Starting phenix.real_space_refine on Fri Jun 20 11:42:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gk4_40179/06_2025/8gk4_40179_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gk4_40179/06_2025/8gk4_40179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gk4_40179/06_2025/8gk4_40179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gk4_40179/06_2025/8gk4_40179.map" model { file = "/net/cci-nas-00/data/ceres_data/8gk4_40179/06_2025/8gk4_40179_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gk4_40179/06_2025/8gk4_40179_trim.cif" } resolution = 3.12 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 84 5.16 5 Cl 2 4.86 5 C 15509 2.51 5 N 3854 2.21 5 O 4462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23911 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 7956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7956 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 989} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 7970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7970 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7965 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 41, 'TRANS': 989} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'CLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.32, per 1000 atoms: 0.60 Number of scatterers: 23911 At special positions: 0 Unit cell: (119.84, 119.84, 150.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 84 16.00 O 4462 8.00 N 3854 7.00 C 15509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.64 Conformation dependent library (CDL) restraints added in 3.3 seconds 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5840 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 26 sheets defined 60.9% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'B' and resid 1 through 9 removed outlier: 4.095A pdb=" N PHE B 6 " --> pdb=" O PHE B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.994A pdb=" N ILE B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 118 removed outlier: 4.399A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.678A pdb=" N LEU B 160 " --> pdb=" O ASN B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.652A pdb=" N GLU B 165 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 200 through 212 Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 263 through 266 No H-bonds generated for 'chain 'B' and resid 263 through 266' Processing helix chain 'B' and resid 299 through 317 removed outlier: 3.827A pdb=" N ASN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 361 removed outlier: 3.768A pdb=" N VAL B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 388 Proline residue: B 369 - end of helix removed outlier: 3.732A pdb=" N ALA B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 392 through 422 removed outlier: 4.386A pdb=" N GLY B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 460 removed outlier: 4.744A pdb=" N SER B 442 " --> pdb=" O ASN B 438 " (cutoff:3.500A) Proline residue: B 443 - end of helix Proline residue: B 457 - end of helix Processing helix chain 'B' and resid 463 through 499 removed outlier: 3.713A pdb=" N PHE B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) Proline residue: B 492 - end of helix Processing helix chain 'B' and resid 508 through 534 removed outlier: 3.666A pdb=" N LYS B 512 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 556 Processing helix chain 'B' and resid 580 through 598 Processing helix chain 'B' and resid 637 through 654 removed outlier: 4.583A pdb=" N ALA B 651 " --> pdb=" O GLY B 647 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASP B 652 " --> pdb=" O GLN B 648 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN B 654 " --> pdb=" O ALA B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 703 Processing helix chain 'B' and resid 725 through 732 Processing helix chain 'B' and resid 735 through 747 Processing helix chain 'B' and resid 777 through 781 Processing helix chain 'B' and resid 794 through 797 No H-bonds generated for 'chain 'B' and resid 794 through 797' Processing helix chain 'B' and resid 829 through 846 Processing helix chain 'B' and resid 855 through 863 Processing helix chain 'B' and resid 867 through 887 removed outlier: 3.896A pdb=" N PHE B 871 " --> pdb=" O GLY B 867 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL B 872 " --> pdb=" O ALA B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 914 removed outlier: 3.874A pdb=" N VAL B 895 " --> pdb=" O MET B 891 " (cutoff:3.500A) Proline residue: B 900 - end of helix removed outlier: 3.616A pdb=" N ALA B 911 " --> pdb=" O ILE B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 949 removed outlier: 3.709A pdb=" N LEU B 926 " --> pdb=" O GLN B 922 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 927 " --> pdb=" O THR B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 985 removed outlier: 4.278A pdb=" N ARG B 967 " --> pdb=" O LYS B 963 " (cutoff:3.500A) Proline residue: B 968 - end of helix Proline residue: B 982 - end of helix Processing helix chain 'B' and resid 990 through 1010 Processing helix chain 'B' and resid 1010 through 1031 Proline residue: B1017 - end of helix Processing helix chain 'A' and resid 2 through 9 removed outlier: 3.599A pdb=" N PHE A 6 " --> pdb=" O PHE A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 54 through 62 Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 99 through 114 removed outlier: 3.507A pdb=" N ALA A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 125 removed outlier: 3.584A pdb=" N LEU A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'A' and resid 161 through 167 removed outlier: 3.909A pdb=" N GLU A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 200 through 212 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 263 through 266 No H-bonds generated for 'chain 'A' and resid 263 through 266' Processing helix chain 'A' and resid 299 through 317 removed outlier: 4.019A pdb=" N ASN A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 361 Processing helix chain 'A' and resid 362 through 387 removed outlier: 3.946A pdb=" N ILE A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix removed outlier: 3.577A pdb=" N ALA A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Proline residue: A 374 - end of helix removed outlier: 3.533A pdb=" N ALA A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 removed outlier: 4.286A pdb=" N GLY A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 461 removed outlier: 4.915A pdb=" N SER A 442 " --> pdb=" O ASN A 438 " (cutoff:3.500A) Proline residue: A 443 - end of helix removed outlier: 3.514A pdb=" N PHE A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Proline residue: A 457 - end of helix removed outlier: 4.133A pdb=" N PHE A 460 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 489 removed outlier: 3.639A pdb=" N THR A 475 " --> pdb=" O GLN A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 507 through 534 removed outlier: 3.559A pdb=" N SER A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 556 removed outlier: 3.516A pdb=" N PHE A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 539 " --> pdb=" O THR A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 598 removed outlier: 3.621A pdb=" N MET A 598 " --> pdb=" O ASN A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 650 Processing helix chain 'A' and resid 685 through 703 removed outlier: 3.760A pdb=" N GLN A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 731 Processing helix chain 'A' and resid 735 through 747 Processing helix chain 'A' and resid 756 through 760 removed outlier: 3.577A pdb=" N GLY A 759 " --> pdb=" O PRO A 756 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 760 " --> pdb=" O MET A 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 756 through 760' Processing helix chain 'A' and resid 774 through 782 removed outlier: 3.644A pdb=" N ALA A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 779 " --> pdb=" O THR A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 797 No H-bonds generated for 'chain 'A' and resid 794 through 797' Processing helix chain 'A' and resid 829 through 845 Processing helix chain 'A' and resid 855 through 863 Processing helix chain 'A' and resid 865 through 887 removed outlier: 3.838A pdb=" N TYR A 869 " --> pdb=" O GLY A 865 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA A 870 " --> pdb=" O ALA A 866 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE A 871 " --> pdb=" O GLY A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 914 removed outlier: 4.307A pdb=" N LEU A 893 " --> pdb=" O TRP A 889 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA A 898 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Proline residue: A 900 - end of helix Processing helix chain 'A' and resid 918 through 949 removed outlier: 3.855A pdb=" N GLY A 930 " --> pdb=" O LEU A 926 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 986 removed outlier: 3.537A pdb=" N ALA A 958 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG A 967 " --> pdb=" O LYS A 963 " (cutoff:3.500A) Proline residue: A 968 - end of helix Proline residue: A 982 - end of helix Processing helix chain 'A' and resid 990 through 1010 Processing helix chain 'A' and resid 1010 through 1032 removed outlier: 3.731A pdb=" N PHE A1014 " --> pdb=" O THR A1010 " (cutoff:3.500A) Proline residue: A1017 - end of helix Processing helix chain 'C' and resid 2 through 9 removed outlier: 3.861A pdb=" N PHE C 6 " --> pdb=" O PHE C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 31 removed outlier: 3.547A pdb=" N ALA C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 62 Processing helix chain 'C' and resid 62 through 70 Processing helix chain 'C' and resid 99 through 114 removed outlier: 3.771A pdb=" N ALA C 114 " --> pdb=" O ARG C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 125 Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.555A pdb=" N GLU C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 197 removed outlier: 3.581A pdb=" N LYS C 196 " --> pdb=" O ASP C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 212 Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 263 through 266 No H-bonds generated for 'chain 'C' and resid 263 through 266' Processing helix chain 'C' and resid 299 through 318 removed outlier: 3.625A pdb=" N LYS C 305 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 360 Processing helix chain 'C' and resid 362 through 388 removed outlier: 3.746A pdb=" N THR C 366 " --> pdb=" O ASN C 362 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE C 367 " --> pdb=" O PHE C 363 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) Proline residue: C 369 - end of helix Proline residue: C 374 - end of helix Processing helix chain 'C' and resid 392 through 424 removed outlier: 3.945A pdb=" N GLY C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 405 " --> pdb=" O LEU C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 461 removed outlier: 4.721A pdb=" N SER C 442 " --> pdb=" O ASN C 438 " (cutoff:3.500A) Proline residue: C 443 - end of helix removed outlier: 3.614A pdb=" N CYS C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) Proline residue: C 457 - end of helix Processing helix chain 'C' and resid 462 through 489 Processing helix chain 'C' and resid 489 through 499 removed outlier: 3.722A pdb=" N SER C 493 " --> pdb=" O THR C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 534 Processing helix chain 'C' and resid 534 through 556 removed outlier: 3.534A pdb=" N LEU C 540 " --> pdb=" O ILE C 536 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 598 removed outlier: 3.542A pdb=" N GLN C 597 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET C 598 " --> pdb=" O ASN C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 650 Processing helix chain 'C' and resid 685 through 703 Processing helix chain 'C' and resid 725 through 732 Processing helix chain 'C' and resid 735 through 747 Processing helix chain 'C' and resid 770 through 774 Processing helix chain 'C' and resid 775 through 776 No H-bonds generated for 'chain 'C' and resid 775 through 776' Processing helix chain 'C' and resid 777 through 782 removed outlier: 4.109A pdb=" N ASN C 781 " --> pdb=" O ASP C 777 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE C 782 " --> pdb=" O ALA C 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 777 through 782' Processing helix chain 'C' and resid 794 through 797 No H-bonds generated for 'chain 'C' and resid 794 through 797' Processing helix chain 'C' and resid 829 through 845 Processing helix chain 'C' and resid 855 through 863 Processing helix chain 'C' and resid 865 through 887 removed outlier: 3.626A pdb=" N VAL C 878 " --> pdb=" O GLY C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 898 removed outlier: 4.035A pdb=" N VAL C 895 " --> pdb=" O MET C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 914 removed outlier: 4.256A pdb=" N ALA C 902 " --> pdb=" O ALA C 898 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C 906 " --> pdb=" O ALA C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 949 removed outlier: 3.557A pdb=" N LEU C 927 " --> pdb=" O THR C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 986 removed outlier: 4.337A pdb=" N ARG C 967 " --> pdb=" O LYS C 963 " (cutoff:3.500A) Proline residue: C 968 - end of helix Proline residue: C 982 - end of helix removed outlier: 3.687A pdb=" N PHE C 985 " --> pdb=" O LEU C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1031 removed outlier: 3.781A pdb=" N ALA C1012 " --> pdb=" O ALA C1008 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE C1013 " --> pdb=" O SER C1009 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE C1014 " --> pdb=" O THR C1010 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C1015 " --> pdb=" O LEU C1011 " (cutoff:3.500A) Proline residue: C1017 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.731A pdb=" N TYR B 78 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS B 810 " --> pdb=" O ALA B 817 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU B 819 " --> pdb=" O THR B 711 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR B 711 " --> pdb=" O LEU B 819 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLN B 821 " --> pdb=" O VAL B 709 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL B 709 " --> pdb=" O GLN B 821 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.731A pdb=" N TYR B 78 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS B 810 " --> pdb=" O ALA B 817 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.733A pdb=" N GLU B 138 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL B 139 " --> pdb=" O PRO B 327 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 267 through 273 removed outlier: 7.004A pdb=" N TYR B 183 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASN B 765 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N MET B 185 " --> pdb=" O ASN B 765 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ARG B 767 " --> pdb=" O MET B 185 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ILE B 187 " --> pdb=" O ARG B 767 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN B 753 " --> pdb=" O VAL B 764 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE B 766 " --> pdb=" O TYR B 751 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N TYR B 751 " --> pdb=" O ILE B 766 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 219 through 220 removed outlier: 3.649A pdb=" N SER B 234 " --> pdb=" O PRO C 718 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 251 through 254 removed outlier: 3.663A pdb=" N ARG B 253 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 285 through 286 removed outlier: 5.820A pdb=" N ALA B 621 " --> pdb=" O GLY B 609 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASP B 611 " --> pdb=" O GLU B 619 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N GLU B 619 " --> pdb=" O ASP B 611 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 798 through 804 removed outlier: 3.633A pdb=" N SER A 234 " --> pdb=" O PRO B 718 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 783 through 785 Processing sheet with id=AB1, first strand: chain 'A' and resid 128 through 132 removed outlier: 4.065A pdb=" N THR A 43 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS A 810 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU A 819 " --> pdb=" O THR A 711 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR A 711 " --> pdb=" O LEU A 819 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN A 821 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL A 709 " --> pdb=" O GLN A 821 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 128 through 132 removed outlier: 4.065A pdb=" N THR A 43 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS A 810 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 818 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU A 675 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.516A pdb=" N ASN A 293 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA A 175 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE A 291 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA A 177 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU A 294 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 136 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A 328 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER A 141 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE A 326 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR A 143 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TYR A 324 " --> pdb=" O TYR A 143 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 267 through 273 removed outlier: 4.025A pdb=" N GLN A 763 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN A 765 " --> pdb=" O MET A 185 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN A 753 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE A 766 " --> pdb=" O TYR A 751 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR A 751 " --> pdb=" O ILE A 766 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 251 through 253 removed outlier: 3.840A pdb=" N ARG A 253 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 279 through 282 removed outlier: 5.924A pdb=" N ALA A 621 " --> pdb=" O GLY A 609 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ASP A 611 " --> pdb=" O GLU A 619 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N GLU A 619 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 798 through 805 removed outlier: 3.558A pdb=" N SER C 234 " --> pdb=" O PRO A 718 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLN C 238 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE A 724 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLY C 239 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLN C 214 " --> pdb=" O GLY C 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 783 through 785 Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.213A pdb=" N LYS C 810 " --> pdb=" O ALA C 817 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 710 through 711 removed outlier: 4.503A pdb=" N GLU C 675 " --> pdb=" O SER C 854 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.179A pdb=" N ALA C 286 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 138 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU C 294 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE C 136 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU C 137 " --> pdb=" O ASP C 329 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP C 329 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL C 139 " --> pdb=" O PRO C 327 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.971A pdb=" N GLY C 280 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 183 through 184 Processing sheet with id=AC5, first strand: chain 'C' and resid 267 through 269 removed outlier: 3.715A pdb=" N ASN C 753 " --> pdb=" O VAL C 764 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE C 766 " --> pdb=" O TYR C 751 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N TYR C 751 " --> pdb=" O ILE C 766 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 251 through 254 removed outlier: 3.852A pdb=" N ARG C 253 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 610 through 611 removed outlier: 3.592A pdb=" N SER C 616 " --> pdb=" O ASP C 611 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 783 through 785 1631 hydrogen bonds defined for protein. 4755 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: 10.03 Time building geometry restraints manager: 7.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7415 1.33 - 1.45: 3126 1.45 - 1.57: 13668 1.57 - 1.69: 0 1.69 - 1.81: 164 Bond restraints: 24373 Sorted by residual: bond pdb=" N9 CLM C1101 " pdb=" O9A CLM C1101 " ideal model delta sigma weight residual 1.209 1.399 -0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" CA SER C 84 " pdb=" C SER C 84 " ideal model delta sigma weight residual 1.520 1.482 0.038 1.02e-02 9.61e+03 1.37e+01 bond pdb=" C ILE A 792 " pdb=" N PRO A 793 " ideal model delta sigma weight residual 1.332 1.375 -0.043 1.33e-02 5.65e+03 1.04e+01 bond pdb=" CA ILE C 456 " pdb=" C ILE C 456 " ideal model delta sigma weight residual 1.520 1.546 -0.027 8.80e-03 1.29e+04 9.10e+00 bond pdb=" CA VAL B 899 " pdb=" C VAL B 899 " ideal model delta sigma weight residual 1.520 1.546 -0.026 8.80e-03 1.29e+04 8.97e+00 ... (remaining 24368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 31023 2.44 - 4.88: 1738 4.88 - 7.33: 282 7.33 - 9.77: 58 9.77 - 12.21: 14 Bond angle restraints: 33115 Sorted by residual: angle pdb=" N ASP A 652 " pdb=" CA ASP A 652 " pdb=" C ASP A 652 " ideal model delta sigma weight residual 111.82 100.93 10.89 1.16e+00 7.43e-01 8.82e+01 angle pdb=" N ILE C 178 " pdb=" CA ILE C 178 " pdb=" C ILE C 178 " ideal model delta sigma weight residual 110.62 119.78 -9.16 1.02e+00 9.61e-01 8.07e+01 angle pdb=" N VAL A 752 " pdb=" CA VAL A 752 " pdb=" C VAL A 752 " ideal model delta sigma weight residual 110.42 117.49 -7.07 9.40e-01 1.13e+00 5.65e+01 angle pdb=" N GLY C 874 " pdb=" CA GLY C 874 " pdb=" C GLY C 874 " ideal model delta sigma weight residual 115.32 105.55 9.77 1.31e+00 5.83e-01 5.56e+01 angle pdb=" N ILE A 162 " pdb=" CA ILE A 162 " pdb=" C ILE A 162 " ideal model delta sigma weight residual 110.62 118.22 -7.60 1.02e+00 9.61e-01 5.56e+01 ... (remaining 33110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.11: 13225 14.11 - 28.22: 1068 28.22 - 42.33: 286 42.33 - 56.43: 57 56.43 - 70.54: 8 Dihedral angle restraints: 14644 sinusoidal: 5611 harmonic: 9033 Sorted by residual: dihedral pdb=" N TYR C 50 " pdb=" C TYR C 50 " pdb=" CA TYR C 50 " pdb=" CB TYR C 50 " ideal model delta harmonic sigma weight residual 122.80 112.44 10.36 0 2.50e+00 1.60e-01 1.72e+01 dihedral pdb=" C PHE C 740 " pdb=" N PHE C 740 " pdb=" CA PHE C 740 " pdb=" CB PHE C 740 " ideal model delta harmonic sigma weight residual -122.60 -132.60 10.00 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" C PHE C1015 " pdb=" N PHE C1015 " pdb=" CA PHE C1015 " pdb=" CB PHE C1015 " ideal model delta harmonic sigma weight residual -122.60 -132.47 9.87 0 2.50e+00 1.60e-01 1.56e+01 ... (remaining 14641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3080 0.097 - 0.194: 717 0.194 - 0.290: 124 0.290 - 0.387: 17 0.387 - 0.484: 4 Chirality restraints: 3942 Sorted by residual: chirality pdb=" CA MET C 891 " pdb=" N MET C 891 " pdb=" C MET C 891 " pdb=" CB MET C 891 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" CA PHE C1015 " pdb=" N PHE C1015 " pdb=" C PHE C1015 " pdb=" CB PHE C1015 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" CA PHE C 740 " pdb=" N PHE C 740 " pdb=" C PHE C 740 " pdb=" CB PHE C 740 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.35e+00 ... (remaining 3939 not shown) Planarity restraints: 4198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 891 " 0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO A 892 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 892 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 892 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 456 " 0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO C 457 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 457 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 457 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 442 " -0.052 5.00e-02 4.00e+02 7.80e-02 9.73e+00 pdb=" N PRO A 443 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 443 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 443 " -0.044 5.00e-02 4.00e+02 ... (remaining 4195 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 8094 2.84 - 3.35: 24960 3.35 - 3.87: 41278 3.87 - 4.38: 50311 4.38 - 4.90: 79765 Nonbonded interactions: 204408 Sorted by model distance: nonbonded pdb=" CB LEU B 948 " pdb=" NZ LYS B 949 " model vdw 2.324 3.520 nonbonded pdb=" O LEU C 699 " pdb=" OG1 THR C 702 " model vdw 2.448 3.040 nonbonded pdb=" O ASN B 362 " pdb=" OG SER B 365 " model vdw 2.455 3.040 nonbonded pdb=" O THR B 491 " pdb=" OG SER B 495 " model vdw 2.460 3.040 nonbonded pdb=" O SER B 991 " pdb=" ND1 HIS B 995 " model vdw 2.474 3.120 ... (remaining 204403 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 1 through 501 or (resid 502 through 503 and (name N or nam \ e CA or name C or name O or name CB )) or resid 504 through 652 or (resid 653 an \ d (name N or name CA or name C or name O or name CB )) or resid 654 through 831 \ or (resid 832 through 833 and (name N or name CA or name C or name O or name CB \ )) or resid 834 through 838 or (resid 839 and (name N or name CA or name C or na \ me O or name CB )) or resid 840 through 863 or (resid 864 and (name N or name CA \ or name C or name O or name CB )) or resid 865 through 1031)) selection = (chain 'B' and (resid 1 through 255 or (resid 256 and (name N or name CA or name \ C or name O or name CB )) or resid 257 or (resid 258 and (name N or name CA or \ name C or name O or name CB )) or resid 259 through 831 or (resid 832 through 83 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 834 through \ 838 or (resid 839 and (name N or name CA or name C or name O or name CB )) or re \ sid 840 through 1031)) selection = (chain 'C' and (resid 1 through 255 or (resid 256 and (name N or name CA or name \ C or name O or name CB )) or resid 257 or (resid 258 and (name N or name CA or \ name C or name O or name CB )) or resid 259 through 501 or (resid 502 through 50 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 504 through \ 652 or (resid 653 and (name N or name CA or name C or name O or name CB )) or re \ sid 654 through 863 or (resid 864 and (name N or name CA or name C or name O or \ name CB )) or resid 865 through 1031)) } 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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 55.600 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.090 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 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 : 0.007 0.190 24373 Z= 0.525 Angle : 1.280 12.208 33115 Z= 0.893 Chirality : 0.085 0.484 3942 Planarity : 0.007 0.084 4198 Dihedral : 11.440 70.542 8804 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.43 % Favored : 97.54 % Rotamer: Outliers : 2.37 % Allowed : 7.10 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 0.46 (0.15), residues: 3088 helix: 0.83 (0.13), residues: 1738 sheet: 0.42 (0.24), residues: 426 loop : -0.59 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 853 HIS 0.005 0.002 HIS A 582 PHE 0.020 0.002 PHE A 755 TYR 0.018 0.002 TYR C 783 ARG 0.004 0.001 ARG C 186 Details of bonding type rmsd hydrogen bonds : bond 0.20669 ( 1572) hydrogen bonds : angle 7.53487 ( 4755) covalent geometry : bond 0.00698 (24373) covalent geometry : angle 1.28008 (33115) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 807 time to evaluate : 2.886 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 64 THR cc_start: 0.7294 (m) cc_final: 0.6774 (p) outliers start: 62 outliers final: 5 residues processed: 852 average time/residue: 0.3639 time to fit residues: 486.2180 Evaluate side-chains 401 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 396 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 450 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 147 optimal weight: 0.4980 chunk 180 optimal weight: 9.9990 chunk 280 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN B 214 GLN B 275 GLN B 299 ASN B 312 GLN B 325 GLN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN A 214 GLN A 320 GLN A 597 GLN C 108 ASN C 308 ASN C 312 GLN C 502 ASN C 582 HIS C 592 ASN C 679 GLN C 691 GLN C 761 ASN C 795 ASN C 922 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.098773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.081728 restraints weight = 48982.464| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.67 r_work: 0.3024 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24373 Z= 0.173 Angle : 0.628 10.077 33115 Z= 0.341 Chirality : 0.044 0.172 3942 Planarity : 0.006 0.065 4198 Dihedral : 4.872 50.160 3307 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.13 % Allowed : 14.54 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.17 (0.15), residues: 3088 helix: 1.61 (0.12), residues: 1750 sheet: 0.07 (0.23), residues: 448 loop : -0.41 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 853 HIS 0.008 0.001 HIS C 582 PHE 0.024 0.002 PHE C1019 TYR 0.038 0.002 TYR A 649 ARG 0.006 0.001 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.05990 ( 1572) hydrogen bonds : angle 5.29650 ( 4755) covalent geometry : bond 0.00372 (24373) covalent geometry : angle 0.62843 (33115) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 457 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 MET cc_start: 0.9057 (tpp) cc_final: 0.8830 (tpp) REVERT: B 408 ASP cc_start: 0.8719 (t70) cc_final: 0.8442 (t0) REVERT: B 412 ILE cc_start: 0.9161 (mt) cc_final: 0.8832 (mt) REVERT: B 435 LYS cc_start: 0.8944 (ptmt) cc_final: 0.8641 (ptpp) REVERT: B 437 MET cc_start: 0.8930 (mmm) cc_final: 0.8554 (mmm) REVERT: B 885 GLN cc_start: 0.9089 (tp40) cc_final: 0.8684 (tm-30) REVERT: B 891 MET cc_start: 0.9024 (mpp) cc_final: 0.8762 (tpp) REVERT: B 916 ASP cc_start: 0.7722 (m-30) cc_final: 0.7507 (m-30) REVERT: B 1005 MET cc_start: 0.8671 (tpp) cc_final: 0.8444 (tpp) REVERT: B 1029 TRP cc_start: 0.8205 (t60) cc_final: 0.7996 (t60) REVERT: A 89 LYS cc_start: 0.8720 (mttp) cc_final: 0.8302 (mptt) REVERT: A 211 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.7624 (mp10) REVERT: A 233 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8553 (mt) REVERT: A 515 ASP cc_start: 0.8438 (m-30) cc_final: 0.8124 (m-30) REVERT: A 675 GLU cc_start: 0.8717 (mp0) cc_final: 0.8509 (mp0) REVERT: A 736 MET cc_start: 0.8197 (ttm) cc_final: 0.7901 (ttm) REVERT: A 757 MET cc_start: 0.9001 (ttp) cc_final: 0.8730 (ptm) REVERT: C 356 MET cc_start: 0.8912 (mmm) cc_final: 0.8562 (mmm) REVERT: C 424 ASP cc_start: 0.7902 (t0) cc_final: 0.7627 (t0) REVERT: C 479 SER cc_start: 0.9531 (m) cc_final: 0.9212 (p) REVERT: C 619 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8026 (mm-30) outliers start: 82 outliers final: 41 residues processed: 515 average time/residue: 0.3430 time to fit residues: 293.3340 Evaluate side-chains 393 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 350 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 993 SER Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1028 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 293 optimal weight: 2.9990 chunk 182 optimal weight: 0.0670 chunk 264 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 277 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 246 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 416 ASN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN C 293 ASN C 679 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.097904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.081511 restraints weight = 48464.897| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.48 r_work: 0.3033 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24373 Z= 0.145 Angle : 0.559 10.240 33115 Z= 0.296 Chirality : 0.042 0.183 3942 Planarity : 0.005 0.052 4198 Dihedral : 4.647 52.931 3303 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.71 % Allowed : 16.76 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.56 (0.15), residues: 3088 helix: 1.95 (0.12), residues: 1760 sheet: 0.11 (0.23), residues: 444 loop : -0.25 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 631 HIS 0.004 0.001 HIS A 582 PHE 0.045 0.001 PHE B 516 TYR 0.021 0.001 TYR C 183 ARG 0.007 0.001 ARG C 703 Details of bonding type rmsd hydrogen bonds : bond 0.04916 ( 1572) hydrogen bonds : angle 4.84738 ( 4755) covalent geometry : bond 0.00302 (24373) covalent geometry : angle 0.55889 (33115) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 403 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 408 ASP cc_start: 0.8729 (t70) cc_final: 0.8385 (t0) REVERT: B 412 ILE cc_start: 0.9107 (mt) cc_final: 0.8859 (mt) REVERT: B 530 TYR cc_start: 0.7575 (t80) cc_final: 0.7313 (t80) REVERT: B 619 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8416 (mt-10) REVERT: B 696 MET cc_start: 0.9146 (ttp) cc_final: 0.8931 (tmm) REVERT: B 834 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8653 (mp) REVERT: B 885 GLN cc_start: 0.9131 (tp40) cc_final: 0.8654 (tm-30) REVERT: B 887 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8173 (mm-30) REVERT: B 891 MET cc_start: 0.9057 (mpp) cc_final: 0.8714 (tpp) REVERT: A 211 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: A 233 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8645 (mt) REVERT: A 515 ASP cc_start: 0.8411 (m-30) cc_final: 0.8067 (m-30) REVERT: A 598 MET cc_start: 0.9099 (tpp) cc_final: 0.8858 (ttm) REVERT: A 675 GLU cc_start: 0.8726 (mp0) cc_final: 0.8525 (mp0) REVERT: A 757 MET cc_start: 0.8828 (ttp) cc_final: 0.8550 (ptm) REVERT: C 479 SER cc_start: 0.9492 (m) cc_final: 0.9187 (p) outliers start: 71 outliers final: 40 residues processed: 455 average time/residue: 0.2998 time to fit residues: 228.1758 Evaluate side-chains 376 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 333 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 991 SER Chi-restraints excluded: chain C residue 1028 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 254 optimal weight: 0.7980 chunk 228 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 291 optimal weight: 0.6980 chunk 165 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 273 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 582 HIS ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN C 108 ASN C 502 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.097015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.080164 restraints weight = 49237.075| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.55 r_work: 0.2976 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24373 Z= 0.148 Angle : 0.556 13.927 33115 Z= 0.288 Chirality : 0.042 0.353 3942 Planarity : 0.004 0.050 4198 Dihedral : 4.553 55.099 3301 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.98 % Allowed : 17.25 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.67 (0.15), residues: 3088 helix: 2.08 (0.12), residues: 1755 sheet: 0.11 (0.23), residues: 443 loop : -0.26 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 889 HIS 0.003 0.001 HIS A 582 PHE 0.023 0.001 PHE B 674 TYR 0.016 0.001 TYR C 183 ARG 0.005 0.000 ARG C 703 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 1572) hydrogen bonds : angle 4.70286 ( 4755) covalent geometry : bond 0.00336 (24373) covalent geometry : angle 0.55599 (33115) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 353 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 408 ASP cc_start: 0.8770 (t70) cc_final: 0.8426 (t0) REVERT: B 412 ILE cc_start: 0.9178 (mt) cc_final: 0.8893 (mt) REVERT: B 514 ASN cc_start: 0.9305 (t0) cc_final: 0.8913 (m-40) REVERT: B 675 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7729 (mm-30) REVERT: B 885 GLN cc_start: 0.9189 (tp40) cc_final: 0.8679 (tm-30) REVERT: B 887 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8308 (mm-30) REVERT: B 891 MET cc_start: 0.9048 (tpp) cc_final: 0.8755 (tpp) REVERT: B 916 ASP cc_start: 0.7761 (m-30) cc_final: 0.7561 (m-30) REVERT: A 211 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.7377 (mp10) REVERT: A 233 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8799 (mt) REVERT: A 675 GLU cc_start: 0.8799 (mp0) cc_final: 0.8550 (mp0) REVERT: A 757 MET cc_start: 0.8813 (ttp) cc_final: 0.8483 (ptm) REVERT: A 891 MET cc_start: 0.7113 (mtt) cc_final: 0.6836 (ttm) REVERT: C 479 SER cc_start: 0.9523 (m) cc_final: 0.9192 (p) outliers start: 78 outliers final: 57 residues processed: 409 average time/residue: 0.2983 time to fit residues: 205.7839 Evaluate side-chains 384 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 325 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 460 PHE Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 502 ASN Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1028 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 44 optimal weight: 8.9990 chunk 241 optimal weight: 0.6980 chunk 207 optimal weight: 0.6980 chunk 300 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 295 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 56 optimal weight: 0.0670 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN A1027 ASN C 108 ASN C 214 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.096203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.079762 restraints weight = 48938.745| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.51 r_work: 0.3017 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24373 Z= 0.123 Angle : 0.531 8.976 33115 Z= 0.275 Chirality : 0.042 0.229 3942 Planarity : 0.004 0.046 4198 Dihedral : 4.469 55.802 3301 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.86 % Allowed : 17.56 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.74 (0.15), residues: 3088 helix: 2.15 (0.12), residues: 1759 sheet: 0.13 (0.23), residues: 439 loop : -0.27 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 853 HIS 0.003 0.001 HIS A 582 PHE 0.021 0.001 PHE C 318 TYR 0.012 0.001 TYR C 183 ARG 0.006 0.000 ARG A 534 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 1572) hydrogen bonds : angle 4.55613 ( 4755) covalent geometry : bond 0.00263 (24373) covalent geometry : angle 0.53081 (33115) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 370 time to evaluate : 3.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 408 ASP cc_start: 0.8776 (t70) cc_final: 0.8398 (t0) REVERT: B 412 ILE cc_start: 0.9190 (mt) cc_final: 0.8883 (mt) REVERT: B 485 PHE cc_start: 0.9099 (t80) cc_final: 0.8819 (t80) REVERT: B 514 ASN cc_start: 0.9320 (t0) cc_final: 0.8992 (m110) REVERT: B 516 PHE cc_start: 0.7607 (p90) cc_final: 0.6883 (p90) REVERT: B 675 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7640 (mm-30) REVERT: B 828 TYR cc_start: 0.7935 (m-10) cc_final: 0.6763 (m-80) REVERT: B 885 GLN cc_start: 0.9180 (tp40) cc_final: 0.8640 (tm-30) REVERT: B 916 ASP cc_start: 0.7743 (m-30) cc_final: 0.7542 (m-30) REVERT: A 211 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.7373 (mp10) REVERT: A 233 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8802 (mt) REVERT: A 323 LYS cc_start: 0.8946 (mtpp) cc_final: 0.8615 (mtpt) REVERT: A 675 GLU cc_start: 0.8748 (mp0) cc_final: 0.8487 (mp0) REVERT: C 479 SER cc_start: 0.9511 (m) cc_final: 0.9182 (p) REVERT: C 560 LEU cc_start: 0.8565 (pt) cc_final: 0.8361 (pp) outliers start: 75 outliers final: 49 residues processed: 426 average time/residue: 0.4414 time to fit residues: 318.8752 Evaluate side-chains 390 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 339 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 460 PHE Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1028 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 57 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 181 optimal weight: 0.0030 chunk 254 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 chunk 294 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.095999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.079541 restraints weight = 48712.935| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.50 r_work: 0.3013 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24373 Z= 0.125 Angle : 0.528 10.064 33115 Z= 0.272 Chirality : 0.042 0.218 3942 Planarity : 0.004 0.048 4198 Dihedral : 4.408 57.106 3301 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.86 % Allowed : 17.90 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.82 (0.15), residues: 3088 helix: 2.23 (0.12), residues: 1757 sheet: 0.20 (0.23), residues: 440 loop : -0.31 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 889 HIS 0.003 0.001 HIS A 582 PHE 0.017 0.001 PHE C 610 TYR 0.026 0.001 TYR B 357 ARG 0.006 0.000 ARG A 534 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 1572) hydrogen bonds : angle 4.49138 ( 4755) covalent geometry : bond 0.00278 (24373) covalent geometry : angle 0.52772 (33115) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 362 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 MET cc_start: 0.9058 (tpp) cc_final: 0.8817 (tpp) REVERT: B 357 TYR cc_start: 0.8493 (t80) cc_final: 0.8278 (t80) REVERT: B 408 ASP cc_start: 0.8745 (t70) cc_final: 0.8106 (t0) REVERT: B 412 ILE cc_start: 0.9170 (mt) cc_final: 0.8690 (mt) REVERT: B 467 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7980 (tp30) REVERT: B 509 PHE cc_start: 0.7846 (m-10) cc_final: 0.7274 (m-10) REVERT: B 513 PHE cc_start: 0.8405 (t80) cc_final: 0.8184 (t80) REVERT: B 514 ASN cc_start: 0.9300 (t0) cc_final: 0.9015 (m110) REVERT: B 516 PHE cc_start: 0.7666 (p90) cc_final: 0.7017 (p90) REVERT: B 546 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8324 (mm) REVERT: B 675 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7651 (mm-30) REVERT: B 885 GLN cc_start: 0.9185 (tp40) cc_final: 0.8614 (tm-30) REVERT: B 916 ASP cc_start: 0.7767 (m-30) cc_final: 0.7560 (m-30) REVERT: A 211 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.7356 (mp10) REVERT: A 233 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8866 (mt) REVERT: A 323 LYS cc_start: 0.8943 (mtpp) cc_final: 0.8614 (mtpt) REVERT: C 211 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.7804 (mp10) REVERT: C 479 SER cc_start: 0.9511 (m) cc_final: 0.9170 (p) outliers start: 75 outliers final: 52 residues processed: 419 average time/residue: 0.2854 time to fit residues: 202.0518 Evaluate side-chains 396 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 340 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 460 PHE Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1028 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 45 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 308 optimal weight: 5.9990 chunk 197 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 232 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 ASN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.077945 restraints weight = 49405.202| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.54 r_work: 0.2966 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24373 Z= 0.143 Angle : 0.540 9.507 33115 Z= 0.278 Chirality : 0.041 0.178 3942 Planarity : 0.004 0.047 4198 Dihedral : 4.385 59.111 3301 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.63 % Allowed : 18.09 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.83 (0.15), residues: 3088 helix: 2.26 (0.12), residues: 1760 sheet: 0.20 (0.23), residues: 441 loop : -0.36 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 853 HIS 0.003 0.001 HIS A 582 PHE 0.016 0.001 PHE B 516 TYR 0.025 0.001 TYR A 649 ARG 0.005 0.000 ARG A 534 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 1572) hydrogen bonds : angle 4.48857 ( 4755) covalent geometry : bond 0.00328 (24373) covalent geometry : angle 0.53967 (33115) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 346 time to evaluate : 2.787 Fit side-chains revert: symmetry clash REVERT: B 357 TYR cc_start: 0.8530 (t80) cc_final: 0.8292 (t80) REVERT: B 408 ASP cc_start: 0.8530 (t70) cc_final: 0.8146 (t0) REVERT: B 412 ILE cc_start: 0.9094 (mt) cc_final: 0.8802 (mt) REVERT: B 467 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7902 (tp30) REVERT: B 509 PHE cc_start: 0.7952 (m-10) cc_final: 0.7359 (m-10) REVERT: B 514 ASN cc_start: 0.9194 (t0) cc_final: 0.8974 (m110) REVERT: B 516 PHE cc_start: 0.7658 (p90) cc_final: 0.7099 (p90) REVERT: B 546 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8446 (mm) REVERT: B 675 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7825 (mm-30) REVERT: B 832 GLN cc_start: 0.9294 (mt0) cc_final: 0.9089 (mt0) REVERT: B 885 GLN cc_start: 0.9215 (tp40) cc_final: 0.8614 (tm-30) REVERT: B 916 ASP cc_start: 0.7832 (m-30) cc_final: 0.7619 (m-30) REVERT: B 931 LEU cc_start: 0.9258 (tp) cc_final: 0.9026 (tt) REVERT: A 211 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.7320 (mp10) REVERT: A 233 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8929 (mt) REVERT: A 323 LYS cc_start: 0.8970 (mtpp) cc_final: 0.8624 (mtpt) REVERT: C 479 SER cc_start: 0.9564 (m) cc_final: 0.9210 (p) REVERT: C 560 LEU cc_start: 0.8597 (pt) cc_final: 0.8376 (pp) outliers start: 69 outliers final: 54 residues processed: 398 average time/residue: 0.3006 time to fit residues: 202.0846 Evaluate side-chains 383 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 326 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 773 ARG Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1028 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 231 optimal weight: 0.2980 chunk 151 optimal weight: 0.0870 chunk 177 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 294 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 268 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 ASN B 180 ASN B 661 ASN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.097473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.080705 restraints weight = 49220.810| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.55 r_work: 0.3013 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24373 Z= 0.117 Angle : 0.527 10.175 33115 Z= 0.270 Chirality : 0.041 0.159 3942 Planarity : 0.004 0.046 4198 Dihedral : 4.295 57.890 3301 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.37 % Allowed : 18.55 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.91 (0.15), residues: 3088 helix: 2.33 (0.12), residues: 1758 sheet: 0.24 (0.23), residues: 443 loop : -0.34 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 853 HIS 0.003 0.001 HIS A 582 PHE 0.025 0.001 PHE C 318 TYR 0.018 0.001 TYR A 649 ARG 0.006 0.000 ARG A 534 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 1572) hydrogen bonds : angle 4.40958 ( 4755) covalent geometry : bond 0.00258 (24373) covalent geometry : angle 0.52686 (33115) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 359 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 185 MET cc_start: 0.9024 (tpp) cc_final: 0.8030 (tpp) REVERT: B 357 TYR cc_start: 0.8484 (t80) cc_final: 0.8238 (t80) REVERT: B 408 ASP cc_start: 0.8716 (t70) cc_final: 0.8469 (t0) REVERT: B 412 ILE cc_start: 0.9037 (mt) cc_final: 0.8807 (mt) REVERT: B 509 PHE cc_start: 0.7851 (m-10) cc_final: 0.7196 (m-10) REVERT: B 514 ASN cc_start: 0.9216 (t0) cc_final: 0.8999 (m110) REVERT: B 516 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7183 (p90) REVERT: B 546 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8435 (mm) REVERT: B 675 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7954 (mm-30) REVERT: B 885 GLN cc_start: 0.9217 (tp40) cc_final: 0.8584 (tm-30) REVERT: B 916 ASP cc_start: 0.7823 (m-30) cc_final: 0.7608 (m-30) REVERT: A 211 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.7390 (mp10) REVERT: A 233 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8920 (mt) REVERT: A 323 LYS cc_start: 0.8978 (mtpp) cc_final: 0.8661 (mtpt) REVERT: C 211 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.7834 (mp10) REVERT: C 479 SER cc_start: 0.9569 (m) cc_final: 0.9193 (p) outliers start: 62 outliers final: 47 residues processed: 406 average time/residue: 0.2878 time to fit residues: 198.0132 Evaluate side-chains 386 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 334 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1028 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 234 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 84 optimal weight: 0.0040 chunk 298 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 125 optimal weight: 0.4980 chunk 109 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 ASN B 661 ASN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.094408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.077797 restraints weight = 48951.964| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.53 r_work: 0.2982 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24373 Z= 0.147 Angle : 0.556 16.924 33115 Z= 0.283 Chirality : 0.041 0.165 3942 Planarity : 0.004 0.046 4198 Dihedral : 4.276 53.429 3301 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.29 % Allowed : 18.74 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.87 (0.15), residues: 3088 helix: 2.31 (0.12), residues: 1760 sheet: 0.26 (0.23), residues: 437 loop : -0.40 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 853 HIS 0.008 0.001 HIS B 422 PHE 0.020 0.001 PHE C 318 TYR 0.024 0.001 TYR A 649 ARG 0.008 0.000 ARG A 534 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 1572) hydrogen bonds : angle 4.46469 ( 4755) covalent geometry : bond 0.00339 (24373) covalent geometry : angle 0.55551 (33115) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 339 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 357 TYR cc_start: 0.8497 (t80) cc_final: 0.8274 (t80) REVERT: B 408 ASP cc_start: 0.8748 (t70) cc_final: 0.8515 (t0) REVERT: B 412 ILE cc_start: 0.9007 (mt) cc_final: 0.8776 (mt) REVERT: B 509 PHE cc_start: 0.7841 (m-10) cc_final: 0.7247 (m-10) REVERT: B 516 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7088 (p90) REVERT: B 546 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8407 (mm) REVERT: B 627 ILE cc_start: 0.9318 (mm) cc_final: 0.9078 (pt) REVERT: B 675 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8066 (mm-30) REVERT: B 676 MET cc_start: 0.8034 (tmm) cc_final: 0.6988 (tpp) REVERT: B 885 GLN cc_start: 0.9217 (tp40) cc_final: 0.8556 (tm-30) REVERT: B 916 ASP cc_start: 0.7842 (m-30) cc_final: 0.7629 (m-30) REVERT: A 211 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.7299 (mp10) REVERT: A 323 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8666 (mtpt) REVERT: A 394 LEU cc_start: 0.9025 (mt) cc_final: 0.8797 (mt) REVERT: A 534 ARG cc_start: 0.7016 (mmt90) cc_final: 0.6610 (mmt90) REVERT: C 211 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.7836 (mp10) REVERT: C 479 SER cc_start: 0.9560 (m) cc_final: 0.9207 (p) outliers start: 60 outliers final: 49 residues processed: 386 average time/residue: 0.3003 time to fit residues: 196.3893 Evaluate side-chains 378 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 325 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 959 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1028 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 143 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 131 optimal weight: 0.7980 chunk 290 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 ASN B 661 ASN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.095074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.078335 restraints weight = 49450.668| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.55 r_work: 0.2956 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24373 Z= 0.142 Angle : 0.558 14.216 33115 Z= 0.283 Chirality : 0.042 0.159 3942 Planarity : 0.004 0.046 4198 Dihedral : 4.241 48.586 3301 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.10 % Allowed : 19.50 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.86 (0.15), residues: 3088 helix: 2.31 (0.12), residues: 1759 sheet: 0.26 (0.23), residues: 439 loop : -0.43 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 631 HIS 0.003 0.001 HIS A 582 PHE 0.023 0.001 PHE C 318 TYR 0.023 0.001 TYR A 649 ARG 0.007 0.000 ARG A 534 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 1572) hydrogen bonds : angle 4.46356 ( 4755) covalent geometry : bond 0.00328 (24373) covalent geometry : angle 0.55788 (33115) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 334 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 MET cc_start: 0.9028 (tpp) cc_final: 0.8063 (tpp) REVERT: B 357 TYR cc_start: 0.8320 (t80) cc_final: 0.8020 (t80) REVERT: B 408 ASP cc_start: 0.8702 (t70) cc_final: 0.8395 (t0) REVERT: B 412 ILE cc_start: 0.9012 (mt) cc_final: 0.8760 (mt) REVERT: B 415 GLU cc_start: 0.8080 (tp30) cc_final: 0.7669 (tp30) REVERT: B 509 PHE cc_start: 0.7781 (m-10) cc_final: 0.7038 (m-10) REVERT: B 516 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7219 (p90) REVERT: B 546 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8413 (mm) REVERT: B 627 ILE cc_start: 0.9311 (mm) cc_final: 0.9087 (pt) REVERT: B 675 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8066 (mm-30) REVERT: B 676 MET cc_start: 0.8062 (tmm) cc_final: 0.7047 (tpp) REVERT: B 885 GLN cc_start: 0.9223 (tp40) cc_final: 0.8527 (tm-30) REVERT: A 211 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: A 394 LEU cc_start: 0.8995 (mt) cc_final: 0.8755 (mt) REVERT: A 534 ARG cc_start: 0.7031 (mmt90) cc_final: 0.6677 (mmt90) REVERT: C 211 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.7818 (mp10) REVERT: C 311 MET cc_start: 0.8927 (mmm) cc_final: 0.8555 (mmm) REVERT: C 479 SER cc_start: 0.9565 (m) cc_final: 0.9219 (p) outliers start: 55 outliers final: 48 residues processed: 378 average time/residue: 0.2943 time to fit residues: 187.5696 Evaluate side-chains 375 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 323 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 1027 ASN Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 460 PHE Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1028 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 269 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 132 optimal weight: 0.0170 chunk 39 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 ASN B 661 ASN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.095138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.078567 restraints weight = 48840.302| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.55 r_work: 0.2996 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24373 Z= 0.125 Angle : 0.553 14.144 33115 Z= 0.279 Chirality : 0.041 0.172 3942 Planarity : 0.004 0.045 4198 Dihedral : 4.165 43.221 3301 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.06 % Allowed : 20.08 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 1.86 (0.15), residues: 3088 helix: 2.31 (0.12), residues: 1759 sheet: 0.20 (0.23), residues: 455 loop : -0.41 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 631 HIS 0.003 0.001 HIS B 422 PHE 0.022 0.001 PHE C 318 TYR 0.022 0.001 TYR A 649 ARG 0.007 0.000 ARG A 534 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 1572) hydrogen bonds : angle 4.42570 ( 4755) covalent geometry : bond 0.00285 (24373) covalent geometry : angle 0.55340 (33115) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10649.67 seconds wall clock time: 186 minutes 48.46 seconds (11208.46 seconds total)