C 581 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 275 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7361 (tp40) REVERT: C 540 GLU cc_start: 0.7804 (pm20) cc_final: 0.7336 (pm20) REVERT: C 581 ARG cc_start: 0.8283 (ttm110) cc_final: 0.7927 (mtm-85) REVERT: B 408 GLN cc_start: 0.8042 (mm110) cc_final: 0.7617 (tp40) REVERT: A 540 GLU cc_start: 0.7521 (pm20) cc_final: 0.6952 (pm20) REVERT: A 554 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.7082 (ptt90) REVERT: D 284 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7247 (tp) REVERT: D 404 ARG cc_start: 0.5947 (mmm-85) cc_final: 0.5627 (tpt-90) REVERT: D 540 GLU cc_start: 0.7555 (pm20) cc_final: 0.6918 (pm20) outliers start: 67 outliers final: 60 residues processed: 320 average time/residue: 0.2158 time to fit residues: 103.0223 Evaluate side-chains 332 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 269 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 457 LEU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain B residue 285 PHE 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 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 413 GLN Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 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 414 VAL Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 519 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 Chi-restraints excluded: chain D residue 564 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 482 ASN B 413 GLN B 478 ASN A 413 GLN D 413 GLN D 463 ASN D 482 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12972 Z= 0.299 Angle : 0.622 9.690 17776 Z= 0.324 Chirality : 0.042 0.184 2064 Planarity : 0.004 0.035 2344 Dihedral : 7.435 131.130 2042 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 7.98 % Allowed : 23.12 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.19), residues: 1848 helix: 2.33 (0.14), residues: 1376 sheet: 1.22 (0.43), residues: 84 loop : -2.39 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 175 HIS 0.005 0.001 HIS C 517 PHE 0.015 0.002 PHE A 538 TYR 0.018 0.001 TYR B 411 ARG 0.003 0.000 ARG D 581 *********************** 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 343 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 275 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9296 (t80) cc_final: 0.9056 (t80) REVERT: C 408 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7255 (tp40) REVERT: C 540 GLU cc_start: 0.7720 (pm20) cc_final: 0.7420 (pm20) REVERT: C 581 ARG cc_start: 0.8258 (ttm110) cc_final: 0.7757 (mtm110) REVERT: B 408 GLN cc_start: 0.8006 (mm110) cc_final: 0.7337 (tp40) REVERT: A 540 GLU cc_start: 0.7477 (pm20) cc_final: 0.7076 (pm20) REVERT: A 554 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6876 (ptt90) REVERT: D 284 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7225 (tp) REVERT: D 404 ARG cc_start: 0.6063 (mmm-85) cc_final: 0.5706 (tpt-90) REVERT: D 540 GLU cc_start: 0.7501 (pm20) cc_final: 0.6980 (pm20) outliers start: 68 outliers final: 60 residues processed: 315 average time/residue: 0.2213 time to fit residues: 104.3885 Evaluate side-chains 331 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 268 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 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 285 PHE 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 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 384 THR Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 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 557 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 557 THR Chi-restraints excluded: chain D residue 564 LEU 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 112 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 115 optimal weight: 30.0000 chunk 123 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 chunk 164 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 GLN A 413 GLN D 413 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12972 Z= 0.238 Angle : 0.599 9.303 17776 Z= 0.311 Chirality : 0.041 0.179 2064 Planarity : 0.003 0.033 2344 Dihedral : 7.419 131.931 2042 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 7.51 % Allowed : 24.18 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.20), residues: 1848 helix: 2.41 (0.14), residues: 1376 sheet: 1.15 (0.42), residues: 84 loop : -2.34 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 175 HIS 0.006 0.001 HIS A 517 PHE 0.012 0.002 PHE A 538 TYR 0.017 0.001 TYR B 411 ARG 0.002 0.000 ARG B 581 *********************** 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 339 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 275 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9287 (t80) cc_final: 0.9041 (t80) REVERT: C 408 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7254 (tp40) REVERT: C 540 GLU cc_start: 0.7672 (pm20) cc_final: 0.7413 (pm20) REVERT: C 581 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7817 (mtm110) REVERT: B 408 GLN cc_start: 0.7922 (mm110) cc_final: 0.7300 (tp40) REVERT: A 540 GLU cc_start: 0.7397 (pm20) cc_final: 0.7033 (pm20) REVERT: A 554 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6879 (ptt90) REVERT: D 280 GLN cc_start: 0.8130 (tp40) cc_final: 0.7891 (tp40) REVERT: D 284 ILE cc_start: 0.7515 (tt) cc_final: 0.7205 (tp) REVERT: D 540 GLU cc_start: 0.7443 (pm20) cc_final: 0.6934 (pm20) outliers start: 64 outliers final: 60 residues processed: 316 average time/residue: 0.2179 time to fit residues: 102.5634 Evaluate side-chains 332 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 270 time to evaluate : 1.474 ------------------------------------------------------------------------------- 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 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 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 519 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain 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 457 LEU Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 557 THR 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 173 optimal weight: 0.0980 chunk 158 optimal weight: 20.0000 chunk 168 optimal weight: 0.5980 chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 51 optimal weight: 0.0670 chunk 152 optimal weight: 50.0000 chunk 159 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 178 optimal weight: 6.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 GLN A 413 GLN D 413 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12972 Z= 0.184 Angle : 0.585 10.625 17776 Z= 0.302 Chirality : 0.041 0.172 2064 Planarity : 0.003 0.031 2344 Dihedral : 7.398 132.234 2042 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 6.57 % Allowed : 25.23 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.20), residues: 1848 helix: 2.47 (0.14), residues: 1376 sheet: 1.21 (0.42), residues: 84 loop : -2.28 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 175 HIS 0.007 0.001 HIS A 517 PHE 0.013 0.001 PHE B 166 TYR 0.017 0.001 TYR D 411 ARG 0.004 0.000 ARG D 581 *********************** 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 332 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 276 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9292 (t80) cc_final: 0.9054 (t80) REVERT: C 408 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7273 (tp40) REVERT: C 562 TYR cc_start: 0.8304 (m-80) cc_final: 0.7269 (m-80) REVERT: C 581 ARG cc_start: 0.8130 (ttm110) cc_final: 0.7722 (mtm110) REVERT: B 280 GLN cc_start: 0.8093 (tp40) cc_final: 0.7881 (tp40) REVERT: B 408 GLN cc_start: 0.7856 (mm110) cc_final: 0.7312 (tp40) REVERT: B 562 TYR cc_start: 0.8352 (m-80) cc_final: 0.7274 (m-80) REVERT: A 531 LYS cc_start: 0.8088 (mtpp) cc_final: 0.7580 (mmtt) REVERT: A 540 GLU cc_start: 0.7296 (pm20) cc_final: 0.6975 (pm20) REVERT: A 554 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6707 (ptt90) REVERT: A 562 TYR cc_start: 0.8259 (m-80) cc_final: 0.7186 (m-80) REVERT: D 280 GLN cc_start: 0.8112 (tp40) cc_final: 0.7875 (tp40) REVERT: D 284 ILE cc_start: 0.7407 (tt) cc_final: 0.7107 (tp) REVERT: D 540 GLU cc_start: 0.7358 (pm20) cc_final: 0.6906 (pm20) REVERT: D 567 ASP cc_start: 0.8362 (m-30) cc_final: 0.8019 (p0) outliers start: 56 outliers final: 52 residues processed: 311 average time/residue: 0.2136 time to fit residues: 99.1904 Evaluate side-chains 321 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 267 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 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 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 413 GLN Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 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 457 LEU Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 564 LEU 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 108 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 124 optimal weight: 0.0870 chunk 187 optimal weight: 50.0000 chunk 172 optimal weight: 0.3980 chunk 149 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 overall best weight: 1.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 GLN A 413 GLN D 413 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12972 Z= 0.286 Angle : 0.627 11.197 17776 Z= 0.324 Chirality : 0.042 0.172 2064 Planarity : 0.003 0.033 2344 Dihedral : 7.325 129.936 2042 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.46 % Allowed : 26.06 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.20), residues: 1848 helix: 2.48 (0.14), residues: 1376 sheet: 1.16 (0.42), residues: 84 loop : -2.33 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 175 HIS 0.005 0.001 HIS C 517 PHE 0.016 0.002 PHE C 538 TYR 0.015 0.001 TYR C 411 ARG 0.005 0.000 ARG D 581 ********************** 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 324 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 269 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 389 PHE cc_start: 0.9295 (t80) cc_final: 0.9049 (t80) REVERT: C 408 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7322 (tp40) REVERT: C 581 ARG cc_start: 0.8163 (ttm110) cc_final: 0.7731 (mtm110) REVERT: B 280 GLN cc_start: 0.8117 (tp40) cc_final: 0.7902 (tp40) REVERT: B 408 GLN cc_start: 0.7906 (mm110) cc_final: 0.7343 (tp40) REVERT: A 531 LYS cc_start: 0.8090 (mtpp) cc_final: 0.7568 (mmtt) REVERT: A 540 GLU cc_start: 0.7428 (pm20) cc_final: 0.7064 (pm20) REVERT: A 554 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6915 (ptt90) REVERT: D 280 GLN cc_start: 0.8141 (tp40) cc_final: 0.7893 (tp40) REVERT: D 284 ILE cc_start: 0.7424 (tt) cc_final: 0.7111 (tp) REVERT: D 540 GLU cc_start: 0.7431 (pm20) cc_final: 0.6939 (pm20) REVERT: D 567 ASP cc_start: 0.8377 (m-30) cc_final: 0.8013 (p0) outliers start: 55 outliers final: 53 residues processed: 303 average time/residue: 0.2148 time to fit residues: 98.0298 Evaluate side-chains 321 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 266 time to evaluate : 1.656 ------------------------------------------------------------------------------- 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 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 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 413 GLN Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 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 457 LEU Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 564 LEU 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 45 optimal weight: 40.0000 chunk 137 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 149 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 131 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 GLN A 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.220749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.148940 restraints weight = 16986.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.152837 restraints weight = 12419.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.152967 restraints weight = 8951.073| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12972 Z= 0.388 Angle : 0.676 11.606 17776 Z= 0.350 Chirality : 0.043 0.170 2064 Planarity : 0.004 0.035 2344 Dihedral : 7.366 129.053 2042 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 7.16 % Allowed : 25.12 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.20), residues: 1848 helix: 2.44 (0.14), residues: 1376 sheet: 1.19 (0.41), residues: 84 loop : -2.43 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 175 HIS 0.007 0.001 HIS B 517 PHE 0.020 0.002 PHE A 538 TYR 0.015 0.002 TYR C 411 ARG 0.009 0.001 ARG B 581 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2720.64 seconds wall clock time: 50 minutes 15.76 seconds (3015.76 seconds total)