Starting phenix.real_space_refine on Sat Oct 11 03:46:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvx_37875/10_2025/8wvx_37875.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvx_37875/10_2025/8wvx_37875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wvx_37875/10_2025/8wvx_37875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvx_37875/10_2025/8wvx_37875.map" model { file = "/net/cci-nas-00/data/ceres_data/8wvx_37875/10_2025/8wvx_37875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvx_37875/10_2025/8wvx_37875.cif" } resolution = 3.32 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= 0.025 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 7155 2.51 5 N 2067 2.21 5 O 2178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11460 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 4931 Classifications: {'peptide': 725} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PTRANS': 35, 'TRANS': 689} Chain breaks: 5 Unresolved non-hydrogen bonds: 783 Unresolved non-hydrogen angles: 1014 Unresolved non-hydrogen dihedrals: 684 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'TRP:plan': 7, 'ARG:plan': 7, 'PHE:plan': 31, 'ASN:plan1': 9, 'TYR:plan': 5, 'ASP:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 407 Chain: "B" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 4964 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 207} Link IDs: {'PTRANS': 36, 'TRANS': 694} Chain breaks: 4 Unresolved non-hydrogen bonds: 789 Unresolved non-hydrogen angles: 1025 Unresolved non-hydrogen dihedrals: 688 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'TYR:plan': 6, 'TRP:plan': 7, 'ARG:plan': 7, 'PHE:plan': 31, 'ASN:plan1': 9, 'ASP:plan': 2, 'GLU:plan': 8, 'HIS:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 414 Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 783 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 782 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Time building chain proxies: 3.08, per 1000 atoms: 0.27 Number of scatterers: 11460 At special positions: 0 Unit cell: (177.65, 113.05, 140.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2178 8.00 N 2067 7.00 C 7155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 35 " distance=2.01 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 43 " distance=2.04 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 364 " distance=2.03 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 693 " distance=2.04 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 35 " distance=1.21 Simple disulfide: pdb=" SG CYS B 33 " - pdb=" SG CYS B 43 " distance=1.67 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 364 " distance=2.34 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 522 " distance=2.02 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 532 " distance=2.03 Simple disulfide: pdb=" SG CYS B 618 " - pdb=" SG CYS B 693 " distance=2.04 Simple disulfide: pdb=" SG CYS C 39 " - pdb=" SG CYS C 96 " distance=1.78 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 110 " distance=2.10 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 126 " distance=1.88 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 128 " distance=2.10 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS D 95 " distance=2.20 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS D 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS D 131 " distance=1.48 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 96 " distance=1.95 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 110 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 126 " distance=2.00 Simple disulfide: pdb=" SG CYS D 69 " - pdb=" SG CYS D 128 " distance=2.10 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 645.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3140 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 14 sheets defined 29.8% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.148A pdb=" N GLY A 127 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 538 through 566 removed outlier: 3.876A pdb=" N PHE A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 558 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 601 removed outlier: 3.562A pdb=" N PHE A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 615 through 647 removed outlier: 4.106A pdb=" N LYS A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 638 " --> pdb=" O PHE A 634 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 639 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 641 " --> pdb=" O MET A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 679 removed outlier: 3.645A pdb=" N ARG A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 682 No H-bonds generated for 'chain 'A' and resid 680 through 682' Processing helix chain 'A' and resid 705 through 731 removed outlier: 3.588A pdb=" N MET A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 768 removed outlier: 3.559A pdb=" N CYS A 761 " --> pdb=" O CYS A 757 " (cutoff:3.500A) Proline residue: A 762 - end of helix removed outlier: 3.798A pdb=" N PHE A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 773 removed outlier: 4.062A pdb=" N ILE A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 776 No H-bonds generated for 'chain 'A' and resid 774 through 776' Processing helix chain 'A' and resid 780 through 790 Processing helix chain 'A' and resid 792 through 800 Proline residue: A 798 - end of helix Processing helix chain 'A' and resid 807 through 820 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.761A pdb=" N GLN B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 468 No H-bonds generated for 'chain 'B' and resid 466 through 468' Processing helix chain 'B' and resid 469 through 474 removed outlier: 4.503A pdb=" N PHE B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 564 removed outlier: 3.729A pdb=" N ARG B 542 " --> pdb=" O SER B 538 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 543 " --> pdb=" O TRP B 539 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE B 554 " --> pdb=" O LEU B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 601 removed outlier: 3.528A pdb=" N GLY B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 601 " --> pdb=" O LEU B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 614 Processing helix chain 'B' and resid 615 through 647 removed outlier: 4.046A pdb=" N LYS B 619 " --> pdb=" O GLY B 615 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 638 " --> pdb=" O PHE B 634 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B 639 " --> pdb=" O LEU B 635 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 641 " --> pdb=" O MET B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 679 removed outlier: 3.777A pdb=" N ARG B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 668 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 731 removed outlier: 3.778A pdb=" N ILE B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR B 725 " --> pdb=" O MET B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 768 Proline residue: B 762 - end of helix removed outlier: 3.571A pdb=" N SER B 767 " --> pdb=" O VAL B 763 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 773 removed outlier: 4.010A pdb=" N ILE B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 776 No H-bonds generated for 'chain 'B' and resid 774 through 776' Processing helix chain 'B' and resid 778 through 790 Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 796 through 804 removed outlier: 3.725A pdb=" N TYR B 801 " --> pdb=" O ASN B 797 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N VAL B 802 " --> pdb=" O PRO B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 820 removed outlier: 3.913A pdb=" N LYS B 809 " --> pdb=" O ASN B 805 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP B 811 " --> pdb=" O LYS B 807 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 7.177A pdb=" N VAL A 41 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU A 110 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 183 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 182 " --> pdb=" O HIS A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 removed outlier: 3.692A pdb=" N ILE A 192 " --> pdb=" O SER A 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA4, first strand: chain 'A' and resid 301 through 304 removed outlier: 6.779A pdb=" N LEU A 348 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU A 394 " --> pdb=" O ASP A 419 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 418 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA6, first strand: chain 'B' and resid 41 through 42 removed outlier: 7.335A pdb=" N VAL B 41 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU B 110 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU B 182 " --> pdb=" O HIS B 207 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.726A pdb=" N ILE B 192 " --> pdb=" O SER B 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 262 through 263 Processing sheet with id=AA9, first strand: chain 'B' and resid 301 through 304 removed outlier: 6.651A pdb=" N LEU B 348 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU B 394 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU B 418 " --> pdb=" O LYS B 440 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AB2, first strand: chain 'C' and resid 40 through 48 removed outlier: 8.215A pdb=" N ALA C 63 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS C 65 " --> pdb=" O SER D 75 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY C 67 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER D 73 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 92 removed outlier: 3.665A pdb=" N ARG C 74 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER C 73 " --> pdb=" O GLY D 67 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY D 67 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ALA D 63 " --> pdb=" O PRO C 77 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 94 through 106 removed outlier: 6.760A pdb=" N SER C 125 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER C 101 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE C 123 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU C 103 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG C 121 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA C 105 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR C 119 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 94 through 107 removed outlier: 6.478A pdb=" N SER D 125 " --> pdb=" O GLN D 99 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER D 101 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE D 123 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU D 103 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG D 121 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA D 105 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR D 119 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG D 107 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR D 117 " --> pdb=" O ARG D 107 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2635 1.32 - 1.45: 2100 1.45 - 1.57: 6844 1.57 - 1.70: 3 1.70 - 1.82: 71 Bond restraints: 11653 Sorted by residual: bond pdb=" C ILE A 541 " pdb=" N ARG A 542 " ideal model delta sigma weight residual 1.334 1.577 -0.242 1.27e-02 6.20e+03 3.64e+02 bond pdb=" C SER B 601 " pdb=" N TRP B 602 " ideal model delta sigma weight residual 1.330 1.595 -0.265 1.40e-02 5.10e+03 3.59e+02 bond pdb=" C SER A 601 " pdb=" N TRP A 602 " ideal model delta sigma weight residual 1.330 1.588 -0.258 1.40e-02 5.10e+03 3.40e+02 bond pdb=" C ALA B 472 " pdb=" N PHE B 473 " ideal model delta sigma weight residual 1.334 1.561 -0.227 1.30e-02 5.92e+03 3.06e+02 bond pdb=" C GLN A 469 " pdb=" N CYS A 470 " ideal model delta sigma weight residual 1.335 1.543 -0.208 1.25e-02 6.40e+03 2.77e+02 ... (remaining 11648 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.39: 15585 6.39 - 12.78: 286 12.78 - 19.17: 36 19.17 - 25.55: 3 25.55 - 31.94: 2 Bond angle restraints: 15912 Sorted by residual: angle pdb=" N SER A 573 " pdb=" CA SER A 573 " pdb=" C SER A 573 " ideal model delta sigma weight residual 114.62 82.68 31.94 1.14e+00 7.69e-01 7.85e+02 angle pdb=" N SER C 92 " pdb=" CA SER C 92 " pdb=" C SER C 92 " ideal model delta sigma weight residual 108.76 79.38 29.38 1.58e+00 4.01e-01 3.46e+02 angle pdb=" O CYS A 471 " pdb=" C CYS A 471 " pdb=" N ALA A 472 " ideal model delta sigma weight residual 122.08 140.74 -18.66 1.07e+00 8.73e-01 3.04e+02 angle pdb=" N GLN A 342 " pdb=" CA GLN A 342 " pdb=" C GLN A 342 " ideal model delta sigma weight residual 109.15 85.11 24.04 1.44e+00 4.82e-01 2.79e+02 angle pdb=" O CYS A 470 " pdb=" C CYS A 470 " pdb=" N CYS A 471 " ideal model delta sigma weight residual 122.09 138.17 -16.08 1.04e+00 9.25e-01 2.39e+02 ... (remaining 15907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6875 17.67 - 35.34: 194 35.34 - 53.01: 41 53.01 - 70.69: 10 70.69 - 88.36: 1 Dihedral angle restraints: 7121 sinusoidal: 2318 harmonic: 4803 Sorted by residual: dihedral pdb=" C ALA B 185 " pdb=" N ALA B 185 " pdb=" CA ALA B 185 " pdb=" CB ALA B 185 " ideal model delta harmonic sigma weight residual -122.60 -101.26 -21.34 0 2.50e+00 1.60e-01 7.29e+01 dihedral pdb=" CB CYS A 29 " pdb=" SG CYS A 29 " pdb=" SG CYS A 35 " pdb=" CB CYS A 35 " ideal model delta sinusoidal sigma weight residual -86.00 -142.50 56.50 1 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" CB CYS A 33 " pdb=" SG CYS A 33 " pdb=" SG CYS A 43 " pdb=" CB CYS A 43 " ideal model delta sinusoidal sigma weight residual -86.00 -31.47 -54.53 1 1.00e+01 1.00e-02 4.03e+01 ... (remaining 7118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.178: 1873 0.178 - 0.356: 43 0.356 - 0.534: 2 0.534 - 0.712: 0 0.712 - 0.890: 1 Chirality restraints: 1919 Sorted by residual: chirality pdb=" CA SER A 572 " pdb=" N SER A 572 " pdb=" C SER A 572 " pdb=" CB SER A 572 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.98e+01 chirality pdb=" CA SER C 82 " pdb=" N SER C 82 " pdb=" C SER C 82 " pdb=" CB SER C 82 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CA ALA B 185 " pdb=" N ALA B 185 " pdb=" C ALA B 185 " pdb=" CB ALA B 185 " both_signs ideal model delta sigma weight residual False 2.48 2.86 -0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 1916 not shown) Planarity restraints: 2118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 806 " -0.042 2.00e-02 2.50e+03 8.38e-02 7.02e+01 pdb=" C PRO B 806 " 0.145 2.00e-02 2.50e+03 pdb=" O PRO B 806 " -0.053 2.00e-02 2.50e+03 pdb=" N LYS B 807 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 703 " -0.025 2.00e-02 2.50e+03 6.06e-02 3.67e+01 pdb=" C SER A 703 " 0.104 2.00e-02 2.50e+03 pdb=" O SER A 703 " -0.042 2.00e-02 2.50e+03 pdb=" N LEU A 704 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 703 " 0.025 2.00e-02 2.50e+03 6.04e-02 3.65e+01 pdb=" C SER B 703 " -0.104 2.00e-02 2.50e+03 pdb=" O SER B 703 " 0.042 2.00e-02 2.50e+03 pdb=" N LEU B 704 " 0.037 2.00e-02 2.50e+03 ... (remaining 2115 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.92: 7 1.92 - 2.67: 359 2.67 - 3.41: 15167 3.41 - 4.16: 25592 4.16 - 4.90: 44871 Nonbonded interactions: 85996 Sorted by model distance: nonbonded pdb=" CD2 LEU A 462 " pdb=" CZ PHE A 473 " model vdw 1.179 3.760 nonbonded pdb=" SG CYS A 470 " pdb=" CG PRO A 524 " model vdw 1.288 3.800 nonbonded pdb=" CD2 LEU A 462 " pdb=" CE1 PHE A 473 " model vdw 1.369 3.760 nonbonded pdb=" CD2 LEU A 462 " pdb=" CE2 PHE A 473 " model vdw 1.727 3.760 nonbonded pdb=" O VAL B 819 " pdb=" O THR B 820 " model vdw 1.814 3.040 ... (remaining 85991 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 29 through 467 or (resid 468 and (name N or name CA or nam \ e C or name O or name CB )) or resid 469 through 820)) selection = (chain 'B' and (resid 29 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 447 or (resid 448 and (name N or n \ ame CA or name C or name O or name CB )) or resid 449 through 474 or resid 519 t \ hrough 567 or resid 572 through 820)) } ncs_group { reference = (chain 'C' and resid 35 through 133) selection = (chain 'D' and (resid 35 through 82 or (resid 83 and (name N or name CA or name \ C or name O or name CB )) or resid 84 through 113 or (resid 114 and (name N or n \ ame CA or name C or name O or name CB )) or resid 115 through 133)) } 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: 3.110 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: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.070 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5285 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 : 0.024 0.822 11675 Z= 1.689 Angle : 2.077 31.943 15954 Z= 1.580 Chirality : 0.069 0.890 1919 Planarity : 0.009 0.084 2118 Dihedral : 8.638 88.358 3918 Min Nonbonded Distance : 1.179 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.48 % Allowed : 4.96 % Favored : 92.56 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.20), residues: 1629 helix: -0.74 (0.23), residues: 426 sheet: -1.88 (0.32), residues: 286 loop : -1.99 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 64 TYR 0.013 0.001 TYR C 122 PHE 0.021 0.001 PHE C 89 TRP 0.004 0.001 TRP A 159 HIS 0.007 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.02155 (11653) covalent geometry : angle 2.06294 (15912) SS BOND : bond 0.25337 ( 21) SS BOND : angle 5.08531 ( 42) hydrogen bonds : bond 0.33112 ( 399) hydrogen bonds : angle 9.51900 ( 1167) Misc. bond : bond 0.08837 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 302 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LYS cc_start: 0.7709 (ptmm) cc_final: 0.7456 (pttp) REVERT: A 79 ASN cc_start: 0.5492 (m-40) cc_final: 0.5204 (t0) REVERT: A 99 LYS cc_start: 0.7841 (mttt) cc_final: 0.7219 (mppt) REVERT: A 252 GLU cc_start: 0.7501 (tt0) cc_final: 0.7140 (mt-10) REVERT: A 286 PHE cc_start: 0.7842 (t80) cc_final: 0.7559 (t80) REVERT: B 78 LYS cc_start: 0.7689 (ptmm) cc_final: 0.7477 (pttp) REVERT: B 79 ASN cc_start: 0.5520 (m-40) cc_final: 0.5183 (t0) REVERT: B 252 GLU cc_start: 0.7502 (tt0) cc_final: 0.7185 (mt-10) REVERT: B 286 PHE cc_start: 0.7845 (t80) cc_final: 0.7530 (t80) REVERT: C 109 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8238 (ptp-170) REVERT: D 114 MET cc_start: 0.6263 (ptp) cc_final: 0.5984 (pmm) outliers start: 26 outliers final: 7 residues processed: 315 average time/residue: 0.1300 time to fit residues: 54.8986 Evaluate side-chains 184 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain D residue 54 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN A 294 ASN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN A 417 ASN B 71 GLN B 218 GLN B 219 HIS B 242 GLN B 294 ASN B 311 GLN B 337 ASN B 342 GLN B 386 GLN B 417 ASN C 87 GLN ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.244524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.216319 restraints weight = 14685.354| |-----------------------------------------------------------------------------| r_work (start): 0.4525 rms_B_bonded: 2.21 r_work: 0.3869 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11675 Z= 0.162 Angle : 0.696 10.911 15954 Z= 0.351 Chirality : 0.046 0.246 1919 Planarity : 0.005 0.055 2118 Dihedral : 5.236 55.204 1734 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.82 % Allowed : 9.54 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.21), residues: 1629 helix: 1.43 (0.25), residues: 444 sheet: -1.91 (0.29), residues: 298 loop : -1.52 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 39 TYR 0.011 0.001 TYR B 280 PHE 0.012 0.001 PHE D 89 TRP 0.011 0.002 TRP A 474 HIS 0.010 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00369 (11653) covalent geometry : angle 0.68894 (15912) SS BOND : bond 0.01006 ( 21) SS BOND : angle 1.99158 ( 42) hydrogen bonds : bond 0.04730 ( 399) hydrogen bonds : angle 5.14236 ( 1167) Misc. bond : bond 0.00512 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.3448 (tpt) cc_final: 0.2850 (ptt) REVERT: A 378 TYR cc_start: 0.7183 (p90) cc_final: 0.6924 (p90) REVERT: B 218 GLN cc_start: 0.7198 (tp40) cc_final: 0.6606 (tp-100) REVERT: B 368 GLU cc_start: 0.5680 (mt-10) cc_final: 0.5476 (pt0) REVERT: B 374 ARG cc_start: 0.6464 (tpp-160) cc_final: 0.6262 (tpp-160) REVERT: B 378 TYR cc_start: 0.6955 (p90) cc_final: 0.6728 (p90) outliers start: 40 outliers final: 27 residues processed: 211 average time/residue: 0.1090 time to fit residues: 32.7863 Evaluate side-chains 170 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 618 CYS Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 25 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 68 optimal weight: 30.0000 chunk 41 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS B 139 ASN B 171 HIS ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.242151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.213373 restraints weight = 14661.707| |-----------------------------------------------------------------------------| r_work (start): 0.4497 rms_B_bonded: 2.16 r_work: 0.3853 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11675 Z= 0.141 Angle : 0.673 15.427 15954 Z= 0.336 Chirality : 0.045 0.297 1919 Planarity : 0.004 0.043 2118 Dihedral : 4.571 52.272 1720 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.20 % Allowed : 10.78 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.21), residues: 1629 helix: 2.06 (0.25), residues: 445 sheet: -1.79 (0.28), residues: 311 loop : -1.56 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 346 TYR 0.010 0.001 TYR A 468 PHE 0.015 0.001 PHE B 312 TRP 0.008 0.001 TRP A 159 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00320 (11653) covalent geometry : angle 0.66505 (15912) SS BOND : bond 0.00728 ( 21) SS BOND : angle 2.07056 ( 42) hydrogen bonds : bond 0.04008 ( 399) hydrogen bonds : angle 4.62242 ( 1167) Misc. bond : bond 0.00088 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ASP cc_start: 0.7159 (m-30) cc_final: 0.6878 (m-30) REVERT: A 445 PHE cc_start: 0.7405 (m-80) cc_final: 0.7015 (m-80) REVERT: B 218 GLN cc_start: 0.7147 (tp40) cc_final: 0.6172 (tp-100) REVERT: B 242 GLN cc_start: 0.6515 (OUTLIER) cc_final: 0.6108 (tm130) REVERT: B 378 TYR cc_start: 0.7032 (p90) cc_final: 0.6773 (p90) REVERT: B 401 ILE cc_start: 0.8422 (mt) cc_final: 0.8187 (mm) REVERT: B 412 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7768 (pp) outliers start: 44 outliers final: 26 residues processed: 180 average time/residue: 0.0953 time to fit residues: 25.3324 Evaluate side-chains 160 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 466 TYR Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 83 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 320 HIS B 115 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 HIS ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.235927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.210886 restraints weight = 14532.960| |-----------------------------------------------------------------------------| r_work (start): 0.4474 rms_B_bonded: 1.77 r_work: 0.4000 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3952 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 11675 Z= 0.239 Angle : 0.767 14.785 15954 Z= 0.376 Chirality : 0.049 0.221 1919 Planarity : 0.005 0.057 2118 Dihedral : 5.071 57.996 1720 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.34 % Allowed : 11.35 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.21), residues: 1629 helix: 2.57 (0.25), residues: 443 sheet: -2.05 (0.27), residues: 301 loop : -1.78 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 374 TYR 0.015 0.002 TYR A 468 PHE 0.020 0.002 PHE D 89 TRP 0.013 0.002 TRP A 159 HIS 0.012 0.002 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00586 (11653) covalent geometry : angle 0.75681 (15912) SS BOND : bond 0.00651 ( 21) SS BOND : angle 2.49323 ( 42) hydrogen bonds : bond 0.04498 ( 399) hydrogen bonds : angle 4.44209 ( 1167) Misc. bond : bond 0.00993 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 150 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ASP cc_start: 0.6540 (m-30) cc_final: 0.6307 (m-30) REVERT: B 368 GLU cc_start: 0.5954 (OUTLIER) cc_final: 0.5645 (mt-10) outliers start: 56 outliers final: 39 residues processed: 189 average time/residue: 0.0930 time to fit residues: 25.8334 Evaluate side-chains 180 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 132 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 6 optimal weight: 5.9990 chunk 146 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 133 optimal weight: 0.0770 chunk 44 optimal weight: 20.0000 chunk 123 optimal weight: 50.0000 chunk 97 optimal weight: 0.0010 chunk 126 optimal weight: 4.9990 chunk 131 optimal weight: 30.0000 chunk 132 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 overall best weight: 1.0746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 199 ASN B 199 ASN B 242 GLN B 342 GLN C 127 HIS D 42 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.238308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.211576 restraints weight = 14632.475| |-----------------------------------------------------------------------------| r_work (start): 0.4476 rms_B_bonded: 1.94 r_work: 0.4013 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3965 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11675 Z= 0.144 Angle : 0.650 14.579 15954 Z= 0.321 Chirality : 0.045 0.274 1919 Planarity : 0.004 0.033 2118 Dihedral : 4.659 53.275 1720 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.68 % Allowed : 12.98 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.22), residues: 1629 helix: 2.78 (0.25), residues: 443 sheet: -2.03 (0.28), residues: 302 loop : -1.67 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 107 TYR 0.014 0.001 TYR A 468 PHE 0.010 0.001 PHE B 529 TRP 0.010 0.001 TRP A 474 HIS 0.015 0.001 HIS D 42 Details of bonding type rmsd covalent geometry : bond 0.00342 (11653) covalent geometry : angle 0.64003 (15912) SS BOND : bond 0.00490 ( 21) SS BOND : angle 2.27101 ( 42) hydrogen bonds : bond 0.03592 ( 399) hydrogen bonds : angle 4.17375 ( 1167) Misc. bond : bond 0.01373 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 37 residues processed: 178 average time/residue: 0.1014 time to fit residues: 26.6130 Evaluate side-chains 173 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 132 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 43 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 71 optimal weight: 0.0370 chunk 2 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 117 optimal weight: 9.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN D 42 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.238455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.212293 restraints weight = 14532.010| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 1.89 r_work: 0.4053 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4011 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11675 Z= 0.124 Angle : 0.622 13.907 15954 Z= 0.307 Chirality : 0.044 0.220 1919 Planarity : 0.004 0.068 2118 Dihedral : 4.318 51.402 1718 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.29 % Allowed : 14.22 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.22), residues: 1629 helix: 2.88 (0.25), residues: 448 sheet: -1.95 (0.28), residues: 302 loop : -1.60 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 107 TYR 0.013 0.001 TYR A 468 PHE 0.009 0.001 PHE B 529 TRP 0.009 0.001 TRP A 474 HIS 0.007 0.001 HIS D 42 Details of bonding type rmsd covalent geometry : bond 0.00295 (11653) covalent geometry : angle 0.61503 (15912) SS BOND : bond 0.00418 ( 21) SS BOND : angle 1.89927 ( 42) hydrogen bonds : bond 0.03285 ( 399) hydrogen bonds : angle 4.07853 ( 1167) Misc. bond : bond 0.00487 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7864 (tt) outliers start: 45 outliers final: 34 residues processed: 172 average time/residue: 0.1013 time to fit residues: 25.6219 Evaluate side-chains 175 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 132 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 29 optimal weight: 0.6980 chunk 139 optimal weight: 0.0770 chunk 39 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 134 optimal weight: 40.0000 chunk 130 optimal weight: 8.9990 chunk 128 optimal weight: 40.0000 chunk 121 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 311 GLN B 199 ASN D 42 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.239269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.212441 restraints weight = 14571.611| |-----------------------------------------------------------------------------| r_work (start): 0.4488 rms_B_bonded: 1.95 r_work: 0.4044 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3991 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11675 Z= 0.110 Angle : 0.613 16.629 15954 Z= 0.298 Chirality : 0.043 0.251 1919 Planarity : 0.004 0.058 2118 Dihedral : 4.168 49.094 1718 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.48 % Allowed : 14.60 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.22), residues: 1629 helix: 3.01 (0.25), residues: 448 sheet: -1.83 (0.28), residues: 307 loop : -1.48 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 107 TYR 0.013 0.001 TYR A 468 PHE 0.007 0.001 PHE B 529 TRP 0.009 0.001 TRP A 474 HIS 0.011 0.001 HIS D 42 Details of bonding type rmsd covalent geometry : bond 0.00254 (11653) covalent geometry : angle 0.60026 (15912) SS BOND : bond 0.00435 ( 21) SS BOND : angle 2.51527 ( 42) hydrogen bonds : bond 0.03038 ( 399) hydrogen bonds : angle 3.90485 ( 1167) Misc. bond : bond 0.00789 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7877 (tt) REVERT: B 374 ARG cc_start: 0.7100 (mmt180) cc_final: 0.6624 (mmt180) REVERT: D 54 LYS cc_start: 0.7400 (pttp) cc_final: 0.7107 (pttt) outliers start: 47 outliers final: 34 residues processed: 174 average time/residue: 0.0989 time to fit residues: 25.5626 Evaluate side-chains 169 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 132 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 30.0000 chunk 41 optimal weight: 8.9990 chunk 161 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 50 optimal weight: 30.0000 chunk 150 optimal weight: 0.0870 chunk 5 optimal weight: 0.0060 chunk 47 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 overall best weight: 1.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN B 199 ASN D 42 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.236614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.212759 restraints weight = 14375.829| |-----------------------------------------------------------------------------| r_work (start): 0.4495 rms_B_bonded: 1.70 r_work: 0.4040 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3961 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 11675 Z= 0.184 Angle : 0.683 16.611 15954 Z= 0.335 Chirality : 0.047 0.355 1919 Planarity : 0.005 0.056 2118 Dihedral : 4.516 59.670 1718 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.48 % Allowed : 14.22 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.22), residues: 1629 helix: 3.25 (0.25), residues: 442 sheet: -1.91 (0.29), residues: 304 loop : -1.60 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 398 TYR 0.013 0.002 TYR A 468 PHE 0.012 0.001 PHE D 89 TRP 0.011 0.001 TRP A 159 HIS 0.019 0.001 HIS D 42 Details of bonding type rmsd covalent geometry : bond 0.00451 (11653) covalent geometry : angle 0.67294 (15912) SS BOND : bond 0.00454 ( 21) SS BOND : angle 2.39489 ( 42) hydrogen bonds : bond 0.03641 ( 399) hydrogen bonds : angle 4.09512 ( 1167) Misc. bond : bond 0.01117 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 LYS cc_start: 0.7586 (pttp) cc_final: 0.7339 (pttm) outliers start: 47 outliers final: 36 residues processed: 172 average time/residue: 0.0942 time to fit residues: 24.4191 Evaluate side-chains 172 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 132 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 77 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 49 optimal weight: 50.0000 chunk 152 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.236258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.211264 restraints weight = 14386.146| |-----------------------------------------------------------------------------| r_work (start): 0.4484 rms_B_bonded: 1.80 r_work: 0.4047 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3996 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11675 Z= 0.173 Angle : 0.670 16.724 15954 Z= 0.330 Chirality : 0.046 0.329 1919 Planarity : 0.004 0.053 2118 Dihedral : 4.504 54.700 1718 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.72 % Allowed : 14.60 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.22), residues: 1629 helix: 3.35 (0.25), residues: 443 sheet: -1.95 (0.29), residues: 298 loop : -1.58 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 398 TYR 0.013 0.002 TYR D 53 PHE 0.010 0.001 PHE D 89 TRP 0.009 0.001 TRP A 159 HIS 0.019 0.001 HIS D 42 Details of bonding type rmsd covalent geometry : bond 0.00427 (11653) covalent geometry : angle 0.65721 (15912) SS BOND : bond 0.00472 ( 21) SS BOND : angle 2.58431 ( 42) hydrogen bonds : bond 0.03539 ( 399) hydrogen bonds : angle 3.89066 ( 1167) Misc. bond : bond 0.01099 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7834 (tt) REVERT: B 412 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7713 (pp) REVERT: D 54 LYS cc_start: 0.7688 (pttp) cc_final: 0.7444 (pttm) outliers start: 39 outliers final: 32 residues processed: 160 average time/residue: 0.0909 time to fit residues: 22.1969 Evaluate side-chains 161 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 132 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 52 optimal weight: 30.0000 chunk 97 optimal weight: 0.0770 chunk 35 optimal weight: 9.9990 chunk 26 optimal weight: 0.2980 chunk 37 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN D 42 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.238300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.212655 restraints weight = 14402.405| |-----------------------------------------------------------------------------| r_work (start): 0.4479 rms_B_bonded: 1.94 r_work: 0.4051 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4004 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11675 Z= 0.123 Angle : 0.631 16.661 15954 Z= 0.309 Chirality : 0.044 0.234 1919 Planarity : 0.004 0.051 2118 Dihedral : 4.281 53.881 1718 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.44 % Allowed : 15.08 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.22), residues: 1629 helix: 3.37 (0.25), residues: 443 sheet: -1.86 (0.29), residues: 304 loop : -1.51 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 107 TYR 0.013 0.001 TYR D 53 PHE 0.011 0.001 PHE A 456 TRP 0.008 0.001 TRP A 474 HIS 0.013 0.001 HIS D 42 Details of bonding type rmsd covalent geometry : bond 0.00295 (11653) covalent geometry : angle 0.62051 (15912) SS BOND : bond 0.00389 ( 21) SS BOND : angle 2.28639 ( 42) hydrogen bonds : bond 0.03060 ( 399) hydrogen bonds : angle 3.94379 ( 1167) Misc. bond : bond 0.00750 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7808 (tt) REVERT: B 412 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7663 (pp) outliers start: 36 outliers final: 31 residues processed: 155 average time/residue: 0.0907 time to fit residues: 21.1910 Evaluate side-chains 159 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 132 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 51 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 158 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.238858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.214035 restraints weight = 14498.745| |-----------------------------------------------------------------------------| r_work (start): 0.4502 rms_B_bonded: 1.87 r_work: 0.4094 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4045 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11675 Z= 0.115 Angle : 0.611 16.353 15954 Z= 0.299 Chirality : 0.044 0.222 1919 Planarity : 0.004 0.082 2118 Dihedral : 4.139 50.791 1718 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.44 % Allowed : 14.89 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.22), residues: 1629 helix: 3.33 (0.25), residues: 449 sheet: -1.78 (0.29), residues: 302 loop : -1.42 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 398 TYR 0.012 0.001 TYR D 53 PHE 0.006 0.001 PHE B 529 TRP 0.008 0.001 TRP A 159 HIS 0.016 0.001 HIS D 42 Details of bonding type rmsd covalent geometry : bond 0.00272 (11653) covalent geometry : angle 0.59827 (15912) SS BOND : bond 0.00394 ( 21) SS BOND : angle 2.44849 ( 42) hydrogen bonds : bond 0.02930 ( 399) hydrogen bonds : angle 3.71958 ( 1167) Misc. bond : bond 0.00718 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3266.90 seconds wall clock time: 56 minutes 26.51 seconds (3386.51 seconds total)