Starting phenix.real_space_refine on Sun Dec 29 20:55:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvx_37875/12_2024/8wvx_37875.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvx_37875/12_2024/8wvx_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_37875/12_2024/8wvx_37875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvx_37875/12_2024/8wvx_37875.map" model { file = "/net/cci-nas-00/data/ceres_data/8wvx_37875/12_2024/8wvx_37875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvx_37875/12_2024/8wvx_37875.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 9, 'TRP:plan': 7, 'ASP:plan': 2, 'PHE:plan': 31, 'GLU:plan': 8, 'ARG:plan': 7} 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: {'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 9, 'TRP:plan': 7, 'ASP:plan': 2, 'PHE:plan': 31, 'GLU:plan': 8, 'ARG:plan': 7} 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: 8.98, per 1000 atoms: 0.78 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: 3.40 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.31 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: 3.53 Time building geometry restraints manager: 3.85 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: 9.670 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: 1.780 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 31.520 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.380 ------------------------------------------------------------------------------- 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 : 0.022 0.265 11653 Z= 1.479 Angle : 2.063 31.943 15912 Z= 1.578 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 : 15.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (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 TRP 0.004 0.001 TRP A 159 HIS 0.007 0.001 HIS D 50 PHE 0.021 0.001 PHE C 89 TYR 0.013 0.001 TYR C 122 ARG 0.006 0.000 ARG D 64 *********************** 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 : 1.412 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: symmetry clash REVERT: A 78 LYS cc_start: 0.7709 (ptmm) cc_final: 0.7459 (pttp) REVERT: A 79 ASN cc_start: 0.5492 (m-40) cc_final: 0.5207 (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: 0.7141 (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: 0.8239 (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: 0.2949 time to fit residues: 124.3253 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 : 1.223 ------------------------------------------------------------------------------- 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 138 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 overall best weight: 2.2782 ------------------------------------------------------------------------------- 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 A 386 GLN A 417 ASN B 71 GLN B 218 GLN B 219 HIS 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5609 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 11653 Z= 0.434 Angle : 0.807 11.812 15912 Z= 0.405 Chirality : 0.050 0.222 1919 Planarity : 0.006 0.069 2118 Dihedral : 5.679 54.575 1734 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.29 % Allowed : 10.21 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.21), residues: 1629 helix: 1.39 (0.25), residues: 444 sheet: -2.20 (0.27), residues: 313 loop : -1.69 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 159 HIS 0.015 0.002 HIS B 209 PHE 0.021 0.002 PHE D 89 TYR 0.015 0.002 TYR B 234 ARG 0.007 0.001 ARG B 39 *********************** 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 236 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.6229 (m-40) cc_final: 0.5984 (t0) REVERT: A 99 LYS cc_start: 0.8313 (mttt) cc_final: 0.7902 (mtmm) REVERT: A 106 GLU cc_start: 0.7577 (tp30) cc_final: 0.7362 (tp30) REVERT: A 344 MET cc_start: 0.3666 (tpt) cc_final: 0.2813 (ptt) REVERT: A 346 ARG cc_start: 0.7151 (tpp-160) cc_final: 0.6813 (mmp80) REVERT: A 368 GLU cc_start: 0.6124 (mt-10) cc_final: 0.5574 (pt0) REVERT: B 79 ASN cc_start: 0.6109 (m-40) cc_final: 0.5895 (t0) REVERT: B 218 GLN cc_start: 0.7120 (tp40) cc_final: 0.6429 (tp-100) REVERT: B 369 GLU cc_start: 0.5314 (mm-30) cc_final: 0.4939 (mm-30) REVERT: C 109 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7982 (ptp-170) REVERT: D 97 ARG cc_start: 0.7709 (mtt180) cc_final: 0.7192 (mtt90) outliers start: 45 outliers final: 28 residues processed: 220 average time/residue: 0.2500 time to fit residues: 78.4424 Evaluate side-chains 178 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 311 GLN Chi-restraints excluded: chain A residue 334 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 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 C residue 109 ARG Chi-restraints excluded: chain C residue 117 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 82 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 132 optimal weight: 0.2980 chunk 147 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 171 HIS ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS B 115 ASN B 139 ASN ** B 199 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5566 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11653 Z= 0.211 Angle : 0.652 15.094 15912 Z= 0.328 Chirality : 0.045 0.290 1919 Planarity : 0.004 0.041 2118 Dihedral : 4.828 51.394 1724 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.39 % Allowed : 11.74 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.21), residues: 1629 helix: 2.03 (0.25), residues: 445 sheet: -2.00 (0.28), residues: 306 loop : -1.62 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 159 HIS 0.010 0.001 HIS B 207 PHE 0.014 0.001 PHE A 312 TYR 0.011 0.001 TYR A 468 ARG 0.004 0.000 ARG B 39 *********************** 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 215 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 1.438 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 36 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6886 (m-30) REVERT: A 79 ASN cc_start: 0.6046 (m-40) cc_final: 0.5787 (t0) REVERT: A 99 LYS cc_start: 0.8316 (mttt) cc_final: 0.7919 (mtmm) REVERT: A 106 GLU cc_start: 0.7461 (tp30) cc_final: 0.7064 (tp30) REVERT: A 225 ASP cc_start: 0.7053 (m-30) cc_final: 0.6844 (m-30) REVERT: A 344 MET cc_start: 0.3775 (tpt) cc_final: 0.2365 (ptt) REVERT: A 445 PHE cc_start: 0.7001 (m-80) cc_final: 0.6768 (m-80) REVERT: B 75 ASP cc_start: 0.7196 (t0) cc_final: 0.6991 (t70) REVERT: B 79 ASN cc_start: 0.6034 (m-40) cc_final: 0.5772 (t0) REVERT: B 106 GLU cc_start: 0.7454 (tp30) cc_final: 0.7152 (tp30) REVERT: B 218 GLN cc_start: 0.7046 (tp40) cc_final: 0.6386 (tp-100) REVERT: B 412 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7725 (pp) REVERT: C 109 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7935 (ptp-170) REVERT: D 97 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7182 (mtt90) outliers start: 46 outliers final: 29 residues processed: 196 average time/residue: 0.2430 time to fit residues: 68.1704 Evaluate side-chains 181 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 120 VAL 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 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 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 466 TYR Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 69 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 0.7980 chunk 112 optimal weight: 0.0050 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 71 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 141 optimal weight: 30.0000 chunk 42 optimal weight: 0.2980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN B 171 HIS ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5545 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11653 Z= 0.171 Angle : 0.610 14.745 15912 Z= 0.301 Chirality : 0.044 0.206 1919 Planarity : 0.004 0.037 2118 Dihedral : 4.517 47.288 1724 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.29 % Allowed : 12.21 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1629 helix: 2.28 (0.25), residues: 448 sheet: -1.91 (0.28), residues: 313 loop : -1.44 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 474 HIS 0.005 0.001 HIS B 207 PHE 0.007 0.001 PHE B 422 TYR 0.013 0.001 TYR D 53 ARG 0.010 0.000 ARG A 346 *********************** 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 202 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 1.230 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: symmetry clash REVERT: A 79 ASN cc_start: 0.6066 (m-40) cc_final: 0.5783 (t0) REVERT: A 99 LYS cc_start: 0.8348 (mttt) cc_final: 0.7939 (mtmm) REVERT: A 106 GLU cc_start: 0.7442 (tp30) cc_final: 0.6937 (tp30) REVERT: A 225 ASP cc_start: 0.7005 (m-30) cc_final: 0.6801 (m-30) REVERT: A 344 MET cc_start: 0.3723 (tpt) cc_final: 0.3311 (ttm) REVERT: A 445 PHE cc_start: 0.7046 (m-80) cc_final: 0.6690 (m-80) REVERT: B 75 ASP cc_start: 0.7184 (t0) cc_final: 0.6959 (t70) REVERT: B 79 ASN cc_start: 0.5977 (m-40) cc_final: 0.5721 (t0) REVERT: B 93 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7145 (tt) REVERT: B 106 GLU cc_start: 0.7355 (tp30) cc_final: 0.6919 (tp30) REVERT: B 412 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7689 (pp) outliers start: 45 outliers final: 33 residues processed: 186 average time/residue: 0.2358 time to fit residues: 63.3656 Evaluate side-chains 196 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 199 ASN 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 398 ARG 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 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 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 372 LEU Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 466 TYR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 69 CYS 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 132 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 135 optimal weight: 50.0000 chunk 109 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 B 218 GLN B 320 HIS ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5694 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 11653 Z= 0.527 Angle : 0.803 14.784 15912 Z= 0.400 Chirality : 0.051 0.303 1919 Planarity : 0.006 0.080 2118 Dihedral : 5.206 45.729 1720 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 5.06 % Allowed : 12.69 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1629 helix: 2.68 (0.25), residues: 449 sheet: -2.24 (0.28), residues: 303 loop : -1.88 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 159 HIS 0.014 0.002 HIS D 68 PHE 0.023 0.002 PHE D 89 TYR 0.016 0.003 TYR A 468 ARG 0.011 0.001 ARG B 374 *********************** 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 213 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 160 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.6482 (m-40) cc_final: 0.5990 (t0) REVERT: A 99 LYS cc_start: 0.8602 (mttt) cc_final: 0.8048 (mtmm) REVERT: A 106 GLU cc_start: 0.7547 (tp30) cc_final: 0.7201 (tp30) REVERT: A 344 MET cc_start: 0.4017 (tpt) cc_final: 0.3595 (ttm) REVERT: A 346 ARG cc_start: 0.6687 (mmt-90) cc_final: 0.6403 (mmt-90) REVERT: B 79 ASN cc_start: 0.6461 (m-40) cc_final: 0.6148 (t0) REVERT: B 106 GLU cc_start: 0.7496 (tp30) cc_final: 0.7193 (tp30) REVERT: B 242 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: D 87 GLN cc_start: 0.6211 (tp40) cc_final: 0.5624 (pt0) outliers start: 53 outliers final: 37 residues processed: 197 average time/residue: 0.2418 time to fit residues: 67.8312 Evaluate side-chains 188 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 119 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 183 THR 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 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 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 372 LEU Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 101 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 53 optimal weight: 40.0000 chunk 142 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 131 optimal weight: 50.0000 chunk 73 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 199 ASN B 342 GLN D 42 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5688 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 11653 Z= 0.424 Angle : 0.743 13.299 15912 Z= 0.368 Chirality : 0.049 0.237 1919 Planarity : 0.005 0.056 2118 Dihedral : 4.946 44.728 1718 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 5.53 % Allowed : 13.55 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.22), residues: 1629 helix: 2.90 (0.25), residues: 449 sheet: -2.26 (0.28), residues: 299 loop : -2.00 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 159 HIS 0.023 0.002 HIS D 42 PHE 0.014 0.001 PHE D 89 TYR 0.015 0.002 TYR A 468 ARG 0.006 0.001 ARG D 107 *********************** 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 208 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 150 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.6802 (pmm) cc_final: 0.6593 (pmm) REVERT: A 79 ASN cc_start: 0.6530 (m-40) cc_final: 0.6174 (t0) REVERT: A 99 LYS cc_start: 0.8654 (mttt) cc_final: 0.8117 (mtmm) REVERT: A 106 GLU cc_start: 0.7522 (tp30) cc_final: 0.7185 (tp30) REVERT: A 344 MET cc_start: 0.4107 (tpt) cc_final: 0.3640 (ttm) REVERT: A 424 GLU cc_start: 0.8139 (mp0) cc_final: 0.7868 (mp0) REVERT: B 79 ASN cc_start: 0.6495 (m-40) cc_final: 0.6234 (t0) REVERT: B 106 GLU cc_start: 0.7535 (tp30) cc_final: 0.7233 (tp30) REVERT: B 445 PHE cc_start: 0.7523 (m-80) cc_final: 0.7171 (m-80) REVERT: C 109 ARG cc_start: 0.8150 (ptt180) cc_final: 0.7744 (ptp-170) REVERT: D 87 GLN cc_start: 0.6205 (tp40) cc_final: 0.5622 (pt0) outliers start: 58 outliers final: 44 residues processed: 193 average time/residue: 0.2419 time to fit residues: 66.8695 Evaluate side-chains 191 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 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 339 CYS Chi-restraints excluded: chain A residue 367 LEU 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 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 276 THR Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 345 LEU 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 C residue 45 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 101 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 101 SER 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 152 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 115 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 D 42 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5624 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 11653 Z= 0.222 Angle : 0.641 16.264 15912 Z= 0.317 Chirality : 0.045 0.220 1919 Planarity : 0.004 0.046 2118 Dihedral : 4.584 45.850 1718 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.20 % Allowed : 15.08 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.22), residues: 1629 helix: 3.13 (0.25), residues: 443 sheet: -2.07 (0.28), residues: 303 loop : -1.77 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 474 HIS 0.016 0.001 HIS D 42 PHE 0.005 0.001 PHE B 255 TYR 0.015 0.001 TYR A 468 ARG 0.004 0.000 ARG D 107 *********************** 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 193 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.6346 (m-40) cc_final: 0.5981 (t0) REVERT: A 92 ASP cc_start: 0.7227 (t0) cc_final: 0.6792 (t0) REVERT: A 99 LYS cc_start: 0.8610 (mttt) cc_final: 0.8090 (mtmm) REVERT: A 106 GLU cc_start: 0.7508 (tp30) cc_final: 0.7113 (tp30) REVERT: A 344 MET cc_start: 0.3604 (tpt) cc_final: 0.3223 (ttm) REVERT: A 445 PHE cc_start: 0.7104 (m-80) cc_final: 0.6767 (m-80) REVERT: B 79 ASN cc_start: 0.6399 (m-40) cc_final: 0.6070 (t0) REVERT: B 93 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7197 (tt) REVERT: B 106 GLU cc_start: 0.7508 (tp30) cc_final: 0.7148 (tp30) REVERT: D 37 ARG cc_start: 0.8553 (mtm110) cc_final: 0.8333 (mtp-110) outliers start: 44 outliers final: 30 residues processed: 180 average time/residue: 0.2575 time to fit residues: 67.1187 Evaluate side-chains 171 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 199 ASN 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 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 B residue 690 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 100 THR 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 101 SER 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 97 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 124 optimal weight: 30.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN D 42 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5674 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11653 Z= 0.372 Angle : 0.719 15.156 15912 Z= 0.355 Chirality : 0.048 0.266 1919 Planarity : 0.005 0.068 2118 Dihedral : 4.859 52.349 1718 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.01 % Allowed : 15.46 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1629 helix: 3.27 (0.25), residues: 443 sheet: -2.11 (0.28), residues: 294 loop : -1.89 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.025 0.002 HIS D 42 PHE 0.013 0.001 PHE D 89 TYR 0.014 0.002 TYR A 468 ARG 0.006 0.001 ARG B 398 *********************** 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 178 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.7065 (tm-30) REVERT: A 79 ASN cc_start: 0.6520 (m-40) cc_final: 0.6197 (t0) REVERT: A 92 ASP cc_start: 0.7357 (t0) cc_final: 0.6914 (t0) REVERT: A 99 LYS cc_start: 0.8681 (mttt) cc_final: 0.8142 (mtmm) REVERT: A 106 GLU cc_start: 0.7534 (tp30) cc_final: 0.7163 (tp30) REVERT: A 344 MET cc_start: 0.3624 (tpt) cc_final: 0.3265 (mtt) REVERT: B 79 ASN cc_start: 0.6484 (m-40) cc_final: 0.6253 (t0) REVERT: B 106 GLU cc_start: 0.7532 (tp30) cc_final: 0.7197 (tp30) REVERT: B 273 LEU cc_start: 0.6091 (OUTLIER) cc_final: 0.5789 (tt) REVERT: B 374 ARG cc_start: 0.6990 (mmt180) cc_final: 0.6230 (mmt180) REVERT: B 398 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7216 (mtt90) REVERT: D 60 VAL cc_start: 0.8277 (p) cc_final: 0.7429 (t) REVERT: D 87 GLN cc_start: 0.6173 (tp40) cc_final: 0.5605 (pt0) outliers start: 42 outliers final: 31 residues processed: 169 average time/residue: 0.2295 time to fit residues: 55.8833 Evaluate side-chains 170 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 LEU 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 464 VAL 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 141 ILE Chi-restraints excluded: chain B residue 183 THR 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 372 LEU Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 100 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 147 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 0.0370 chunk 139 optimal weight: 5.9990 chunk 146 optimal weight: 0.0020 overall best weight: 0.5468 ------------------------------------------------------------------------------- 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** B 199 ASN D 42 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5601 moved from start: 0.5521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11653 Z= 0.180 Angle : 0.614 16.713 15912 Z= 0.302 Chirality : 0.044 0.241 1919 Planarity : 0.004 0.050 2118 Dihedral : 4.369 48.734 1718 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.08 % Favored : 93.86 % Rotamer: Outliers : 3.34 % Allowed : 16.41 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.22), residues: 1629 helix: 3.34 (0.25), residues: 443 sheet: -1.99 (0.28), residues: 303 loop : -1.62 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 474 HIS 0.018 0.001 HIS D 42 PHE 0.006 0.001 PHE B 422 TYR 0.013 0.001 TYR A 468 ARG 0.010 0.001 ARG A 346 *********************** 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 183 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.6440 (m-40) cc_final: 0.6068 (t0) REVERT: A 92 ASP cc_start: 0.7135 (t0) cc_final: 0.6723 (t0) REVERT: A 99 LYS cc_start: 0.8636 (mttt) cc_final: 0.8128 (mtmm) REVERT: A 106 GLU cc_start: 0.7493 (tp30) cc_final: 0.7097 (tp30) REVERT: A 344 MET cc_start: 0.3591 (tpt) cc_final: 0.3361 (ttt) REVERT: B 79 ASN cc_start: 0.6358 (m-40) cc_final: 0.6094 (t0) REVERT: B 93 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7158 (tt) REVERT: B 106 GLU cc_start: 0.7502 (tp30) cc_final: 0.7150 (tp30) REVERT: B 374 ARG cc_start: 0.6893 (mmt180) cc_final: 0.5978 (mmt180) REVERT: D 37 ARG cc_start: 0.8512 (mtm110) cc_final: 0.8298 (mtp-110) REVERT: D 115 ARG cc_start: 0.6865 (ttt180) cc_final: 0.6663 (ttt180) outliers start: 35 outliers final: 27 residues processed: 168 average time/residue: 0.2535 time to fit residues: 60.3076 Evaluate side-chains 169 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 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 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 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 372 LEU Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 59 MET 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 96 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 0.0030 overall best weight: 0.9194 ------------------------------------------------------------------------------- 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** B 199 ASN D 42 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5617 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11653 Z= 0.222 Angle : 0.645 17.182 15912 Z= 0.315 Chirality : 0.045 0.236 1919 Planarity : 0.005 0.083 2118 Dihedral : 4.418 54.147 1718 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.71 % Favored : 94.23 % Rotamer: Outliers : 3.05 % Allowed : 17.08 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.22), residues: 1629 helix: 3.39 (0.25), residues: 443 sheet: -1.98 (0.29), residues: 301 loop : -1.59 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 159 HIS 0.014 0.001 HIS D 42 PHE 0.008 0.001 PHE B 422 TYR 0.012 0.001 TYR A 468 ARG 0.011 0.001 ARG A 346 ********************** 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 177 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.6421 (m-40) cc_final: 0.6123 (t0) REVERT: A 92 ASP cc_start: 0.7184 (t0) cc_final: 0.6756 (t0) REVERT: A 99 LYS cc_start: 0.8627 (mttt) cc_final: 0.8118 (mtmm) REVERT: A 106 GLU cc_start: 0.7500 (tp30) cc_final: 0.7106 (tp30) REVERT: B 93 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7079 (tt) REVERT: B 106 GLU cc_start: 0.7517 (tp30) cc_final: 0.7163 (tp30) REVERT: C 54 LYS cc_start: 0.8022 (pptt) cc_final: 0.7768 (pptt) REVERT: D 115 ARG cc_start: 0.6879 (ttt180) cc_final: 0.6666 (ttt180) outliers start: 32 outliers final: 26 residues processed: 167 average time/residue: 0.2307 time to fit residues: 56.5456 Evaluate side-chains 167 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 262 VAL Chi-restraints excluded: chain A residue 273 LEU 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 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 242 GLN 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 57 SER Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 59 MET 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: 0.9980 chunk 138 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** B 79 ASN 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 = 0.4720 r_free = 0.4720 target = 0.238185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.211206 restraints weight = 14356.726| |-----------------------------------------------------------------------------| r_work (start): 0.4483 rms_B_bonded: 1.96 r_work: 0.3922 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11653 Z= 0.214 Angle : 0.635 17.132 15912 Z= 0.311 Chirality : 0.044 0.229 1919 Planarity : 0.005 0.078 2118 Dihedral : 4.385 56.277 1718 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.95 % Favored : 93.98 % Rotamer: Outliers : 3.15 % Allowed : 17.08 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1629 helix: 3.47 (0.25), residues: 443 sheet: -1.90 (0.29), residues: 301 loop : -1.49 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 159 HIS 0.011 0.001 HIS D 42 PHE 0.006 0.001 PHE D 89 TYR 0.012 0.001 TYR A 468 ARG 0.010 0.001 ARG B 398 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2572.89 seconds wall clock time: 48 minutes 25.16 seconds (2905.16 seconds total)