Starting phenix.real_space_refine on Tue Jun 10 05:57:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wvx_37875/06_2025/8wvx_37875.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wvx_37875/06_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_37875/06_2025/8wvx_37875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wvx_37875/06_2025/8wvx_37875.map" model { file = "/net/cci-nas-00/data/ceres_data/8wvx_37875/06_2025/8wvx_37875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wvx_37875/06_2025/8wvx_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-5710/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: 8.00, per 1000 atoms: 0.70 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: 2.97 Conformation dependent library (CDL) restraints added in 1.7 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: 1.43 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: 3.28 Time building geometry restraints manager: 3.50 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.940 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.600 ------------------------------------------------------------------------------- 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 : 15.41 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 Details of bonding type rmsd hydrogen bonds : bond 0.33112 ( 399) hydrogen bonds : angle 9.51900 ( 1167) SS BOND : bond 0.25337 ( 21) SS BOND : angle 5.08531 ( 42) covalent geometry : bond 0.02155 (11653) covalent geometry : angle 2.06294 (15912) 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 : 1.198 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: 0.2927 time to fit residues: 123.7013 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 : 1.232 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.239360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.207330 restraints weight = 14472.825| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 3.10 r_work: 0.3732 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 11675 Z= 0.261 Angle : 0.814 11.812 15954 Z= 0.409 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 Details of bonding type rmsd hydrogen bonds : bond 0.05377 ( 399) hydrogen bonds : angle 5.23836 ( 1167) SS BOND : bond 0.00923 ( 21) SS BOND : angle 2.28137 ( 42) covalent geometry : bond 0.00632 (11653) covalent geometry : angle 0.80704 (15912) Misc. bond : bond 0.00401 ( 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 236 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8553 (mttt) cc_final: 0.8146 (mtmm) REVERT: A 344 MET cc_start: 0.3943 (tpt) cc_final: 0.3028 (ptt) REVERT: A 346 ARG cc_start: 0.7340 (tpp-160) cc_final: 0.6997 (mmp80) REVERT: A 368 GLU cc_start: 0.6220 (mt-10) cc_final: 0.5540 (pt0) REVERT: B 218 GLN cc_start: 0.7286 (tp40) cc_final: 0.6604 (tp-100) REVERT: B 368 GLU cc_start: 0.5837 (mt-10) cc_final: 0.5606 (pt0) REVERT: B 369 GLU cc_start: 0.5798 (mm-30) cc_final: 0.5370 (mm-30) REVERT: B 402 HIS cc_start: 0.7355 (p90) cc_final: 0.7133 (p90) REVERT: B 529 PHE cc_start: 0.7484 (m-80) cc_final: 0.7264 (m-80) REVERT: D 97 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7640 (mtt90) outliers start: 45 outliers final: 28 residues processed: 220 average time/residue: 0.3381 time to fit residues: 108.1812 Evaluate side-chains 176 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 2.321 ------------------------------------------------------------------------------- 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 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 43 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 63 optimal weight: 30.0000 chunk 69 optimal weight: 0.0970 chunk 95 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 overall best weight: 3.2184 ------------------------------------------------------------------------------- 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 311 GLN B 115 ASN B 139 ASN B 171 HIS ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.233568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.206204 restraints weight = 14595.329| |-----------------------------------------------------------------------------| r_work (start): 0.4442 rms_B_bonded: 2.03 r_work: 0.3759 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 11675 Z= 0.339 Angle : 0.858 14.872 15954 Z= 0.430 Chirality : 0.053 0.311 1919 Planarity : 0.006 0.069 2118 Dihedral : 5.529 54.135 1720 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 6.39 % Allowed : 11.26 % Favored : 82.35 % 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: -1.37 (0.21), residues: 1629 helix: 2.21 (0.25), residues: 442 sheet: -2.45 (0.27), residues: 294 loop : -2.08 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 159 HIS 0.013 0.002 HIS D 68 PHE 0.022 0.002 PHE D 89 TYR 0.015 0.003 TYR B 280 ARG 0.006 0.001 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.05339 ( 399) hydrogen bonds : angle 4.79995 ( 1167) SS BOND : bond 0.00673 ( 21) SS BOND : angle 2.59718 ( 42) covalent geometry : bond 0.00838 (11653) covalent geometry : angle 0.84856 (15912) Misc. bond : bond 0.00241 ( 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 237 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 170 time to evaluate : 1.233 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.8659 (mttt) cc_final: 0.8301 (mtmm) REVERT: B 369 GLU cc_start: 0.5778 (mm-30) cc_final: 0.5554 (mm-30) REVERT: D 87 GLN cc_start: 0.6344 (tp40) cc_final: 0.6030 (pt0) outliers start: 67 outliers final: 44 residues processed: 216 average time/residue: 0.2472 time to fit residues: 77.0301 Evaluate side-chains 195 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 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 339 CYS 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 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 215 SER 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 342 GLN 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 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 45 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 108 LEU 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 84 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 137 optimal weight: 0.0040 chunk 16 optimal weight: 0.4980 chunk 52 optimal weight: 30.0000 chunk 55 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 129 optimal weight: 50.0000 chunk 23 optimal weight: 0.6980 chunk 145 optimal weight: 0.0470 chunk 12 optimal weight: 2.9990 overall best weight: 0.6492 ------------------------------------------------------------------------------- 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** ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.239557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.205744 restraints weight = 14602.985| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 2.52 r_work: 0.3765 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 11675 Z= 0.129 Angle : 0.648 14.370 15954 Z= 0.322 Chirality : 0.045 0.209 1919 Planarity : 0.004 0.037 2118 Dihedral : 4.775 52.198 1720 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.40 % Favored : 94.54 % Rotamer: Outliers : 4.58 % Allowed : 14.12 % 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 (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: -1.00 (0.21), residues: 1629 helix: 2.39 (0.25), residues: 448 sheet: -2.27 (0.27), residues: 301 loop : -1.77 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 474 HIS 0.024 0.001 HIS D 42 PHE 0.006 0.001 PHE A 255 TYR 0.013 0.001 TYR A 468 ARG 0.005 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 399) hydrogen bonds : angle 4.37138 ( 1167) SS BOND : bond 0.00707 ( 21) SS BOND : angle 2.26982 ( 42) covalent geometry : bond 0.00296 (11653) covalent geometry : angle 0.63789 (15912) Misc. bond : bond 0.00742 ( 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 210 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 1.247 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 99 LYS cc_start: 0.8638 (mttt) cc_final: 0.8207 (mtmm) REVERT: A 346 ARG cc_start: 0.7854 (tpp80) cc_final: 0.7361 (mmm160) REVERT: A 369 GLU cc_start: 0.6509 (pm20) cc_final: 0.6166 (pm20) outliers start: 48 outliers final: 32 residues processed: 195 average time/residue: 0.3286 time to fit residues: 94.0729 Evaluate side-chains 186 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 1.495 ------------------------------------------------------------------------------- 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 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 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 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 75 ASP 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 342 GLN 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 100 THR Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 108 LEU 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 103 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 61 optimal weight: 0.0030 chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 127 optimal weight: 30.0000 chunk 148 optimal weight: 2.9990 chunk 14 optimal weight: 0.0670 overall best weight: 0.8130 ------------------------------------------------------------------------------- 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 242 GLN B 320 HIS C 127 HIS D 42 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.239351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.213607 restraints weight = 14352.486| |-----------------------------------------------------------------------------| r_work (start): 0.4475 rms_B_bonded: 1.95 r_work: 0.4048 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4006 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 11675 Z= 0.129 Angle : 0.640 14.235 15954 Z= 0.317 Chirality : 0.045 0.290 1919 Planarity : 0.004 0.064 2118 Dihedral : 4.582 44.268 1720 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.77 % Favored : 94.17 % Rotamer: Outliers : 4.96 % Allowed : 14.03 % Favored : 81.01 % 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: -0.76 (0.21), residues: 1629 helix: 2.84 (0.25), residues: 438 sheet: -2.17 (0.27), residues: 307 loop : -1.69 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 474 HIS 0.016 0.001 HIS D 42 PHE 0.006 0.001 PHE D 89 TYR 0.014 0.001 TYR A 468 ARG 0.006 0.000 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 399) hydrogen bonds : angle 4.13896 ( 1167) SS BOND : bond 0.00751 ( 21) SS BOND : angle 2.04199 ( 42) covalent geometry : bond 0.00307 (11653) covalent geometry : angle 0.63198 (15912) Misc. bond : bond 0.00735 ( 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 204 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 152 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7866 (tt) outliers start: 52 outliers final: 33 residues processed: 187 average time/residue: 0.2425 time to fit residues: 65.5047 Evaluate side-chains 178 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 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 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 345 LEU 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 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 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 14 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 154 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 ASN B 242 GLN B 342 GLN D 42 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.237678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.212446 restraints weight = 14355.730| |-----------------------------------------------------------------------------| r_work (start): 0.4496 rms_B_bonded: 1.83 r_work: 0.4051 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3992 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11675 Z= 0.140 Angle : 0.662 15.381 15954 Z= 0.325 Chirality : 0.046 0.434 1919 Planarity : 0.004 0.055 2118 Dihedral : 4.474 44.747 1718 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.34 % Favored : 94.60 % Rotamer: Outliers : 5.06 % Allowed : 14.22 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.62 (0.22), residues: 1629 helix: 3.02 (0.25), residues: 442 sheet: -2.09 (0.28), residues: 312 loop : -1.65 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 159 HIS 0.018 0.001 HIS D 42 PHE 0.007 0.001 PHE D 89 TYR 0.013 0.001 TYR A 468 ARG 0.004 0.000 ARG D 41 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 399) hydrogen bonds : angle 4.11174 ( 1167) SS BOND : bond 0.00597 ( 21) SS BOND : angle 2.63457 ( 42) covalent geometry : bond 0.00334 (11653) covalent geometry : angle 0.64875 (15912) Misc. bond : bond 0.00871 ( 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 200 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 147 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7881 (tt) outliers start: 53 outliers final: 38 residues processed: 185 average time/residue: 0.2092 time to fit residues: 57.8356 Evaluate side-chains 179 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 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 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 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 412 LEU Chi-restraints excluded: chain B residue 690 SER 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 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 110 CYS 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 79 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 40.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 ASN B 342 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 = 0.4700 r_free = 0.4700 target = 0.236172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.211580 restraints weight = 14596.026| |-----------------------------------------------------------------------------| r_work (start): 0.4487 rms_B_bonded: 1.75 r_work: 0.4026 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3978 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11675 Z= 0.187 Angle : 0.705 14.848 15954 Z= 0.347 Chirality : 0.047 0.369 1919 Planarity : 0.005 0.073 2118 Dihedral : 4.617 44.170 1718 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.77 % Allowed : 15.08 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.59 (0.22), residues: 1629 helix: 3.16 (0.25), residues: 443 sheet: -2.09 (0.28), residues: 298 loop : -1.72 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.010 0.001 HIS D 42 PHE 0.011 0.001 PHE D 89 TYR 0.014 0.002 TYR A 468 ARG 0.004 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 399) hydrogen bonds : angle 4.01629 ( 1167) SS BOND : bond 0.00644 ( 21) SS BOND : angle 3.22092 ( 42) covalent geometry : bond 0.00459 (11653) covalent geometry : angle 0.68600 (15912) Misc. bond : bond 0.00889 ( 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 187 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 LYS cc_start: 0.7526 (pttp) cc_final: 0.7136 (pttt) REVERT: D 60 VAL cc_start: 0.8871 (p) cc_final: 0.7953 (t) outliers start: 50 outliers final: 37 residues processed: 173 average time/residue: 0.2117 time to fit residues: 54.2425 Evaluate side-chains 171 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 227 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 273 LEU 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 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 227 LEU 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 412 LEU Chi-restraints excluded: chain B residue 690 SER 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 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 110 CYS 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 7 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 129 optimal weight: 50.0000 chunk 42 optimal weight: 30.0000 chunk 63 optimal weight: 7.9990 chunk 9 optimal weight: 0.0570 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 40.0000 chunk 69 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 ASN D 42 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.239376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.216794 restraints weight = 14438.217| |-----------------------------------------------------------------------------| r_work (start): 0.4526 rms_B_bonded: 1.61 r_work: 0.4068 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3970 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.5408 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= 0.117 Angle : 0.629 14.000 15954 Z= 0.311 Chirality : 0.045 0.312 1919 Planarity : 0.004 0.067 2118 Dihedral : 4.341 44.240 1718 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.16 % Favored : 94.78 % Rotamer: Outliers : 3.91 % Allowed : 15.74 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.40 (0.22), residues: 1629 helix: 3.24 (0.25), residues: 443 sheet: -1.96 (0.28), residues: 312 loop : -1.55 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 474 HIS 0.012 0.001 HIS D 42 PHE 0.005 0.001 PHE A 255 TYR 0.013 0.001 TYR A 468 ARG 0.003 0.000 ARG D 41 Details of bonding type rmsd hydrogen bonds : bond 0.03061 ( 399) hydrogen bonds : angle 3.98881 ( 1167) SS BOND : bond 0.00475 ( 21) SS BOND : angle 2.58958 ( 42) covalent geometry : bond 0.00268 (11653) covalent geometry : angle 0.61601 (15912) Misc. bond : bond 0.00993 ( 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 183 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7879 (tt) REVERT: D 54 LYS cc_start: 0.7373 (pttp) cc_final: 0.6984 (pttt) outliers start: 41 outliers final: 30 residues processed: 171 average time/residue: 0.2886 time to fit residues: 75.2677 Evaluate side-chains 169 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 262 VAL Chi-restraints excluded: chain A residue 273 LEU 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 464 VAL Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain A residue 471 CYS 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 412 LEU 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 125 SER Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 110 CYS 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 118 optimal weight: 9.9990 chunk 67 optimal weight: 30.0000 chunk 142 optimal weight: 0.0270 chunk 31 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 50.0000 chunk 15 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 overall best weight: 0.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 ASN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.239001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.215688 restraints weight = 14508.467| |-----------------------------------------------------------------------------| r_work (start): 0.4511 rms_B_bonded: 1.67 r_work: 0.4042 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3933 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.5503 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= 0.126 Angle : 0.648 14.078 15954 Z= 0.317 Chirality : 0.045 0.283 1919 Planarity : 0.004 0.074 2118 Dihedral : 4.293 47.756 1718 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % 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: -0.29 (0.22), residues: 1629 helix: 3.34 (0.25), residues: 443 sheet: -1.94 (0.28), residues: 307 loop : -1.47 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 159 HIS 0.015 0.001 HIS D 42 PHE 0.008 0.001 PHE B 312 TYR 0.012 0.001 TYR A 468 ARG 0.005 0.000 ARG D 41 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 399) hydrogen bonds : angle 3.80453 ( 1167) SS BOND : bond 0.00496 ( 21) SS BOND : angle 3.02927 ( 42) covalent geometry : bond 0.00301 (11653) covalent geometry : angle 0.62967 (15912) Misc. bond : bond 0.00780 ( 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 182 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7869 (tt) REVERT: D 54 LYS cc_start: 0.7435 (pttp) cc_final: 0.7035 (pttt) outliers start: 44 outliers final: 36 residues processed: 168 average time/residue: 0.2660 time to fit residues: 68.3307 Evaluate side-chains 166 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 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 466 TYR Chi-restraints excluded: chain A residue 471 CYS 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 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 412 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 57 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 101 SER 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 110 CYS 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 155 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 124 optimal weight: 30.0000 chunk 107 optimal weight: 8.9990 chunk 129 optimal weight: 20.0000 chunk 109 optimal weight: 0.8980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN C 42 HIS D 42 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.235245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.206010 restraints weight = 14377.471| |-----------------------------------------------------------------------------| r_work (start): 0.4440 rms_B_bonded: 2.24 r_work: 0.3766 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 11675 Z= 0.224 Angle : 0.746 13.938 15954 Z= 0.366 Chirality : 0.048 0.282 1919 Planarity : 0.005 0.077 2118 Dihedral : 4.739 51.842 1718 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.91 % Allowed : 15.74 % Favored : 80.34 % 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: -0.43 (0.22), residues: 1629 helix: 3.43 (0.25), residues: 443 sheet: -2.06 (0.28), residues: 298 loop : -1.68 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.023 0.002 HIS D 42 PHE 0.016 0.001 PHE A 456 TYR 0.013 0.002 TYR A 468 ARG 0.005 0.001 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 399) hydrogen bonds : angle 4.08178 ( 1167) SS BOND : bond 0.00525 ( 21) SS BOND : angle 2.89052 ( 42) covalent geometry : bond 0.00555 (11653) covalent geometry : angle 0.73162 (15912) Misc. bond : bond 0.01047 ( 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 176 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 GLU cc_start: 0.7893 (tp30) cc_final: 0.7532 (tp30) REVERT: D 60 VAL cc_start: 0.8948 (p) cc_final: 0.8032 (t) REVERT: D 87 GLN cc_start: 0.6339 (tp40) cc_final: 0.6004 (pt0) outliers start: 41 outliers final: 36 residues processed: 167 average time/residue: 0.3302 time to fit residues: 83.0613 Evaluate side-chains 164 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 2.995 ------------------------------------------------------------------------------- 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 183 THR Chi-restraints excluded: chain A residue 227 LEU 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 466 TYR Chi-restraints excluded: chain A residue 471 CYS 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 227 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 273 LEU 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 412 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 57 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 101 SER 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 110 CYS 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 116 optimal weight: 0.0770 chunk 84 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 154 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 113 optimal weight: 8.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.238853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.209041 restraints weight = 14484.032| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 2.17 r_work: 0.3816 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11675 Z= 0.114 Angle : 0.643 14.223 15954 Z= 0.316 Chirality : 0.044 0.252 1919 Planarity : 0.004 0.076 2118 Dihedral : 4.318 47.450 1718 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.34 % Allowed : 16.22 % Favored : 80.44 % 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: 3.46 (0.25), residues: 443 sheet: -1.92 (0.28), residues: 312 loop : -1.47 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 474 HIS 0.014 0.001 HIS D 42 PHE 0.004 0.001 PHE B 255 TYR 0.011 0.001 TYR D 53 ARG 0.006 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.02852 ( 399) hydrogen bonds : angle 3.76429 ( 1167) SS BOND : bond 0.00434 ( 21) SS BOND : angle 2.95765 ( 42) covalent geometry : bond 0.00266 (11653) covalent geometry : angle 0.62604 (15912) Misc. bond : bond 0.00674 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7377.73 seconds wall clock time: 132 minutes 13.08 seconds (7933.08 seconds total)