Starting phenix.real_space_refine on Wed Mar 4 14:07:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lvc_0989/03_2026/6lvc_0989.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lvc_0989/03_2026/6lvc_0989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lvc_0989/03_2026/6lvc_0989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lvc_0989/03_2026/6lvc_0989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lvc_0989/03_2026/6lvc_0989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lvc_0989/03_2026/6lvc_0989.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 Fe 2 7.16 5 S 48 5.16 5 C 8916 2.51 5 N 2484 2.21 5 O 2688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14138 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5987 Classifications: {'peptide': 762} Link IDs: {'PTRANS': 39, 'TRANS': 722} Chain: "B" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1080 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "C" Number of atoms: 5987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5987 Classifications: {'peptide': 762} Link IDs: {'PTRANS': 39, 'TRANS': 722} Chain: "D" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1080 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.18, per 1000 atoms: 0.22 Number of scatterers: 14138 At special positions: 0 Unit cell: (120.91, 123.05, 95.23, 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) Fe 2 26.01 S 48 16.00 O 2688 8.00 N 2484 7.00 C 8916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 611.7 milliseconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3208 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 18 sheets defined 24.5% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 224 through 228 removed outlier: 4.151A pdb=" N GLY A 227 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.687A pdb=" N ARG A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.527A pdb=" N GLN A 326 " --> pdb=" O CYS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 410 through 415 removed outlier: 3.707A pdb=" N ALA A 415 " --> pdb=" O GLY A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.725A pdb=" N VAL A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 435 Processing helix chain 'A' and resid 475 through 488 removed outlier: 4.366A pdb=" N LEU A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.052A pdb=" N LEU A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 537 removed outlier: 3.739A pdb=" N ASP A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 597 Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 623 through 631 removed outlier: 3.619A pdb=" N GLN A 626 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N GLU A 628 " --> pdb=" O SER A 625 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG A 629 " --> pdb=" O GLN A 626 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 631 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 688 through 691 removed outlier: 3.609A pdb=" N LYS A 691 " --> pdb=" O PRO A 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 691' Processing helix chain 'A' and resid 726 through 733 removed outlier: 3.726A pdb=" N TRP A 729 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 730 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 731 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 733 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 754 removed outlier: 3.538A pdb=" N ILE A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.774A pdb=" N TYR B 15 " --> pdb=" O PRO B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 41 removed outlier: 4.374A pdb=" N TRP B 22 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 51 Processing helix chain 'B' and resid 60 through 71 Processing helix chain 'B' and resid 111 through 130 removed outlier: 3.572A pdb=" N ALA B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 removed outlier: 4.167A pdb=" N GLY C 227 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 removed outlier: 3.687A pdb=" N ARG C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 327 removed outlier: 3.527A pdb=" N GLN C 326 " --> pdb=" O CYS C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 410 through 415 removed outlier: 3.708A pdb=" N ALA C 415 " --> pdb=" O GLY C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 431 removed outlier: 3.725A pdb=" N VAL C 426 " --> pdb=" O ASN C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 435 Processing helix chain 'C' and resid 475 through 488 removed outlier: 4.367A pdb=" N LEU C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 504 through 509 removed outlier: 4.051A pdb=" N LEU C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 537 removed outlier: 3.745A pdb=" N ASP C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 597 Processing helix chain 'C' and resid 600 through 605 Processing helix chain 'C' and resid 623 through 631 removed outlier: 3.618A pdb=" N GLN C 626 " --> pdb=" O PRO C 623 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU C 628 " --> pdb=" O SER C 625 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG C 629 " --> pdb=" O GLN C 626 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 631 " --> pdb=" O GLU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 666 Processing helix chain 'C' and resid 688 through 691 removed outlier: 3.609A pdb=" N LYS C 691 " --> pdb=" O PRO C 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 688 through 691' Processing helix chain 'C' and resid 726 through 733 removed outlier: 3.738A pdb=" N TRP C 729 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 730 " --> pdb=" O ILE C 727 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY C 731 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 733 " --> pdb=" O LEU C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 754 removed outlier: 3.537A pdb=" N ILE C 754 " --> pdb=" O LEU C 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.778A pdb=" N TYR D 15 " --> pdb=" O PRO D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 41 removed outlier: 4.375A pdb=" N TRP D 22 " --> pdb=" O ARG D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 51 Processing helix chain 'D' and resid 60 through 71 Processing helix chain 'D' and resid 111 through 130 removed outlier: 3.572A pdb=" N ALA D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 10 removed outlier: 3.536A pdb=" N PHE A 346 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15 removed outlier: 4.939A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU A 38 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS A 54 " --> pdb=" O ILE A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 15 removed outlier: 4.939A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 64 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 148 removed outlier: 6.770A pdb=" N SER A 122 " --> pdb=" O TRP A 116 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TRP A 116 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TRP A 124 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER A 114 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A 126 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 244 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N HIS A 271 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ASP A 273 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 10.123A pdb=" N ASP A 240 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL A 239 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TRP A 101 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ALA A 241 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE A 99 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 308 removed outlier: 3.966A pdb=" N SER A 308 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.345A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 514 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 618 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N MET A 608 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ARG A 660 " --> pdb=" O MET A 608 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 612 " --> pdb=" O TYR A 656 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 656 " --> pdb=" O GLY A 612 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N ASP A 614 " --> pdb=" O GLY A 654 " (cutoff:3.500A) removed outlier: 11.879A pdb=" N GLY A 654 " --> pdb=" O ASP A 614 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.345A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 514 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 618 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 611 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 420 through 421 removed outlier: 6.782A pdb=" N ALA B 89 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AB1, first strand: chain 'C' and resid 9 through 10 removed outlier: 3.535A pdb=" N PHE C 346 " --> pdb=" O PHE C 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.938A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU C 38 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS C 54 " --> pdb=" O ILE C 42 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.938A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY C 64 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.770A pdb=" N SER C 122 " --> pdb=" O TRP C 116 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TRP C 116 " --> pdb=" O SER C 122 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TRP C 124 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER C 114 " --> pdb=" O TRP C 124 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU C 126 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL C 289 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE C 244 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N HIS C 271 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ASP C 273 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N ASP C 240 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N VAL C 239 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N TRP C 101 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ALA C 241 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE C 99 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 306 through 308 removed outlier: 3.976A pdb=" N SER C 308 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.357A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL C 514 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N MET C 608 " --> pdb=" O ARG C 660 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ARG C 660 " --> pdb=" O MET C 608 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY C 612 " --> pdb=" O TYR C 656 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR C 656 " --> pdb=" O GLY C 612 " (cutoff:3.500A) removed outlier: 9.480A pdb=" N ASP C 614 " --> pdb=" O GLY C 654 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N GLY C 654 " --> pdb=" O ASP C 614 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.357A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL C 514 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE C 611 " --> pdb=" O THR C 685 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 420 through 421 removed outlier: 6.781A pdb=" N ALA D 89 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 451 through 453 514 hydrogen bonds defined for protein. 1392 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: 2.83 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4321 1.33 - 1.45: 2735 1.45 - 1.57: 7404 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 14538 Sorted by residual: bond pdb=" C PRO A 577 " pdb=" N PRO A 578 " ideal model delta sigma weight residual 1.334 1.393 -0.059 1.51e-02 4.39e+03 1.51e+01 bond pdb=" C PRO C 577 " pdb=" N PRO C 578 " ideal model delta sigma weight residual 1.334 1.393 -0.058 1.51e-02 4.39e+03 1.50e+01 bond pdb=" CG ARG A 707 " pdb=" CD ARG A 707 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.35e+00 bond pdb=" CG ARG C 707 " pdb=" CD ARG C 707 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.32e+00 bond pdb=" CB VAL A 15 " pdb=" CG1 VAL A 15 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.85e+00 ... (remaining 14533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 18733 2.06 - 4.12: 896 4.12 - 6.18: 97 6.18 - 8.24: 22 8.24 - 10.30: 6 Bond angle restraints: 19754 Sorted by residual: angle pdb=" C GLY A 655 " pdb=" N TYR A 656 " pdb=" CA TYR A 656 " ideal model delta sigma weight residual 121.54 131.84 -10.30 1.91e+00 2.74e-01 2.91e+01 angle pdb=" C GLY C 655 " pdb=" N TYR C 656 " pdb=" CA TYR C 656 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 angle pdb=" N PRO C 578 " pdb=" CA PRO C 578 " pdb=" C PRO C 578 " ideal model delta sigma weight residual 113.75 121.61 -7.86 1.49e+00 4.50e-01 2.78e+01 angle pdb=" N PRO A 578 " pdb=" CA PRO A 578 " pdb=" C PRO A 578 " ideal model delta sigma weight residual 113.75 121.59 -7.84 1.49e+00 4.50e-01 2.77e+01 angle pdb=" CA TYR C 24 " pdb=" CB TYR C 24 " pdb=" CG TYR C 24 " ideal model delta sigma weight residual 113.90 120.75 -6.85 1.80e+00 3.09e-01 1.45e+01 ... (remaining 19749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 7992 15.53 - 31.05: 400 31.05 - 46.57: 58 46.57 - 62.10: 6 62.10 - 77.62: 4 Dihedral angle restraints: 8460 sinusoidal: 3394 harmonic: 5066 Sorted by residual: dihedral pdb=" CA PRO A 577 " pdb=" C PRO A 577 " pdb=" N PRO A 578 " pdb=" CA PRO A 578 " ideal model delta harmonic sigma weight residual 180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA PRO C 577 " pdb=" C PRO C 577 " pdb=" N PRO C 578 " pdb=" CA PRO C 578 " ideal model delta harmonic sigma weight residual -180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA SER C 114 " pdb=" C SER C 114 " pdb=" N ARG C 115 " pdb=" CA ARG C 115 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 8457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1746 0.097 - 0.195: 233 0.195 - 0.292: 17 0.292 - 0.390: 0 0.390 - 0.487: 2 Chirality restraints: 1998 Sorted by residual: chirality pdb=" CB ILE C 283 " pdb=" CA ILE C 283 " pdb=" CG1 ILE C 283 " pdb=" CG2 ILE C 283 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" CB ILE A 283 " pdb=" CA ILE A 283 " pdb=" CG1 ILE A 283 " pdb=" CG2 ILE A 283 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CB ILE C 21 " pdb=" CA ILE C 21 " pdb=" CG1 ILE C 21 " pdb=" CG2 ILE C 21 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1995 not shown) Planarity restraints: 2628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 522 " 0.039 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR A 522 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TYR A 522 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 522 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 522 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 522 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 522 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 522 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 522 " -0.038 2.00e-02 2.50e+03 3.03e-02 1.83e+01 pdb=" CG TYR C 522 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TYR C 522 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR C 522 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 522 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR C 522 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR C 522 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR C 522 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 440 " 0.030 2.00e-02 2.50e+03 2.95e-02 1.73e+01 pdb=" CG TYR A 440 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR A 440 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 440 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 440 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 440 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 440 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 440 " -0.001 2.00e-02 2.50e+03 ... (remaining 2625 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 57 2.44 - 3.06: 8092 3.06 - 3.67: 21336 3.67 - 4.29: 34360 4.29 - 4.90: 57880 Nonbonded interactions: 121725 Sorted by model distance: nonbonded pdb=" OH TYR C 440 " pdb="FE FE C 801 " model vdw 1.831 2.260 nonbonded pdb=" OH TYR A 440 " pdb="FE FE A 801 " model vdw 1.833 2.260 nonbonded pdb=" OE1 GLU A 521 " pdb="FE FE A 801 " model vdw 1.915 2.260 nonbonded pdb=" OE1 GLU C 521 " pdb="FE FE C 801 " model vdw 1.918 2.260 nonbonded pdb=" OE2 GLU C 521 " pdb="FE FE C 801 " model vdw 1.959 2.260 ... (remaining 121720 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.950 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 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 : 0.011 0.091 14538 Z= 0.464 Angle : 1.001 10.305 19754 Z= 0.561 Chirality : 0.066 0.487 1998 Planarity : 0.008 0.060 2628 Dihedral : 9.662 77.624 5252 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.48 % Allowed : 1.98 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.17), residues: 1764 helix: -2.05 (0.23), residues: 284 sheet: -1.37 (0.28), residues: 326 loop : -2.04 (0.15), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG B 30 TYR 0.072 0.005 TYR A 522 PHE 0.030 0.005 PHE A 358 TRP 0.054 0.004 TRP C 331 HIS 0.021 0.004 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.01120 (14538) covalent geometry : angle 1.00052 (19754) hydrogen bonds : bond 0.21369 ( 452) hydrogen bonds : angle 8.41925 ( 1392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 264 time to evaluate : 0.415 Fit side-chains REVERT: A 4 ILE cc_start: 0.8956 (mm) cc_final: 0.8698 (mp) REVERT: A 170 LYS cc_start: 0.8620 (mtpt) cc_final: 0.8171 (mtmp) REVERT: A 761 ARG cc_start: 0.7403 (mtt-85) cc_final: 0.7202 (mmm-85) REVERT: B 32 LYS cc_start: 0.8393 (mtmt) cc_final: 0.8079 (mtmm) REVERT: B 116 MET cc_start: 0.8895 (mtt) cc_final: 0.8647 (mtm) REVERT: C 4 ILE cc_start: 0.8953 (mm) cc_final: 0.8682 (mp) REVERT: C 170 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8171 (mtmp) REVERT: D 32 LYS cc_start: 0.8391 (mtmt) cc_final: 0.8076 (mtmm) REVERT: D 116 MET cc_start: 0.8882 (mtt) cc_final: 0.8632 (mtm) outliers start: 7 outliers final: 1 residues processed: 271 average time/residue: 0.7129 time to fit residues: 208.6421 Evaluate side-chains 151 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 121 GLN ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN A 695 HIS B 14 ASN C 71 GLN C 121 GLN ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 547 ASN C 695 HIS D 14 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.100945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.081745 restraints weight = 19226.073| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 1.62 r_work: 0.2668 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14538 Z= 0.133 Angle : 0.570 6.995 19754 Z= 0.312 Chirality : 0.045 0.209 1998 Planarity : 0.006 0.048 2628 Dihedral : 5.425 36.593 1983 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.32 % Allowed : 7.72 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.18), residues: 1764 helix: -0.23 (0.27), residues: 302 sheet: -0.93 (0.27), residues: 344 loop : -1.45 (0.17), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 364 TYR 0.022 0.002 TYR C 661 PHE 0.015 0.002 PHE C 75 TRP 0.023 0.001 TRP B 22 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00296 (14538) covalent geometry : angle 0.57030 (19754) hydrogen bonds : bond 0.04686 ( 452) hydrogen bonds : angle 5.38207 ( 1392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.530 Fit side-chains REVERT: A 65 GLN cc_start: 0.8306 (mt0) cc_final: 0.7895 (mt0) REVERT: A 170 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8200 (mtmp) REVERT: A 402 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: A 422 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8605 (p0) REVERT: A 721 MET cc_start: 0.9382 (tpt) cc_final: 0.9088 (tpt) REVERT: A 761 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.7714 (mmm-85) REVERT: C 65 GLN cc_start: 0.8306 (mt0) cc_final: 0.7888 (mt0) REVERT: C 170 LYS cc_start: 0.8678 (mtpt) cc_final: 0.8193 (mtmp) REVERT: C 402 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: C 422 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8608 (p0) REVERT: C 634 MET cc_start: 0.8758 (mmt) cc_final: 0.8521 (mmt) REVERT: C 721 MET cc_start: 0.9425 (tpt) cc_final: 0.9077 (tpt) outliers start: 34 outliers final: 20 residues processed: 175 average time/residue: 0.6281 time to fit residues: 120.0869 Evaluate side-chains 160 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 512 LYS Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 37 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 118 optimal weight: 0.0770 chunk 90 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 110 optimal weight: 0.0970 chunk 46 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN C 225 GLN ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.094303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.073551 restraints weight = 19859.944| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 1.80 r_work: 0.2669 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14538 Z= 0.128 Angle : 0.539 7.129 19754 Z= 0.292 Chirality : 0.045 0.197 1998 Planarity : 0.005 0.053 2628 Dihedral : 5.098 37.777 1983 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.60 % Allowed : 8.81 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.19), residues: 1764 helix: 0.79 (0.29), residues: 302 sheet: -0.57 (0.28), residues: 344 loop : -1.21 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 364 TYR 0.022 0.001 TYR C 661 PHE 0.017 0.002 PHE B 53 TRP 0.017 0.001 TRP B 22 HIS 0.005 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00293 (14538) covalent geometry : angle 0.53925 (19754) hydrogen bonds : bond 0.04215 ( 452) hydrogen bonds : angle 4.97193 ( 1392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.644 Fit side-chains REVERT: A 65 GLN cc_start: 0.8434 (mt0) cc_final: 0.8042 (mt0) REVERT: A 170 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8177 (mtmp) REVERT: A 402 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: A 592 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8096 (ptt-90) REVERT: A 761 ARG cc_start: 0.7970 (mtt-85) cc_final: 0.7701 (mmm-85) REVERT: C 65 GLN cc_start: 0.8434 (mt0) cc_final: 0.8039 (mt0) REVERT: C 170 LYS cc_start: 0.8698 (mtpt) cc_final: 0.8170 (mtmp) REVERT: C 402 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: C 592 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8060 (ptt-90) outliers start: 38 outliers final: 22 residues processed: 171 average time/residue: 0.6115 time to fit residues: 114.4303 Evaluate side-chains 167 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 512 LYS Chi-restraints excluded: chain C residue 592 ARG Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 37 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 87 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.091044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.069867 restraints weight = 19928.635| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 1.83 r_work: 0.2530 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2399 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 14538 Z= 0.230 Angle : 0.612 7.735 19754 Z= 0.330 Chirality : 0.048 0.212 1998 Planarity : 0.006 0.050 2628 Dihedral : 5.298 40.234 1983 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.66 % Allowed : 10.31 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.19), residues: 1764 helix: 1.35 (0.30), residues: 304 sheet: -0.75 (0.28), residues: 340 loop : -1.16 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 364 TYR 0.029 0.002 TYR A 661 PHE 0.017 0.002 PHE B 53 TRP 0.014 0.002 TRP B 22 HIS 0.009 0.002 HIS D 67 Details of bonding type rmsd covalent geometry : bond 0.00552 (14538) covalent geometry : angle 0.61176 (19754) hydrogen bonds : bond 0.04679 ( 452) hydrogen bonds : angle 4.97462 ( 1392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.583 Fit side-chains REVERT: A 65 GLN cc_start: 0.8474 (mt0) cc_final: 0.8072 (mt0) REVERT: A 170 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8155 (mtmp) REVERT: A 402 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: A 422 ASN cc_start: 0.9190 (OUTLIER) cc_final: 0.8855 (p0) REVERT: A 592 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8160 (ptt-90) REVERT: A 761 ARG cc_start: 0.8080 (mtt-85) cc_final: 0.7800 (mmm-85) REVERT: B 72 MET cc_start: 0.9347 (ptm) cc_final: 0.9045 (ptp) REVERT: C 65 GLN cc_start: 0.8472 (mt0) cc_final: 0.8021 (mt0) REVERT: C 170 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8154 (mtmp) REVERT: C 402 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: C 422 ASN cc_start: 0.9158 (OUTLIER) cc_final: 0.8832 (p0) REVERT: C 592 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8170 (ptt-90) REVERT: D 72 MET cc_start: 0.9342 (ptm) cc_final: 0.9040 (ptp) outliers start: 39 outliers final: 21 residues processed: 173 average time/residue: 0.6486 time to fit residues: 122.7329 Evaluate side-chains 170 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 592 ARG Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 8 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 173 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 73 optimal weight: 0.0000 chunk 109 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.092340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.071523 restraints weight = 19904.382| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 1.84 r_work: 0.2607 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14538 Z= 0.132 Angle : 0.531 7.169 19754 Z= 0.290 Chirality : 0.045 0.195 1998 Planarity : 0.005 0.049 2628 Dihedral : 5.023 41.062 1983 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.80 % Allowed : 11.95 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.20), residues: 1764 helix: 1.78 (0.30), residues: 302 sheet: -0.69 (0.27), residues: 364 loop : -1.01 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 364 TYR 0.021 0.001 TYR C 661 PHE 0.015 0.002 PHE D 53 TRP 0.017 0.001 TRP B 22 HIS 0.004 0.001 HIS D 67 Details of bonding type rmsd covalent geometry : bond 0.00309 (14538) covalent geometry : angle 0.53136 (19754) hydrogen bonds : bond 0.03957 ( 452) hydrogen bonds : angle 4.77387 ( 1392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.527 Fit side-chains REVERT: A 65 GLN cc_start: 0.8433 (mt0) cc_final: 0.7987 (mt0) REVERT: A 170 LYS cc_start: 0.8700 (mtpt) cc_final: 0.8173 (mtmp) REVERT: A 364 ARG cc_start: 0.8525 (tpp80) cc_final: 0.8319 (ttm-80) REVERT: A 402 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: A 422 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8672 (p0) REVERT: A 592 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8069 (ptt-90) REVERT: A 761 ARG cc_start: 0.8062 (mtt-85) cc_final: 0.7790 (mmm-85) REVERT: B 28 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8257 (tm-30) REVERT: B 72 MET cc_start: 0.9329 (ptm) cc_final: 0.9012 (ptp) REVERT: B 112 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: C 65 GLN cc_start: 0.8433 (mt0) cc_final: 0.7986 (mt0) REVERT: C 170 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8176 (mtmp) REVERT: C 364 ARG cc_start: 0.8531 (tpp80) cc_final: 0.8323 (ttm-80) REVERT: C 402 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7642 (tm-30) REVERT: C 422 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8673 (p0) REVERT: C 592 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8071 (ptt-90) REVERT: D 28 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: D 72 MET cc_start: 0.9329 (ptm) cc_final: 0.9011 (ptp) REVERT: D 112 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8100 (mt-10) outliers start: 41 outliers final: 25 residues processed: 172 average time/residue: 0.6438 time to fit residues: 120.7137 Evaluate side-chains 178 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 592 ARG Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 112 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 138 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.090178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.069287 restraints weight = 19923.083| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 1.79 r_work: 0.2580 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2448 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14538 Z= 0.204 Angle : 0.578 7.214 19754 Z= 0.314 Chirality : 0.047 0.206 1998 Planarity : 0.005 0.049 2628 Dihedral : 5.140 42.620 1983 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.14 % Allowed : 11.27 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.20), residues: 1764 helix: 1.81 (0.30), residues: 304 sheet: -0.64 (0.27), residues: 364 loop : -0.96 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 364 TYR 0.025 0.002 TYR C 661 PHE 0.018 0.002 PHE B 53 TRP 0.014 0.001 TRP B 22 HIS 0.007 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00489 (14538) covalent geometry : angle 0.57751 (19754) hydrogen bonds : bond 0.04306 ( 452) hydrogen bonds : angle 4.80107 ( 1392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 0.533 Fit side-chains REVERT: A 65 GLN cc_start: 0.8465 (mt0) cc_final: 0.8029 (mt0) REVERT: A 170 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8171 (mtmp) REVERT: A 402 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: A 592 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8154 (ptt-90) REVERT: A 761 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7858 (mmm-85) REVERT: B 28 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8293 (tm-30) REVERT: B 72 MET cc_start: 0.9322 (ptm) cc_final: 0.9047 (ptp) REVERT: B 100 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: C 65 GLN cc_start: 0.8466 (mt0) cc_final: 0.8029 (mt0) REVERT: C 170 LYS cc_start: 0.8729 (mtpt) cc_final: 0.8183 (mtmp) REVERT: C 402 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: C 592 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8158 (ptt-90) REVERT: D 28 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8307 (tm-30) REVERT: D 72 MET cc_start: 0.9323 (ptm) cc_final: 0.9045 (ptp) REVERT: D 100 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7719 (mp0) outliers start: 46 outliers final: 30 residues processed: 169 average time/residue: 0.6346 time to fit residues: 117.1846 Evaluate side-chains 179 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 592 ARG Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 112 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 18 optimal weight: 0.5980 chunk 173 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.092392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.072426 restraints weight = 19634.157| |-----------------------------------------------------------------------------| r_work (start): 0.2577 rms_B_bonded: 1.70 r_work: 0.2461 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2328 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14538 Z= 0.218 Angle : 0.587 7.310 19754 Z= 0.319 Chirality : 0.047 0.208 1998 Planarity : 0.005 0.047 2628 Dihedral : 5.218 45.328 1983 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.66 % Allowed : 12.50 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.20), residues: 1764 helix: 1.86 (0.30), residues: 302 sheet: -0.62 (0.27), residues: 364 loop : -0.98 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 364 TYR 0.025 0.002 TYR A 661 PHE 0.017 0.002 PHE A 187 TRP 0.015 0.001 TRP B 22 HIS 0.007 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00524 (14538) covalent geometry : angle 0.58678 (19754) hydrogen bonds : bond 0.04427 ( 452) hydrogen bonds : angle 4.81977 ( 1392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.584 Fit side-chains REVERT: A 65 GLN cc_start: 0.8432 (mt0) cc_final: 0.7958 (mt0) REVERT: A 170 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8136 (mtmp) REVERT: A 364 ARG cc_start: 0.8370 (ttm-80) cc_final: 0.7557 (ttp80) REVERT: A 402 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: A 422 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8703 (p0) REVERT: A 592 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8123 (ptt-90) REVERT: A 717 ASN cc_start: 0.9113 (t0) cc_final: 0.8798 (t0) REVERT: A 761 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.7767 (mmm160) REVERT: B 28 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8234 (tm-30) REVERT: B 72 MET cc_start: 0.9303 (ptm) cc_final: 0.9066 (ptp) REVERT: B 100 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: C 65 GLN cc_start: 0.8436 (mt0) cc_final: 0.7959 (mt0) REVERT: C 170 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8145 (mtmp) REVERT: C 364 ARG cc_start: 0.8384 (ttm-80) cc_final: 0.7570 (ttp80) REVERT: C 402 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: C 422 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8712 (p0) REVERT: C 592 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8126 (ptt-90) REVERT: C 717 ASN cc_start: 0.9099 (t0) cc_final: 0.8803 (t0) REVERT: D 28 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8249 (tm-30) REVERT: D 72 MET cc_start: 0.9296 (ptm) cc_final: 0.9058 (ptp) REVERT: D 100 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7687 (mp0) outliers start: 39 outliers final: 29 residues processed: 168 average time/residue: 0.6402 time to fit residues: 117.5217 Evaluate side-chains 174 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 592 ARG Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 112 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 173 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.091250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.070487 restraints weight = 19858.003| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 1.82 r_work: 0.2576 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2444 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14538 Z= 0.151 Angle : 0.545 6.939 19754 Z= 0.297 Chirality : 0.045 0.195 1998 Planarity : 0.005 0.047 2628 Dihedral : 5.056 46.068 1983 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.46 % Allowed : 13.25 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.20), residues: 1764 helix: 1.89 (0.30), residues: 312 sheet: -0.61 (0.27), residues: 364 loop : -0.95 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 364 TYR 0.022 0.001 TYR C 661 PHE 0.016 0.002 PHE B 53 TRP 0.017 0.001 TRP B 22 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00358 (14538) covalent geometry : angle 0.54546 (19754) hydrogen bonds : bond 0.03987 ( 452) hydrogen bonds : angle 4.70392 ( 1392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.489 Fit side-chains REVERT: A 65 GLN cc_start: 0.8423 (mt0) cc_final: 0.7997 (mt0) REVERT: A 170 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8158 (mtmp) REVERT: A 364 ARG cc_start: 0.8375 (ttm-80) cc_final: 0.7593 (ttp80) REVERT: A 402 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: A 592 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8080 (ptt-90) REVERT: A 761 ARG cc_start: 0.8149 (mtt-85) cc_final: 0.7874 (mmm-85) REVERT: B 13 SER cc_start: 0.9285 (m) cc_final: 0.9007 (p) REVERT: B 28 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: B 72 MET cc_start: 0.9331 (ptm) cc_final: 0.9094 (ptp) REVERT: B 100 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: C 65 GLN cc_start: 0.8426 (mt0) cc_final: 0.8002 (mt0) REVERT: C 170 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8159 (mtmp) REVERT: C 364 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.7602 (ttp80) REVERT: C 402 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: C 592 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8082 (ptt-90) REVERT: D 13 SER cc_start: 0.9280 (m) cc_final: 0.8998 (p) REVERT: D 28 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: D 72 MET cc_start: 0.9329 (ptm) cc_final: 0.9091 (ptp) REVERT: D 100 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7684 (mp0) outliers start: 36 outliers final: 25 residues processed: 170 average time/residue: 0.6492 time to fit residues: 120.2380 Evaluate side-chains 171 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 592 ARG Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 112 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 4 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 135 optimal weight: 0.1980 chunk 168 optimal weight: 0.2980 chunk 101 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 431 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 431 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.093025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.072740 restraints weight = 19907.108| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 1.75 r_work: 0.2518 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2387 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14538 Z= 0.109 Angle : 0.524 7.340 19754 Z= 0.284 Chirality : 0.044 0.186 1998 Planarity : 0.004 0.047 2628 Dihedral : 4.815 44.637 1983 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.12 % Allowed : 13.87 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1764 helix: 2.07 (0.30), residues: 312 sheet: -0.56 (0.27), residues: 364 loop : -0.84 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 364 TYR 0.018 0.001 TYR A 661 PHE 0.015 0.001 PHE B 53 TRP 0.019 0.001 TRP B 22 HIS 0.002 0.001 HIS C 582 Details of bonding type rmsd covalent geometry : bond 0.00250 (14538) covalent geometry : angle 0.52385 (19754) hydrogen bonds : bond 0.03556 ( 452) hydrogen bonds : angle 4.55615 ( 1392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.544 Fit side-chains REVERT: A 65 GLN cc_start: 0.8376 (mt0) cc_final: 0.7929 (mt0) REVERT: A 170 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8027 (mtmp) REVERT: A 364 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.7558 (ttp80) REVERT: A 402 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: A 405 MET cc_start: 0.9169 (mmt) cc_final: 0.8841 (mmt) REVERT: A 592 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8080 (ptt-90) REVERT: A 761 ARG cc_start: 0.8145 (mtt-85) cc_final: 0.7863 (mmm-85) REVERT: B 13 SER cc_start: 0.9283 (m) cc_final: 0.8990 (p) REVERT: B 28 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: B 72 MET cc_start: 0.9288 (ptm) cc_final: 0.9087 (ptp) REVERT: C 65 GLN cc_start: 0.8358 (mt0) cc_final: 0.7910 (mt0) REVERT: C 170 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8041 (mtmp) REVERT: C 364 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.7561 (ttp80) REVERT: C 402 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: C 592 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8088 (ptt-90) REVERT: C 721 MET cc_start: 0.9422 (tpt) cc_final: 0.9114 (tpt) REVERT: D 13 SER cc_start: 0.9294 (m) cc_final: 0.8989 (p) REVERT: D 28 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: D 72 MET cc_start: 0.9285 (ptm) cc_final: 0.9081 (ptp) outliers start: 31 outliers final: 21 residues processed: 163 average time/residue: 0.6382 time to fit residues: 113.7099 Evaluate side-chains 169 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 592 ARG Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 112 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.090830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.070846 restraints weight = 19869.232| |-----------------------------------------------------------------------------| r_work (start): 0.2558 rms_B_bonded: 1.70 r_work: 0.2442 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2311 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14538 Z= 0.265 Angle : 0.631 7.514 19754 Z= 0.342 Chirality : 0.049 0.216 1998 Planarity : 0.005 0.046 2628 Dihedral : 5.286 47.619 1983 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.12 % Allowed : 13.59 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.20), residues: 1764 helix: 1.78 (0.30), residues: 314 sheet: -0.55 (0.27), residues: 360 loop : -0.89 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 364 TYR 0.030 0.002 TYR A 661 PHE 0.019 0.002 PHE A 187 TRP 0.013 0.002 TRP A 101 HIS 0.008 0.002 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00640 (14538) covalent geometry : angle 0.63083 (19754) hydrogen bonds : bond 0.04629 ( 452) hydrogen bonds : angle 4.83222 ( 1392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.504 Fit side-chains REVERT: A 65 GLN cc_start: 0.8437 (mt0) cc_final: 0.7976 (mt0) REVERT: A 170 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8152 (mtmp) REVERT: A 294 TYR cc_start: 0.7941 (m-10) cc_final: 0.7646 (m-80) REVERT: A 364 ARG cc_start: 0.8325 (ttm-80) cc_final: 0.7525 (ttp80) REVERT: A 402 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: A 445 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.7124 (m-30) REVERT: A 592 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8112 (ptt-90) REVERT: A 717 ASN cc_start: 0.9102 (t0) cc_final: 0.8781 (t0) REVERT: A 721 MET cc_start: 0.9490 (tpt) cc_final: 0.9117 (tpt) REVERT: A 761 ARG cc_start: 0.8225 (mtt-85) cc_final: 0.7771 (mmm160) REVERT: B 28 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: B 72 MET cc_start: 0.9305 (ptm) cc_final: 0.9064 (ptp) REVERT: B 100 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: C 3 ASP cc_start: 0.7584 (t0) cc_final: 0.7358 (OUTLIER) REVERT: C 65 GLN cc_start: 0.8424 (mt0) cc_final: 0.7962 (mt0) REVERT: C 170 LYS cc_start: 0.8722 (mtpt) cc_final: 0.8160 (mtmp) REVERT: C 294 TYR cc_start: 0.7946 (m-10) cc_final: 0.7650 (m-80) REVERT: C 364 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.7535 (ttp80) REVERT: C 402 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: C 445 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.7063 (m-30) REVERT: C 592 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8118 (ptt-90) REVERT: C 717 ASN cc_start: 0.9121 (t0) cc_final: 0.8807 (t0) REVERT: D 28 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8261 (tm-30) REVERT: D 72 MET cc_start: 0.9304 (ptm) cc_final: 0.9062 (ptp) REVERT: D 100 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7722 (mp0) outliers start: 31 outliers final: 18 residues processed: 154 average time/residue: 0.6579 time to fit residues: 110.8219 Evaluate side-chains 156 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 8 CYS Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 592 ARG Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 112 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.091027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.070702 restraints weight = 19993.197| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 1.76 r_work: 0.2541 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2408 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14538 Z= 0.142 Angle : 0.552 7.181 19754 Z= 0.299 Chirality : 0.045 0.192 1998 Planarity : 0.005 0.043 2628 Dihedral : 5.023 48.855 1983 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.84 % Allowed : 13.80 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1764 helix: 1.95 (0.30), residues: 312 sheet: -0.53 (0.27), residues: 364 loop : -0.87 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 364 TYR 0.019 0.001 TYR C 661 PHE 0.016 0.002 PHE B 53 TRP 0.017 0.001 TRP B 22 HIS 0.004 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00338 (14538) covalent geometry : angle 0.55158 (19754) hydrogen bonds : bond 0.03895 ( 452) hydrogen bonds : angle 4.64049 ( 1392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4228.98 seconds wall clock time: 72 minutes 49.62 seconds (4369.62 seconds total)