Starting phenix.real_space_refine on Fri Sep 19 10:13:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vuj_43531/09_2025/8vuj_43531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vuj_43531/09_2025/8vuj_43531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vuj_43531/09_2025/8vuj_43531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vuj_43531/09_2025/8vuj_43531.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vuj_43531/09_2025/8vuj_43531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vuj_43531/09_2025/8vuj_43531.map" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 16059 2.51 5 N 4412 2.21 5 O 4607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25184 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 5691 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 33, 'TRANS': 753} Chain breaks: 2 Unresolved non-hydrogen bonds: 555 Unresolved non-hydrogen angles: 705 Unresolved non-hydrogen dihedrals: 463 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLU:plan': 24, 'GLN:plan1': 5, 'TRP:plan': 4, 'ASN:plan1': 9, 'ASP:plan': 13, 'ARG:plan': 9, 'HIS:plan': 3, 'PHE:plan': 9, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 346 Chain: "B" Number of atoms: 5498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 5498 Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 198} Link IDs: {'PTRANS': 30, 'TRANS': 750} Chain breaks: 2 Unresolved non-hydrogen bonds: 711 Unresolved non-hydrogen angles: 910 Unresolved non-hydrogen dihedrals: 593 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'HIS:plan': 4, 'ASP:plan': 22, 'ARG:plan': 6, 'GLU:plan': 26, 'GLN:plan1': 8, 'ASN:plan1': 11, 'PHE:plan': 13, 'TRP:plan': 5, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 436 Chain: "C" Number of atoms: 5457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 5457 Classifications: {'peptide': 788} Incomplete info: {'truncation_to_alanine': 215} Link IDs: {'PTRANS': 33, 'TRANS': 754} Chain breaks: 2 Unresolved non-hydrogen bonds: 804 Unresolved non-hydrogen angles: 1007 Unresolved non-hydrogen dihedrals: 671 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLU:plan': 35, 'GLN:plan1': 12, 'ASN:plan1': 14, 'TRP:plan': 5, 'ASP:plan': 17, 'ARG:plan': 14, 'HIS:plan': 4, 'PHE:plan': 9, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 491 Chain: "D" Number of atoms: 5382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 5382 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 242} Link IDs: {'PTRANS': 30, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 819 Unresolved non-hydrogen angles: 1043 Unresolved non-hydrogen dihedrals: 674 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'HIS:plan': 5, 'GLU:plan': 25, 'ARG:plan': 7, 'GLN:plan1': 8, 'ASP:plan': 28, 'ASN:plan1': 18, 'TYR:plan': 5, 'PHE:plan': 13, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 479 Chain: "H" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 867 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 110} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 773 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "L" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 792 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 102} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "M" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 724 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 102} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 53 Time building chain proxies: 6.69, per 1000 atoms: 0.27 Number of scatterers: 25184 At special positions: 0 Unit cell: (127.6, 218.9, 187, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 106 16.00 O 4607 8.00 N 4412 7.00 C 16059 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 779 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 780 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.04 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 779 " distance=2.03 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 725 " - pdb=" SG CYS D 780 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 251 " - pdb=" SG CYS I 325 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.04 Simple disulfide: pdb=" SG CYS M 251 " - pdb=" SG CYS M 320 " distance=2.03 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: 2.31 Conformation dependent library (CDL) restraints added in 845.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6680 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 43 sheets defined 36.6% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 Processing helix chain 'A' and resid 71 through 84 Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.691A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.710A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.565A pdb=" N LEU A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 237 removed outlier: 3.853A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.612A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 removed outlier: 3.512A pdb=" N SER A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.748A pdb=" N GLN A 525 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 582 removed outlier: 3.867A pdb=" N TRP A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 582 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 590 removed outlier: 3.619A pdb=" N PHE A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 598 Processing helix chain 'A' and resid 607 through 639 Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 668 through 676 Processing helix chain 'A' and resid 680 through 689 removed outlier: 3.572A pdb=" N TYR A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 704 removed outlier: 3.590A pdb=" N ASP A 704 " --> pdb=" O GLN A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 749 through 760 removed outlier: 4.288A pdb=" N LEU A 755 " --> pdb=" O GLN A 751 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 756 " --> pdb=" O ASN A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 774 Processing helix chain 'A' and resid 781 through 784 Processing helix chain 'A' and resid 785 through 797 removed outlier: 4.040A pdb=" N LEU A 791 " --> pdb=" O GLY A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 813 Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.569A pdb=" N LEU B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 90 Processing helix chain 'B' and resid 106 through 119 removed outlier: 4.053A pdb=" N ALA B 110 " --> pdb=" O GLN B 106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS B 119 " --> pdb=" O PHE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 165 Processing helix chain 'B' and resid 179 through 192 removed outlier: 3.717A pdb=" N PHE B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 184 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 220 Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.671A pdb=" N SER B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 311 removed outlier: 3.597A pdb=" N ARG B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 472 removed outlier: 3.670A pdb=" N ILE B 463 " --> pdb=" O PHE B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.869A pdb=" N TYR B 502 " --> pdb=" O GLY B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 522 removed outlier: 3.574A pdb=" N VAL B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 578 removed outlier: 3.823A pdb=" N TYR B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 591 Processing helix chain 'B' and resid 604 through 635 Processing helix chain 'B' and resid 652 through 656 Processing helix chain 'B' and resid 669 through 678 removed outlier: 3.502A pdb=" N TYR B 678 " --> pdb=" O ILE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 686 removed outlier: 3.929A pdb=" N HIS B 682 " --> pdb=" O TYR B 678 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR B 684 " --> pdb=" O TYR B 680 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR B 686 " --> pdb=" O HIS B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 703 removed outlier: 4.174A pdb=" N THR B 702 " --> pdb=" O VAL B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 721 Processing helix chain 'B' and resid 722 through 726 removed outlier: 4.195A pdb=" N LYS B 726 " --> pdb=" O GLU B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 766 Processing helix chain 'B' and resid 767 through 776 Processing helix chain 'B' and resid 787 through 789 No H-bonds generated for 'chain 'B' and resid 787 through 789' Processing helix chain 'B' and resid 790 through 814 removed outlier: 3.645A pdb=" N PHE B 814 " --> pdb=" O TRP B 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 Processing helix chain 'C' and resid 70 through 83 Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.727A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 159 removed outlier: 3.903A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.504A pdb=" N ALA C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 213 removed outlier: 4.045A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 removed outlier: 4.014A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.872A pdb=" N ILE C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 removed outlier: 3.885A pdb=" N ARG C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 261' Processing helix chain 'C' and resid 277 through 297 removed outlier: 3.945A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 327 removed outlier: 3.812A pdb=" N PHE C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 499 through 504 Processing helix chain 'C' and resid 520 through 524 Processing helix chain 'C' and resid 559 through 582 removed outlier: 3.873A pdb=" N ARG C 582 " --> pdb=" O TYR C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 596 removed outlier: 3.712A pdb=" N LEU C 596 " --> pdb=" O TRP C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 639 Processing helix chain 'C' and resid 650 through 655 Processing helix chain 'C' and resid 669 through 677 Processing helix chain 'C' and resid 681 through 688 Processing helix chain 'C' and resid 694 through 702 removed outlier: 4.458A pdb=" N ALA C 698 " --> pdb=" O SER C 694 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE C 699 " --> pdb=" O ALA C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 724 removed outlier: 3.634A pdb=" N PHE C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 763 removed outlier: 4.650A pdb=" N ASN C 752 " --> pdb=" O PRO C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 764 through 775 Processing helix chain 'C' and resid 781 through 812 removed outlier: 3.541A pdb=" N MET C 785 " --> pdb=" O THR C 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.572A pdb=" N SER D 91 " --> pdb=" O CYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.688A pdb=" N MET D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 133 removed outlier: 3.711A pdb=" N MET D 133 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 removed outlier: 3.948A pdb=" N GLN D 154 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 193 Processing helix chain 'D' and resid 213 through 221 Processing helix chain 'D' and resid 233 through 247 removed outlier: 4.026A pdb=" N SER D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 3.934A pdb=" N SER D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 258 through 263' Processing helix chain 'D' and resid 288 through 310 removed outlier: 3.722A pdb=" N LYS D 309 " --> pdb=" O SER D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 338 removed outlier: 3.929A pdb=" N PHE D 337 " --> pdb=" O THR D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 448 removed outlier: 4.527A pdb=" N GLU D 448 " --> pdb=" O SER D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 472 Processing helix chain 'D' and resid 496 through 502 Processing helix chain 'D' and resid 556 through 578 removed outlier: 3.511A pdb=" N MET D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 594 Processing helix chain 'D' and resid 605 through 634 removed outlier: 3.994A pdb=" N ILE D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 652 removed outlier: 4.384A pdb=" N ARG D 652 " --> pdb=" O LYS D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 678 removed outlier: 4.078A pdb=" N ILE D 674 " --> pdb=" O THR D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 689 removed outlier: 4.124A pdb=" N ASN D 689 " --> pdb=" O THR D 686 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 702 removed outlier: 3.531A pdb=" N THR D 702 " --> pdb=" O VAL D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 720 removed outlier: 3.833A pdb=" N TYR D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 765 Processing helix chain 'D' and resid 766 through 776 removed outlier: 3.895A pdb=" N GLU D 770 " --> pdb=" O GLY D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 814 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.197A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.932A pdb=" N ASP L 85 " --> pdb=" O LYS L 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 311 through 315 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 65 removed outlier: 3.503A pdb=" N VAL A 65 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 91 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 219 removed outlier: 3.504A pdb=" N ILE A 219 " --> pdb=" O VAL A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 340 removed outlier: 4.815A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 356 Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 367 Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 Processing sheet with id=AA7, first strand: chain 'A' and resid 409 through 412 removed outlier: 3.705A pdb=" N CYS A 455 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 434 " --> pdb=" O CYS A 455 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA9, first strand: chain 'A' and resid 710 through 712 removed outlier: 3.799A pdb=" N ILE A 540 " --> pdb=" O THR A 730 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AB2, first strand: chain 'B' and resid 124 through 125 removed outlier: 6.900A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 173 through 175 removed outlier: 3.626A pdb=" N LEU B 206 " --> pdb=" O THR B 174 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 255 through 256 removed outlier: 6.314A pdb=" N TRP B 255 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL B 279 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 364 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 409 through 410 Processing sheet with id=AB6, first strand: chain 'B' and resid 418 through 419 Processing sheet with id=AB7, first strand: chain 'C' and resid 27 through 28 removed outlier: 6.844A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 64 through 65 removed outlier: 6.960A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 91 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 194 through 196 removed outlier: 3.548A pdb=" N LEU C 195 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 248 through 249 removed outlier: 4.034A pdb=" N VAL C 249 " --> pdb=" O LEU C 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 270 through 271 removed outlier: 3.714A pdb=" N GLN C 270 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 362 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 401 through 402 removed outlier: 3.798A pdb=" N THR C 402 " --> pdb=" O HIS C 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 409 through 412 removed outlier: 3.582A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 434 " --> pdb=" O CYS C 455 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 488 through 489 removed outlier: 3.794A pdb=" N GLU C 488 " --> pdb=" O GLU C 497 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 497 " --> pdb=" O GLU C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 662 through 663 removed outlier: 6.880A pdb=" N ALA C 663 " --> pdb=" O ILE C 711 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N ASP C 713 " --> pdb=" O ALA C 663 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP C 712 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER C 737 " --> pdb=" O GLN C 536 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU C 538 " --> pdb=" O PHE C 735 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N PHE C 735 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N ILE C 540 " --> pdb=" O LEU C 733 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N LEU C 733 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N VAL C 542 " --> pdb=" O GLY C 731 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N GLY C 731 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 227 through 228 removed outlier: 6.095A pdb=" N ILE D 227 " --> pdb=" O ILE D 256 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 278 through 280 removed outlier: 3.575A pdb=" N ILE D 364 " --> pdb=" O SER D 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 342 through 343 Processing sheet with id=AD1, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AD2, first strand: chain 'D' and resid 409 through 410 removed outlier: 3.706A pdb=" N THR D 410 " --> pdb=" O TYR D 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 417 through 419 removed outlier: 3.666A pdb=" N VAL D 434 " --> pdb=" O CYS D 456 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 708 through 710 removed outlier: 4.049A pdb=" N VAL D 537 " --> pdb=" O VAL D 728 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL D 728 " --> pdb=" O VAL D 537 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.680A pdb=" N TRP H 35 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TRP H 34 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP H 99 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TRP H 106 " --> pdb=" O VAL H 100 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 39 through 40 Processing sheet with id=AD8, first strand: chain 'I' and resid 232 through 236 Processing sheet with id=AD9, first strand: chain 'I' and resid 245 through 247 removed outlier: 6.848A pdb=" N GLN I 245 " --> pdb=" O SER I 314 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER I 314 " --> pdb=" O GLN I 245 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU I 247 " --> pdb=" O LEU I 312 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU I 312 " --> pdb=" O LEU I 247 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 276 through 281 removed outlier: 5.185A pdb=" N TRP I 277 " --> pdb=" O ARG I 268 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG I 268 " --> pdb=" O TRP I 277 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY I 279 " --> pdb=" O TRP I 266 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER I 265 " --> pdb=" O ALA I 326 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA I 326 " --> pdb=" O SER I 265 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.879A pdb=" N THR L 23 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 10 through 11 removed outlier: 7.318A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'L' and resid 46 through 50 removed outlier: 6.850A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 233 through 234 Processing sheet with id=AE6, first strand: chain 'M' and resid 238 through 240 removed outlier: 7.875A pdb=" N VAL M 263 " --> pdb=" O TYR M 279 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N TYR M 279 " --> pdb=" O VAL M 263 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TRP M 265 " --> pdb=" O VAL M 277 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 238 through 240 977 hydrogen bonds defined for protein. 2784 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: 5.29 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8329 1.34 - 1.47: 6244 1.47 - 1.59: 10995 1.59 - 1.71: 0 1.71 - 1.83: 167 Bond restraints: 25735 Sorted by residual: bond pdb=" CB PRO D 57 " pdb=" CG PRO D 57 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.88e+00 bond pdb=" C GLN I 269 " pdb=" O GLN I 269 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 1.95e+00 bond pdb=" CG PRO D 57 " pdb=" CD PRO D 57 " ideal model delta sigma weight residual 1.503 1.541 -0.038 3.40e-02 8.65e+02 1.28e+00 bond pdb=" C ALA B 414 " pdb=" N PRO B 415 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.17e+00 bond pdb=" CA LYS D 270 " pdb=" CB LYS D 270 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.31e-02 5.83e+03 1.13e+00 ... (remaining 25730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 34718 2.19 - 4.38: 417 4.38 - 6.57: 58 6.57 - 8.76: 11 8.76 - 10.95: 7 Bond angle restraints: 35211 Sorted by residual: angle pdb=" C ARG D 49 " pdb=" CA ARG D 49 " pdb=" CB ARG D 49 " ideal model delta sigma weight residual 117.23 110.44 6.79 1.36e+00 5.41e-01 2.49e+01 angle pdb=" CA LYS D 270 " pdb=" CB LYS D 270 " pdb=" CG LYS D 270 " ideal model delta sigma weight residual 114.10 123.64 -9.54 2.00e+00 2.50e-01 2.28e+01 angle pdb=" C TYR B 656 " pdb=" N SER B 657 " pdb=" CA SER B 657 " ideal model delta sigma weight residual 121.80 131.92 -10.12 2.44e+00 1.68e-01 1.72e+01 angle pdb=" N ALA L 30 " pdb=" CA ALA L 30 " pdb=" C ALA L 30 " ideal model delta sigma weight residual 114.62 109.99 4.63 1.14e+00 7.69e-01 1.65e+01 angle pdb=" N GLY H 56 " pdb=" CA GLY H 56 " pdb=" C GLY H 56 " ideal model delta sigma weight residual 113.18 122.48 -9.30 2.37e+00 1.78e-01 1.54e+01 ... (remaining 35206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 13117 17.92 - 35.84: 1501 35.84 - 53.76: 424 53.76 - 71.68: 62 71.68 - 89.60: 25 Dihedral angle restraints: 15129 sinusoidal: 4771 harmonic: 10358 Sorted by residual: dihedral pdb=" CB CYS D 436 " pdb=" SG CYS D 436 " pdb=" SG CYS D 456 " pdb=" CB CYS D 456 " ideal model delta sinusoidal sigma weight residual 93.00 -177.40 -89.60 1 1.00e+01 1.00e-02 9.53e+01 dihedral pdb=" CB CYS B 87 " pdb=" SG CYS B 87 " pdb=" SG CYS B 320 " pdb=" CB CYS B 320 " ideal model delta sinusoidal sigma weight residual -86.00 -1.34 -84.66 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CB CYS D 725 " pdb=" SG CYS D 725 " pdb=" SG CYS D 780 " pdb=" CB CYS D 780 " ideal model delta sinusoidal sigma weight residual -86.00 -151.85 65.85 1 1.00e+01 1.00e-02 5.67e+01 ... (remaining 15126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2990 0.040 - 0.080: 848 0.080 - 0.119: 297 0.119 - 0.159: 20 0.159 - 0.199: 1 Chirality restraints: 4156 Sorted by residual: chirality pdb=" CA THR C 105 " pdb=" N THR C 105 " pdb=" C THR C 105 " pdb=" CB THR C 105 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CB VAL A 157 " pdb=" CA VAL A 157 " pdb=" CG1 VAL A 157 " pdb=" CG2 VAL A 157 " both_signs ideal model delta sigma weight residual False -2.63 -2.79 0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA VAL C 141 " pdb=" N VAL C 141 " pdb=" C VAL C 141 " pdb=" CB VAL C 141 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 4153 not shown) Planarity restraints: 4547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 310 " -0.014 2.00e-02 2.50e+03 2.31e-02 9.32e+00 pdb=" CG PHE B 310 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE B 310 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE B 310 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE B 310 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 310 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 310 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 56 " -0.038 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO D 57 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 57 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 57 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 265 " -0.016 2.00e-02 2.50e+03 1.34e-02 4.52e+00 pdb=" CG TRP M 265 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP M 265 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP M 265 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP M 265 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP M 265 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP M 265 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 265 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 265 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP M 265 " -0.001 2.00e-02 2.50e+03 ... (remaining 4544 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1648 2.73 - 3.27: 24911 3.27 - 3.82: 39031 3.82 - 4.36: 39056 4.36 - 4.90: 71469 Nonbonded interactions: 176115 Sorted by model distance: nonbonded pdb=" O LYS D 648 " pdb=" OH TYR D 656 " model vdw 2.190 3.040 nonbonded pdb=" O ASP D 114 " pdb=" OG SER D 118 " model vdw 2.226 3.040 nonbonded pdb=" O LEU H 20 " pdb=" OG SER H 80 " model vdw 2.239 3.040 nonbonded pdb=" O THR H 91 " pdb=" OG1 THR H 91 " model vdw 2.251 3.040 nonbonded pdb=" OG SER D 118 " pdb=" OG SER D 142 " model vdw 2.256 3.040 ... (remaining 176110 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 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 46 or (resid 47 through 49 and (na \ me N or name CA or name C or name O or name CB )) or resid 50 through 54 or (res \ id 55 through 60 and (name N or name CA or name C or name O or name CB )) or res \ id 61 through 62 or (resid 63 through 66 and (name N or name CA or name C or nam \ e O or name CB )) or resid 67 through 80 or (resid 81 and (name N or name CA or \ name C or name O or name CB )) or resid 82 or (resid 83 and (name N or name CA o \ r name C or name O or name CB )) or resid 84 through 85 or (resid 86 and (name N \ or name CA or name C or name O or name CB )) or resid 87 through 152 or (resid \ 153 and (name N or name CA or name C or name O or name CB )) or resid 154 throug \ h 182 or (resid 183 and (name N or name CA or name C or name O or name CB )) or \ resid 184 or (resid 185 through 188 and (name N or name CA or name C or name O o \ r name CB )) or resid 189 or (resid 190 through 193 and (name N or name CA or na \ me C or name O or name CB )) or resid 194 through 208 or (resid 209 and (name N \ or name CA or name C or name O or name CB )) or resid 210 through 214 or (resid \ 215 through 216 and (name N or name CA or name C or name O or name CB )) or resi \ d 217 through 251 or (resid 252 through 253 and (name N or name CA or name C or \ name O or name CB )) or resid 254 through 259 or (resid 260 and (name N or name \ CA or name C or name O or name CB )) or resid 261 through 274 or (resid 275 and \ (name N or name CA or name C or name O or name CB )) or resid 276 through 293 or \ (resid 294 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 5 through 305 or (resid 306 and (name N or name CA or name C or name O or name C \ B )) or resid 307 through 308 or (resid 309 and (name N or name CA or name C or \ name O or name CB )) or resid 310 through 315 or (resid 316 and (name N or name \ CA or name C or name O or name CB )) or resid 317 through 328 or (resid 329 and \ (name N or name CA or name C or name O or name CB )) or resid 330 through 336 or \ (resid 337 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 8 through 353 or (resid 354 and (name N or name CA or name C or name O or name C \ B )) or resid 355 through 357 or resid 359 or (resid 360 and (name N or name CA \ or name C or name O or name CB )) or resid 361 through 362 or (resid 363 and (na \ me N or name CA or name C or name O or name CB )) or resid 364 through 370 or (r \ esid 371 and (name N or name CA or name C or name O or name CB )) or resid 372 t \ hrough 375 or (resid 376 and (name N or name CA or name C or name O or name CB ) \ ) or resid 377 through 384 or (resid 385 and (name N or name CA or name C or nam \ e O or name CB )) or resid 386 or (resid 387 through 388 and (name N or name CA \ or name C or name O or name CB )) or resid 389 or (resid 390 and (name N or name \ CA or name C or name O or name CB )) or resid 391 through 393 or (resid 394 and \ (name N or name CA or name C or name O or name CB )) or resid 395 through 411 o \ r (resid 412 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 13 through 414 or (resid 415 through 417 and (name N or name CA or name C or nam \ e O or name CB )) or resid 418 through 420 or (resid 421 through 423 and (name N \ or name CA or name C or name O or name CB )) or resid 424 through 425 or (resid \ 426 through 427 and (name N or name CA or name C or name O or name CB )) or res \ id 428 through 440 or (resid 441 through 443 and (name N or name CA or name C or \ name O or name CB )) or resid 444 through 445 or (resid 446 and (name N or name \ CA or name C or name O or name CB )) or resid 447 through 449 or (resid 450 and \ (name N or name CA or name C or name O or name CB )) or resid 451 through 464 o \ r (resid 465 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 66 through 487 or (resid 488 through 489 and (name N or name CA or name C or nam \ e O or name CB )) or resid 490 or (resid 491 through 492 and (name N or name CA \ or name C or name O or name CB )) or resid 493 through 510 or (resid 511 and (na \ me N or name CA or name C or name O or name CB )) or resid 512 through 535 or (r \ esid 536 and (name N or name CA or name C or name O or name CB )) or resid 537 t \ hrough 542 or (resid 543 and (name N or name CA or name C or name O or name CB ) \ ) or resid 544 through 550 or (resid 551 through 556 and (name N or name CA or n \ ame C or name O or name CB )) or resid 557 through 572 or (resid 573 through 582 \ and (name N or name CA or name C or name O or name CB )) or resid 583 or (resid \ 584 through 592 and (name N or name CA or name C or name O or name CB )) or res \ id 593 through 606 or (resid 607 through 613 and (name N or name CA or name C or \ name O or name CB )) or (resid 614 through 628 and (name N or name CA or name C \ or name O or name CB )) or resid 629 through 630 or (resid 631 through 640 and \ (name N or name CA or name C or name O or name CB )) or resid 641 through 644 or \ (resid 645 through 646 and (name N or name CA or name C or name O or name CB )) \ or resid 647 through 656 or (resid 657 through 659 and (name N or name CA or na \ me C or name O or name CB )) or resid 660 through 663 or (resid 664 through 667 \ and (name N or name CA or name C or name O or name CB )) or resid 668 through 67 \ 4 or (resid 675 and (name N or name CA or name C or name O or name CB )) or resi \ d 676 through 686 or (resid 687 through 688 and (name N or name CA or name C or \ name O or name CB )) or resid 689 through 704 or (resid 705 and (name N or name \ CA or name C or name O or name CB )) or resid 706 through 712 or (resid 713 and \ (name N or name CA or name C or name O or name CB )) or resid 714 through 722 or \ (resid 723 through 724 and (name N or name CA or name C or name O or name CB )) \ or resid 725 through 731 or (resid 732 and (name N or name CA or name C or name \ O or name CB )) or resid 733 through 744 or (resid 745 through 746 and (name N \ or name CA or name C or name O or name CB )) or resid 747 through 750 or (resid \ 751 and (name N or name CA or name C or name O or name CB )) or resid 752 throug \ h 761 or (resid 762 and (name N or name CA or name C or name O or name CB )) or \ resid 763 through 767 or (resid 768 and (name N or name CA or name C or name O o \ r name CB )) or resid 769 through 802 or (resid 803 through 813 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 27 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 169 or (resid 170 and (name N or n \ ame CA or name C or name O or name CB )) or resid 171 through 197 or (resid 198 \ and (name N or name CA or name C or name O or name CB )) or resid 199 through 21 \ 2 or (resid 213 and (name N or name CA or name C or name O or name CB )) or resi \ d 214 through 258 or (resid 259 through 260 and (name N or name CA or name C or \ name O or name CB )) or resid 261 through 298 or (resid 299 through 300 and (nam \ e N or name CA or name C or name O or name CB )) or resid 301 through 322 or (re \ sid 323 and (name N or name CA or name C or name O or name CB )) or resid 324 th \ rough 357 or resid 359 through 447 or (resid 448 through 450 and (name N or name \ CA or name C or name O or name CB )) or resid 451 through 494 or (resid 495 and \ (name N or name CA or name C or name O or name CB )) or resid 496 through 560 o \ r (resid 561 through 566 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 567 through 582 and (name N or name CA or name C or name O or name C \ B )) or resid 583 through 584 or (resid 585 through 592 and (name N or name CA o \ r name C or name O or name CB )) or (resid 593 through 598 and (name N or name C \ A or name C or name O or name CB )) or resid 599 through 611 or (resid 612 throu \ gh 613 and (name N or name CA or name C or name O or name CB )) or (resid 614 th \ rough 628 and (name N or name CA or name C or name O or name CB )) or resid 629 \ through 631 or (resid 632 through 640 and (name N or name CA or name C or name O \ or name CB )) or resid 641 through 643 or (resid 644 through 646 and (name N or \ name CA or name C or name O or name CB )) or resid 647 through 723 or (resid 72 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 725 through \ 729 or (resid 730 and (name N or name CA or name C or name O or name CB )) or re \ sid 731 through 813)) } ncs_group { reference = (chain 'B' and (resid 35 through 42 or (resid 43 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 75 or (resid 76 through \ 78 and (name N or name CA or name C or name O or name CB )) or resid 79 through \ 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or (re \ sid 92 through 96 and (name N or name CA or name C or name O or name CB )) or re \ sid 97 through 104 or (resid 105 through 108 and (name N or name CA or name C or \ name O or name CB )) or resid 109 through 113 or (resid 114 and (name N or name \ CA or name C or name O or name CB )) or resid 115 through 132 or (resid 133 and \ (name N or name CA or name C or name O or name CB )) or resid 134 through 136 o \ r (resid 137 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 38 or (resid 139 and (name N or name CA or name C or name O or name CB )) or res \ id 140 through 192 or (resid 193 and (name N or name CA or name C or name O or n \ ame CB )) or resid 194 through 198 or (resid 199 and (name N or name CA or name \ C or name O or name CB )) or resid 200 through 201 or (resid 202 and (name N or \ name CA or name C or name O or name CB )) or resid 203 through 206 or (resid 207 \ through 209 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 10 through 213 or (resid 214 and (name N or name CA or name C or name O or name \ CB )) or resid 215 through 263 or (resid 264 and (name N or name CA or name C or \ name O or name CB )) or resid 265 through 270 or (resid 271 and (name N or name \ CA or name C or name O or name CB )) or resid 272 through 284 or (resid 285 and \ (name N or name CA or name C or name O or name CB )) or resid 286 or (resid 287 \ and (name N or name CA or name C or name O or name CB )) or resid 288 through 3 \ 03 or (resid 304 through 309 and (name N or name CA or name C or name O or name \ CB )) or resid 310 or (resid 311 and (name N or name CA or name C or name O or n \ ame CB )) or resid 312 through 316 or (resid 317 through 319 and (name N or name \ CA or name C or name O or name CB )) or resid 320 or (resid 321 and (name N or \ name CA or name C or name O or name CB )) or resid 322 through 330 or (resid 331 \ through 333 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 34 through 338 or (resid 339 and (name N or name CA or name C or name O or name \ CB )) or resid 340 through 367 or (resid 368 through 369 and (name N or name CA \ or name C or name O or name CB )) or resid 370 or (resid 371 and (name N or name \ CA or name C or name O or name CB )) or resid 372 through 381 or (resid 382 and \ (name N or name CA or name C or name O or name CB )) or resid 383 through 388 o \ r (resid 389 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 90 through 394 or (resid 395 and (name N or name CA or name C or name O or name \ CB )) or resid 396 through 398 or (resid 399 through 400 and (name N or name CA \ or name C or name O or name CB )) or resid 401 through 411 or (resid 412 through \ 414 and (name N or name CA or name C or name O or name CB )) or resid 415 throu \ gh 424 or (resid 425 through 428 and (name N or name CA or name C or name O or n \ ame CB )) or resid 429 through 430 or (resid 431 and (name N or name CA or name \ C or name O or name CB )) or resid 432 through 437 or (resid 438 and (name N or \ name CA or name C or name O or name CB )) or resid 439 or (resid 440 through 448 \ and (name N or name CA or name C or name O or name CB )) or resid 449 or (resid \ 450 and (name N or name CA or name C or name O or name CB )) or resid 451 throu \ gh 469 or (resid 470 and (name N or name CA or name C or name O or name CB )) or \ resid 471 through 480 or (resid 481 through 482 and (name N or name CA or name \ C or name O or name CB )) or resid 483 or (resid 484 and (name N or name CA or n \ ame C or name O or name CB )) or resid 485 through 510 or (resid 511 and (name N \ or name CA or name C or name O or name CB )) or resid 512 through 515 or (resid \ 516 and (name N or name CA or name C or name O or name CB )) or resid 517 throu \ gh 519 or (resid 520 and (name N or name CA or name C or name O or name CB )) or \ resid 521 through 522 or (resid 523 and (name N or name CA or name C or name O \ or name CB )) or resid 524 or (resid 525 and (name N or name CA or name C or nam \ e O or name CB )) or resid 526 through 537 or (resid 538 and (name N or name CA \ or name C or name O or name CB )) or resid 539 through 540 or (resid 541 and (na \ me N or name CA or name C or name O or name CB )) or resid 542 through 579 or (r \ esid 580 through 581 and (name N or name CA or name C or name O or name CB )) or \ (resid 582 through 587 and (name N or name CA or name C or name O or name CB )) \ or resid 588 through 590 or (resid 591 through 597 and (name N or name CA or na \ me C or name O or name CB )) or resid 598 through 606 or (resid 607 through 609 \ and (name N or name CA or name C or name O or name CB )) or resid 610 through 61 \ 8 or (resid 619 through 621 and (name N or name CA or name C or name O or name C \ B )) or resid 622 through 624 or (resid 625 and (name N or name CA or name C or \ name O or name CB )) or resid 626 through 627 or (resid 628 through 633 and (nam \ e N or name CA or name C or name O or name CB )) or resid 634 through 640 or (re \ sid 641 through 643 and (name N or name CA or name C or name O or name CB )) or \ resid 644 or (resid 645 through 649 and (name N or name CA or name C or name O o \ r name CB )) or resid 650 through 663 or (resid 664 through 665 and (name N or n \ ame CA or name C or name O or name CB )) or resid 666 through 669 or (resid 670 \ through 671 and (name N or name CA or name C or name O or name CB )) or resid 67 \ 2 through 674 or (resid 675 through 677 and (name N or name CA or name C or name \ O or name CB )) or resid 678 through 682 or (resid 683 and (name N or name CA o \ r name C or name O or name CB )) or resid 684 through 685 or (resid 686 through \ 687 and (name N or name CA or name C or name O or name CB )) or resid 688 throug \ h 710 or (resid 711 through 713 and (name N or name CA or name C or name O or na \ me CB )) or resid 714 through 733 or (resid 734 and (name N or name CA or name C \ or name O or name CB )) or resid 735 through 766 or (resid 767 and (name N or n \ ame CA or name C or name O or name CB )) or resid 768 through 771 or (resid 772 \ through 774 and (name N or name CA or name C or name O or name CB )) or resid 77 \ 5 through 780 or (resid 781 through 791 and (name N or name CA or name C or name \ O or name CB )) or resid 792 through 793 or (resid 794 through 814 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 35 through 44 or (resid 45 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 103 or (resid 104 throu \ gh 108 and (name N or name CA or name C or name O or name CB )) or resid 109 thr \ ough 149 or (resid 150 and (name N or name CA or name C or name O or name CB )) \ or resid 151 through 181 or (resid 182 and (name N or name CA or name C or name \ O or name CB )) or resid 183 through 210 or (resid 211 and (name N or name CA or \ name C or name O or name CB )) or resid 212 through 223 or (resid 224 and (name \ N or name CA or name C or name O or name CB )) or resid 225 through 233 or (res \ id 234 through 236 and (name N or name CA or name C or name O or name CB )) or r \ esid 237 through 241 or (resid 242 through 243 and (name N or name CA or name C \ or name O or name CB )) or resid 244 through 282 or (resid 283 and (name N or na \ me CA or name C or name O or name CB )) or resid 284 through 325 or (resid 326 a \ nd (name N or name CA or name C or name O or name CB )) or resid 327 through 343 \ or (resid 344 and (name N or name CA or name C or name O or name CB )) or resid \ 345 through 351 or (resid 352 through 353 and (name N or name CA or name C or n \ ame O or name CB )) or resid 354 through 412 or (resid 413 through 414 and (name \ N or name CA or name C or name O or name CB )) or resid 415 through 427 or (res \ id 428 and (name N or name CA or name C or name O or name CB )) or resid 429 thr \ ough 471 or (resid 472 and (name N or name CA or name C or name O or name CB )) \ or resid 473 or (resid 474 and (name N or name CA or name C or name O or name CB \ )) or resid 475 through 535 or (resid 536 and (name N or name CA or name C or n \ ame O or name CB )) or resid 537 through 553 or (resid 554 through 581 and (name \ N or name CA or name C or name O or name CB )) or resid 582 through 616 or (res \ id 617 through 621 and (name N or name CA or name C or name O or name CB )) or r \ esid 622 through 651 or (resid 652 and (name N or name CA or name C or name O or \ name CB )) or resid 653 through 655 or (resid 656 through 657 and (name N or na \ me CA or name C or name O or name CB )) or resid 658 through 670 or (resid 671 a \ nd (name N or name CA or name C or name O or name CB )) or resid 672 through 689 \ or (resid 690 through 691 and (name N or name CA or name C or name O or name CB \ )) or (resid 692 through 696 and (name N or name CA or name C or name O or name \ CB )) or resid 697 through 700 or (resid 701 through 702 and (name N or name CA \ or name C or name O or name CB )) or resid 703 through 704 or (resid 705 throug \ h 707 and (name N or name CA or name C or name O or name CB )) or resid 708 thro \ ugh 752 or (resid 753 and (name N or name CA or name C or name O or name CB )) o \ r resid 754 through 773 or (resid 774 and (name N or name CA or name C or name O \ or name CB )) or resid 775 through 776 or (resid 777 and (name N or name CA or \ name C or name O or name CB )) or resid 778 or (resid 779 and (name N or name CA \ or name C or name O or name CB )) or resid 780 through 781 or (resid 782 throug \ h 791 and (name N or name CA or name C or name O or name CB )) or resid 792 thro \ ugh 794 or (resid 795 through 814 and (name N or name CA or name C or name O or \ name CB )))) } ncs_group { reference = (chain 'H' and ((resid 2 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 10 or (resid 11 through 13 and (name N or name CA \ or name C or name O or name CB )) or resid 14 or (resid 15 through 16 and (name \ N or name CA or name C or name O or name CB )) or resid 17 or (resid 18 through \ 21 and (name N or name CA or name C or name O or name CB )) or resid 22 or (res \ id 23 through 25 and (name N or name CA or name C or name O or name CB )) or res \ id 26 through 27 or (resid 28 through 32 and (name N or name CA or name C or nam \ e O or name CB )) or resid 33 through 35 or (resid 36 and (name N or name CA or \ name C or name O or name CB )) or resid 37 or (resid 38 and (name N or name CA o \ r name C or name O or name CB )) or resid 39 or (resid 40 and (name N or name CA \ or name C or name O or name CB )) or resid 41 through 43 or (resid 44 and (name \ N or name CA or name C or name O or name CB )) or resid 45 through 62 or (resid \ 63 through 65 and (name N or name CA or name C or name O or name CB )) or resid \ 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or res \ id 68 through 72 or (resid 73 and (name N or name CA or name C or name O or name \ CB )) or resid 74 through 75 or (resid 76 and (name N or name CA or name C or n \ ame O or name CB )) or resid 77 through 81 or (resid 82 through 93 and (name N o \ r name CA or name C or name O or name CB )) or resid 94 through 103 or (resid 10 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 105 through \ 113 or (resid 114 through 118 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'I' and (resid 231 through 241 or (resid 242 and (name N or name CA or na \ me C or name O or name CB )) or resid 243 through 275 or (resid 276 and (name N \ or name CA or name C or name O or name CB )) or resid 277 through 336 or (resid \ 337 and (name N or name CA or name C or name O or name CB )) or resid 338 throug \ h 347)) } ncs_group { reference = (chain 'L' and (resid 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name O or name CB )) or resid 4 or (resid 5 through 6 and (name N or name CA o \ r name C or name O or name CB )) or resid 7 or (resid 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 28 or (resid 29 through 30 a \ nd (name N or name CA or name C or name O or name CB )) or resid 31 through 54 o \ r (resid 55 and (name N or name CA or name C or name O or name CB )) or resid 56 \ or (resid 57 and (name N or name CA or name C or name O or name CB )) or resid \ 58 or (resid 59 and (name N or name CA or name C or name O or name CB )) or resi \ d 60 through 61 or (resid 62 and (name N or name CA or name C or name O or name \ CB )) or resid 63 through 67 or (resid 68 and (name N or name CA or name C or na \ me O or name CB )) or resid 69 through 70 or (resid 71 and (name N or name CA or \ name C or name O or name CB )) or resid 72 through 75 or (resid 76 and (name N \ or name CA or name C or name O or name CB )) or resid 77 or (resid 78 and (name \ N or name CA or name C or name O or name CB )) or resid 79 through 80 or (resid \ 81 through 84 and (name N or name CA or name C or name O or name CB )) or resid \ 85 or (resid 86 through 88 and (name N or name CA or name C or name O or name CB \ )) or resid 89 through 91 or (resid 92 and (name N or name CA or name C or name \ O or name CB )) or resid 93 through 94 or (resid 95 and (name N or name CA or n \ ame C or name O or name CB )) or resid 96 through 98 or (resid 99 and (name N or \ name CA or name C or name O or name CB )) or resid 100 through 104 or (resid 10 \ 5 through 106 and (name N or name CA or name C or name O or name CB )) or resid \ 107 through 109)) selection = (chain 'M' and (resid 230 through 280 or (resid 281 through 284 and (name N or n \ ame CA or name C or name O or name CB )) or resid 285 through 289 or (resid 290 \ through 291 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 2 through 338)) } 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 group one per residue 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: 6.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.310 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.002 0.085 25755 Z= 0.108 Angle : 0.585 10.947 35251 Z= 0.300 Chirality : 0.041 0.199 4156 Planarity : 0.003 0.057 4547 Dihedral : 16.846 89.424 8389 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.08 % Favored : 88.61 % Rotamer: Outliers : 0.40 % Allowed : 41.25 % Favored : 58.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.15), residues: 3556 helix: 2.10 (0.16), residues: 1140 sheet: -1.71 (0.25), residues: 491 loop : -2.42 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 36 TYR 0.015 0.001 TYR B 321 PHE 0.052 0.001 PHE B 310 TRP 0.036 0.001 TRP M 265 HIS 0.002 0.000 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00239 (25735) covalent geometry : angle 0.58406 (35211) SS BOND : bond 0.00270 ( 20) SS BOND : angle 1.07269 ( 40) hydrogen bonds : bond 0.16978 ( 973) hydrogen bonds : angle 5.98015 ( 2784) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 239 time to evaluate : 1.034 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 245 average time/residue: 0.1440 time to fit residues: 60.9491 Evaluate side-chains 242 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 235 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain I residue 289 TYR Chi-restraints excluded: chain L residue 32 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0170 chunk 155 optimal weight: 50.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 1.9990 overall best weight: 1.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 357 GLN I 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.132413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.096615 restraints weight = 59605.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.092734 restraints weight = 49701.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.093925 restraints weight = 51409.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094270 restraints weight = 44628.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094319 restraints weight = 40592.454| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25755 Z= 0.147 Angle : 0.582 10.017 35251 Z= 0.302 Chirality : 0.042 0.189 4156 Planarity : 0.004 0.051 4547 Dihedral : 4.678 58.525 3798 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.18 % Favored : 87.51 % Rotamer: Outliers : 5.07 % Allowed : 36.40 % Favored : 58.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.15), residues: 3556 helix: 2.26 (0.16), residues: 1166 sheet: -1.83 (0.24), residues: 519 loop : -2.46 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 654 TYR 0.014 0.001 TYR A 367 PHE 0.014 0.001 PHE C 533 TRP 0.013 0.001 TRP C 315 HIS 0.004 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00343 (25735) covalent geometry : angle 0.58125 (35211) SS BOND : bond 0.00307 ( 20) SS BOND : angle 1.16091 ( 40) hydrogen bonds : bond 0.03750 ( 973) hydrogen bonds : angle 4.53873 ( 2784) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 239 time to evaluate : 0.976 Fit side-chains REVERT: B 410 THR cc_start: 0.9405 (t) cc_final: 0.9068 (m) REVERT: C 226 ASP cc_start: 0.8605 (m-30) cc_final: 0.8022 (t0) REVERT: H 2 LEU cc_start: 0.8350 (pt) cc_final: 0.7822 (pp) REVERT: H 73 ASP cc_start: 0.8361 (t0) cc_final: 0.8136 (t0) REVERT: L 33 TYR cc_start: 0.7138 (OUTLIER) cc_final: 0.6633 (p90) REVERT: M 336 LEU cc_start: 0.3903 (OUTLIER) cc_final: 0.3688 (pt) outliers start: 113 outliers final: 58 residues processed: 338 average time/residue: 0.1396 time to fit residues: 80.9088 Evaluate side-chains 294 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 234 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 734 TYR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 779 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 289 TYR Chi-restraints excluded: chain L residue 8 HIS Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 252 THR Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 337 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 39 optimal weight: 6.9990 chunk 279 optimal weight: 0.0570 chunk 188 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 69 optimal weight: 0.0030 chunk 324 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 261 optimal weight: 9.9990 chunk 165 optimal weight: 0.0980 chunk 240 optimal weight: 2.9990 chunk 208 optimal weight: 40.0000 overall best weight: 0.6110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 286 ASN ** I 341 GLN ** 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 = 0.4001 r_free = 0.4001 target = 0.133866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.100539 restraints weight = 59643.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.099424 restraints weight = 60797.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.100097 restraints weight = 48257.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.099515 restraints weight = 35710.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.099676 restraints weight = 36975.192| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25755 Z= 0.104 Angle : 0.559 12.725 35251 Z= 0.284 Chirality : 0.041 0.183 4156 Planarity : 0.003 0.050 4547 Dihedral : 4.524 55.500 3795 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.55 % Favored : 89.12 % Rotamer: Outliers : 5.70 % Allowed : 35.28 % Favored : 59.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.15), residues: 3556 helix: 2.32 (0.16), residues: 1167 sheet: -1.90 (0.23), residues: 509 loop : -2.40 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 654 TYR 0.015 0.001 TYR B 684 PHE 0.017 0.001 PHE A 152 TRP 0.014 0.001 TRP C 315 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00233 (25735) covalent geometry : angle 0.55737 (35211) SS BOND : bond 0.00281 ( 20) SS BOND : angle 1.22998 ( 40) hydrogen bonds : bond 0.03164 ( 973) hydrogen bonds : angle 4.25089 ( 2784) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 250 time to evaluate : 0.929 Fit side-chains REVERT: B 138 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7623 (mmtp) REVERT: B 221 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8200 (pttm) REVERT: B 410 THR cc_start: 0.9308 (t) cc_final: 0.9028 (m) REVERT: C 226 ASP cc_start: 0.8581 (m-30) cc_final: 0.8067 (t0) REVERT: C 315 TRP cc_start: 0.7722 (OUTLIER) cc_final: 0.7181 (p-90) REVERT: H 2 LEU cc_start: 0.8349 (pt) cc_final: 0.7824 (pp) REVERT: H 73 ASP cc_start: 0.8034 (t0) cc_final: 0.7812 (t0) outliers start: 127 outliers final: 70 residues processed: 362 average time/residue: 0.1439 time to fit residues: 88.8052 Evaluate side-chains 310 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 237 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 734 TYR Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 678 TYR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 289 TYR Chi-restraints excluded: chain L residue 8 HIS Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 252 THR Chi-restraints excluded: chain M residue 296 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 280 optimal weight: 4.9990 chunk 226 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 153 optimal weight: 40.0000 chunk 309 optimal weight: 40.0000 chunk 79 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 chunk 316 optimal weight: 0.0270 chunk 190 optimal weight: 0.6980 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.132704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.097132 restraints weight = 59405.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.093134 restraints weight = 54451.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.094222 restraints weight = 52851.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.094489 restraints weight = 46109.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.094666 restraints weight = 42066.801| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25755 Z= 0.134 Angle : 0.573 10.159 35251 Z= 0.293 Chirality : 0.042 0.190 4156 Planarity : 0.003 0.050 4547 Dihedral : 4.574 58.310 3795 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.84 % Favored : 87.80 % Rotamer: Outliers : 6.69 % Allowed : 34.52 % Favored : 58.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.15), residues: 3556 helix: 2.33 (0.16), residues: 1169 sheet: -1.99 (0.23), residues: 508 loop : -2.42 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 124 TYR 0.015 0.001 TYR B 684 PHE 0.014 0.001 PHE A 472 TRP 0.015 0.001 TRP M 265 HIS 0.004 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00317 (25735) covalent geometry : angle 0.57158 (35211) SS BOND : bond 0.00299 ( 20) SS BOND : angle 1.25137 ( 40) hydrogen bonds : bond 0.03300 ( 973) hydrogen bonds : angle 4.18556 ( 2784) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 242 time to evaluate : 0.875 Fit side-chains REVERT: B 410 THR cc_start: 0.9320 (t) cc_final: 0.9023 (m) REVERT: C 226 ASP cc_start: 0.8692 (m-30) cc_final: 0.8088 (t0) REVERT: C 315 TRP cc_start: 0.7864 (OUTLIER) cc_final: 0.7250 (p-90) REVERT: C 495 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6951 (mtmm) REVERT: H 2 LEU cc_start: 0.8315 (pt) cc_final: 0.7832 (pp) REVERT: H 39 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7106 (ttm-80) REVERT: H 73 ASP cc_start: 0.8353 (t0) cc_final: 0.8028 (t0) REVERT: L 33 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.6590 (p90) outliers start: 149 outliers final: 106 residues processed: 376 average time/residue: 0.1246 time to fit residues: 80.5411 Evaluate side-chains 345 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 235 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 631 ASN Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 734 TYR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 289 TYR Chi-restraints excluded: chain L residue 8 HIS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 252 THR Chi-restraints excluded: chain M residue 296 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 39 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 216 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 295 optimal weight: 4.9990 chunk 342 optimal weight: 6.9990 chunk 226 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.131637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.096185 restraints weight = 59363.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.092550 restraints weight = 52501.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.093063 restraints weight = 52031.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.093666 restraints weight = 46329.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.093775 restraints weight = 42182.547| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25755 Z= 0.164 Angle : 0.602 10.120 35251 Z= 0.307 Chirality : 0.043 0.196 4156 Planarity : 0.004 0.068 4547 Dihedral : 4.718 55.467 3795 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.06 % Favored : 87.51 % Rotamer: Outliers : 7.18 % Allowed : 34.47 % Favored : 58.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.15), residues: 3556 helix: 2.32 (0.16), residues: 1171 sheet: -2.18 (0.23), residues: 518 loop : -2.44 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 518 TYR 0.017 0.001 TYR B 684 PHE 0.019 0.001 PHE A 152 TRP 0.016 0.001 TRP M 265 HIS 0.004 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00391 (25735) covalent geometry : angle 0.60059 (35211) SS BOND : bond 0.00290 ( 20) SS BOND : angle 1.38583 ( 40) hydrogen bonds : bond 0.03559 ( 973) hydrogen bonds : angle 4.18963 ( 2784) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 233 time to evaluate : 0.745 Fit side-chains REVERT: A 208 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8191 (mp) REVERT: A 240 MET cc_start: 0.8699 (mmm) cc_final: 0.8153 (tpp) REVERT: B 334 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8119 (pp) REVERT: B 337 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.6920 (t80) REVERT: C 226 ASP cc_start: 0.8704 (m-30) cc_final: 0.8120 (t0) REVERT: C 315 TRP cc_start: 0.7921 (OUTLIER) cc_final: 0.7278 (p-90) REVERT: C 495 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6993 (mtmm) REVERT: D 768 MET cc_start: 0.8448 (mpp) cc_final: 0.8231 (mpp) REVERT: H 2 LEU cc_start: 0.8371 (pt) cc_final: 0.7899 (pp) REVERT: H 73 ASP cc_start: 0.8265 (t0) cc_final: 0.7948 (t0) REVERT: L 33 TYR cc_start: 0.7092 (OUTLIER) cc_final: 0.6650 (p90) outliers start: 160 outliers final: 123 residues processed: 379 average time/residue: 0.1284 time to fit residues: 83.3796 Evaluate side-chains 353 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 224 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 631 ASN Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 355 TYR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 734 TYR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 678 TYR Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 779 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 289 TYR Chi-restraints excluded: chain L residue 8 HIS Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 252 THR Chi-restraints excluded: chain M residue 296 ILE Chi-restraints excluded: chain M residue 337 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 93 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 324 optimal weight: 9.9990 chunk 165 optimal weight: 0.0980 chunk 337 optimal weight: 0.7980 chunk 294 optimal weight: 30.0000 chunk 317 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 331 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.133107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.097763 restraints weight = 59701.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.093637 restraints weight = 53781.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.094123 restraints weight = 54121.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.094494 restraints weight = 48727.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.094675 restraints weight = 45292.627| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25755 Z= 0.112 Angle : 0.568 10.068 35251 Z= 0.289 Chirality : 0.042 0.185 4156 Planarity : 0.003 0.054 4547 Dihedral : 4.616 53.984 3795 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.14 % Favored : 88.50 % Rotamer: Outliers : 6.28 % Allowed : 35.50 % Favored : 58.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.15), residues: 3556 helix: 2.36 (0.16), residues: 1169 sheet: -2.07 (0.23), residues: 509 loop : -2.42 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 518 TYR 0.012 0.001 TYR B 684 PHE 0.011 0.001 PHE C 533 TRP 0.018 0.001 TRP M 265 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00263 (25735) covalent geometry : angle 0.56700 (35211) SS BOND : bond 0.00238 ( 20) SS BOND : angle 1.35069 ( 40) hydrogen bonds : bond 0.03035 ( 973) hydrogen bonds : angle 4.04418 ( 2784) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 236 time to evaluate : 0.847 Fit side-chains REVERT: A 208 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8173 (mp) REVERT: B 337 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.6814 (t80) REVERT: C 226 ASP cc_start: 0.8674 (m-30) cc_final: 0.8099 (t0) REVERT: C 315 TRP cc_start: 0.7875 (OUTLIER) cc_final: 0.7226 (p-90) REVERT: H 2 LEU cc_start: 0.8319 (pt) cc_final: 0.7845 (pp) REVERT: H 73 ASP cc_start: 0.8396 (t0) cc_final: 0.8048 (t0) REVERT: L 33 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6640 (p90) outliers start: 140 outliers final: 111 residues processed: 364 average time/residue: 0.1353 time to fit residues: 85.7193 Evaluate side-chains 345 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 230 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 631 ASN Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 355 TYR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 734 TYR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 678 TYR Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 289 TYR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 252 THR Chi-restraints excluded: chain M residue 296 ILE Chi-restraints excluded: chain M residue 337 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 325 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 197 optimal weight: 9.9990 chunk 127 optimal weight: 0.4980 chunk 322 optimal weight: 0.0170 chunk 330 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 214 optimal weight: 20.0000 chunk 282 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 341 GLN ** 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 = 0.4000 r_free = 0.4000 target = 0.133752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.098929 restraints weight = 59161.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.094865 restraints weight = 51828.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.095889 restraints weight = 53171.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.096448 restraints weight = 44454.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.096464 restraints weight = 40564.342| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 25755 Z= 0.103 Angle : 0.565 10.039 35251 Z= 0.286 Chirality : 0.042 0.191 4156 Planarity : 0.003 0.050 4547 Dihedral : 4.543 51.595 3795 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.88 % Favored : 88.78 % Rotamer: Outliers : 6.37 % Allowed : 35.46 % Favored : 58.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.15), residues: 3556 helix: 2.40 (0.16), residues: 1168 sheet: -2.01 (0.24), residues: 490 loop : -2.38 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 55 TYR 0.012 0.001 TYR C 776 PHE 0.025 0.001 PHE A 152 TRP 0.020 0.001 TRP M 265 HIS 0.003 0.000 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00240 (25735) covalent geometry : angle 0.56302 (35211) SS BOND : bond 0.00238 ( 20) SS BOND : angle 1.51907 ( 40) hydrogen bonds : bond 0.02842 ( 973) hydrogen bonds : angle 3.94257 ( 2784) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 248 time to evaluate : 1.024 Fit side-chains REVERT: B 337 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.6672 (t80) REVERT: C 226 ASP cc_start: 0.8677 (m-30) cc_final: 0.8081 (t0) REVERT: C 315 TRP cc_start: 0.7796 (OUTLIER) cc_final: 0.7159 (p-90) REVERT: H 2 LEU cc_start: 0.8330 (pt) cc_final: 0.7849 (pp) REVERT: H 73 ASP cc_start: 0.8332 (t0) cc_final: 0.7985 (t0) REVERT: L 33 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.6597 (p90) REVERT: M 264 GLN cc_start: 0.8296 (pm20) cc_final: 0.7798 (mm-40) outliers start: 142 outliers final: 116 residues processed: 373 average time/residue: 0.1396 time to fit residues: 89.6317 Evaluate side-chains 357 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 238 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 631 ASN Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 734 TYR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 678 TYR Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 289 TYR Chi-restraints excluded: chain L residue 8 HIS Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 252 THR Chi-restraints excluded: chain M residue 296 ILE Chi-restraints excluded: chain M residue 337 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 124 optimal weight: 0.4980 chunk 309 optimal weight: 40.0000 chunk 113 optimal weight: 0.7980 chunk 234 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 347 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 190 optimal weight: 0.0370 chunk 283 optimal weight: 0.9980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.133408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.098451 restraints weight = 59451.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.094585 restraints weight = 51707.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.095596 restraints weight = 50101.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.095855 restraints weight = 44282.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.095962 restraints weight = 40559.370| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25755 Z= 0.115 Angle : 0.578 10.532 35251 Z= 0.292 Chirality : 0.042 0.188 4156 Planarity : 0.004 0.064 4547 Dihedral : 4.535 50.845 3795 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.22 % Favored : 88.47 % Rotamer: Outliers : 6.42 % Allowed : 35.50 % Favored : 58.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.15), residues: 3556 helix: 2.45 (0.16), residues: 1165 sheet: -1.96 (0.24), residues: 495 loop : -2.37 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 518 TYR 0.011 0.001 TYR B 321 PHE 0.012 0.001 PHE A 472 TRP 0.019 0.001 TRP M 265 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00274 (25735) covalent geometry : angle 0.57605 (35211) SS BOND : bond 0.00241 ( 20) SS BOND : angle 1.38455 ( 40) hydrogen bonds : bond 0.02958 ( 973) hydrogen bonds : angle 3.93782 ( 2784) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 246 time to evaluate : 0.881 Fit side-chains REVERT: A 240 MET cc_start: 0.8559 (tpp) cc_final: 0.8200 (mmm) REVERT: B 337 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.6670 (t80) REVERT: C 226 ASP cc_start: 0.8672 (m-30) cc_final: 0.8080 (t0) REVERT: C 315 TRP cc_start: 0.7777 (OUTLIER) cc_final: 0.7175 (p-90) REVERT: C 495 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7001 (mtmm) REVERT: H 2 LEU cc_start: 0.8361 (pt) cc_final: 0.7887 (pp) REVERT: H 73 ASP cc_start: 0.8352 (t0) cc_final: 0.8000 (t0) REVERT: I 276 GLU cc_start: 0.8298 (pm20) cc_final: 0.8029 (pm20) REVERT: L 33 TYR cc_start: 0.7120 (OUTLIER) cc_final: 0.6622 (p90) outliers start: 143 outliers final: 123 residues processed: 375 average time/residue: 0.1318 time to fit residues: 85.1216 Evaluate side-chains 368 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 241 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 631 ASN Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 734 TYR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 678 TYR Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 289 TYR Chi-restraints excluded: chain I residue 301 VAL Chi-restraints excluded: chain L residue 8 HIS Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 252 THR Chi-restraints excluded: chain M residue 296 ILE Chi-restraints excluded: chain M residue 337 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 90 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 47 optimal weight: 0.2980 chunk 210 optimal weight: 6.9990 chunk 337 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 chunk 266 optimal weight: 0.0050 chunk 307 optimal weight: 1.9990 chunk 338 optimal weight: 0.9980 chunk 183 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 54 HIS ** I 341 GLN ** 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 = 0.4019 r_free = 0.4019 target = 0.135003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.099868 restraints weight = 59279.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096355 restraints weight = 50554.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.096773 restraints weight = 51716.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.097186 restraints weight = 47645.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.097354 restraints weight = 43798.294| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25755 Z= 0.097 Angle : 0.574 11.238 35251 Z= 0.288 Chirality : 0.041 0.184 4156 Planarity : 0.004 0.063 4547 Dihedral : 4.470 52.267 3795 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.35 % Favored : 89.34 % Rotamer: Outliers : 5.21 % Allowed : 36.54 % Favored : 58.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.15), residues: 3556 helix: 2.45 (0.16), residues: 1172 sheet: -1.99 (0.23), residues: 508 loop : -2.35 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 652 TYR 0.012 0.001 TYR B 321 PHE 0.009 0.001 PHE B 170 TRP 0.028 0.001 TRP M 265 HIS 0.002 0.000 HIS D 223 Details of bonding type rmsd covalent geometry : bond 0.00220 (25735) covalent geometry : angle 0.57230 (35211) SS BOND : bond 0.00274 ( 20) SS BOND : angle 1.34706 ( 40) hydrogen bonds : bond 0.02635 ( 973) hydrogen bonds : angle 3.83977 ( 2784) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 252 time to evaluate : 1.011 Fit side-chains REVERT: A 240 MET cc_start: 0.8489 (tpp) cc_final: 0.8130 (mmm) REVERT: B 337 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.6576 (t80) REVERT: C 226 ASP cc_start: 0.8665 (m-30) cc_final: 0.8030 (t0) REVERT: C 315 TRP cc_start: 0.7876 (OUTLIER) cc_final: 0.7255 (p-90) REVERT: H 2 LEU cc_start: 0.8306 (pt) cc_final: 0.7880 (pp) REVERT: H 73 ASP cc_start: 0.8368 (t0) cc_final: 0.8018 (t0) REVERT: I 276 GLU cc_start: 0.8338 (pm20) cc_final: 0.8063 (pm20) REVERT: L 33 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6554 (p90) outliers start: 116 outliers final: 93 residues processed: 351 average time/residue: 0.1333 time to fit residues: 80.8199 Evaluate side-chains 341 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 245 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 734 TYR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 678 TYR Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 289 TYR Chi-restraints excluded: chain I residue 325 CYS Chi-restraints excluded: chain L residue 8 HIS Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 252 THR Chi-restraints excluded: chain M residue 296 ILE Chi-restraints excluded: chain M residue 337 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 251 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 151 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 319 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 293 optimal weight: 20.0000 chunk 201 optimal weight: 0.0980 chunk 70 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.133853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.097576 restraints weight = 59550.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.093718 restraints weight = 54804.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.095046 restraints weight = 53063.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.095103 restraints weight = 46468.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.095311 restraints weight = 43245.683| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25755 Z= 0.117 Angle : 0.589 11.154 35251 Z= 0.296 Chirality : 0.042 0.186 4156 Planarity : 0.004 0.062 4547 Dihedral : 4.482 53.356 3795 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.08 % Favored : 88.58 % Rotamer: Outliers : 4.76 % Allowed : 37.34 % Favored : 57.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.15), residues: 3556 helix: 2.49 (0.16), residues: 1171 sheet: -1.98 (0.24), residues: 495 loop : -2.36 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 652 TYR 0.031 0.001 TYR H 53 PHE 0.028 0.001 PHE A 152 TRP 0.041 0.001 TRP H 37 HIS 0.003 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00277 (25735) covalent geometry : angle 0.58652 (35211) SS BOND : bond 0.00273 ( 20) SS BOND : angle 1.71511 ( 40) hydrogen bonds : bond 0.02871 ( 973) hydrogen bonds : angle 3.84415 ( 2784) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 246 time to evaluate : 1.002 Fit side-chains REVERT: A 240 MET cc_start: 0.8552 (tpp) cc_final: 0.8189 (mmm) REVERT: B 337 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6661 (t80) REVERT: C 226 ASP cc_start: 0.8672 (m-30) cc_final: 0.8083 (t70) REVERT: C 315 TRP cc_start: 0.7808 (OUTLIER) cc_final: 0.7125 (p-90) REVERT: H 2 LEU cc_start: 0.8376 (pt) cc_final: 0.8013 (pp) REVERT: H 73 ASP cc_start: 0.8432 (t0) cc_final: 0.8051 (t0) REVERT: I 276 GLU cc_start: 0.8347 (pm20) cc_final: 0.8070 (pm20) REVERT: L 33 TYR cc_start: 0.7103 (OUTLIER) cc_final: 0.6587 (p90) outliers start: 106 outliers final: 97 residues processed: 339 average time/residue: 0.1405 time to fit residues: 82.6379 Evaluate side-chains 343 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 243 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 734 TYR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 315 TRP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 392 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 42 HIS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 678 TYR Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 289 TYR Chi-restraints excluded: chain L residue 8 HIS Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 252 THR Chi-restraints excluded: chain M residue 296 ILE Chi-restraints excluded: chain M residue 337 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 345 optimal weight: 20.0000 chunk 118 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 52 optimal weight: 0.0270 chunk 63 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 126 optimal weight: 0.0020 chunk 61 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 overall best weight: 0.2646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 341 GLN ** 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 = 0.4032 r_free = 0.4032 target = 0.135987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.100377 restraints weight = 59441.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.097090 restraints weight = 49178.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.097934 restraints weight = 49830.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.098260 restraints weight = 46597.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.098364 restraints weight = 41226.338| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25755 Z= 0.095 Angle : 0.575 10.519 35251 Z= 0.288 Chirality : 0.041 0.182 4156 Planarity : 0.003 0.060 4547 Dihedral : 4.377 54.941 3795 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.90 % Favored : 89.79 % Rotamer: Outliers : 4.35 % Allowed : 37.52 % Favored : 58.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.15), residues: 3556 helix: 2.47 (0.15), residues: 1179 sheet: -1.83 (0.24), residues: 512 loop : -2.34 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 652 TYR 0.012 0.001 TYR B 321 PHE 0.009 0.001 PHE A 734 TRP 0.032 0.001 TRP M 265 HIS 0.002 0.000 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00215 (25735) covalent geometry : angle 0.57311 (35211) SS BOND : bond 0.00282 ( 20) SS BOND : angle 1.58306 ( 40) hydrogen bonds : bond 0.02425 ( 973) hydrogen bonds : angle 3.73247 ( 2784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4413.64 seconds wall clock time: 76 minutes 43.16 seconds (4603.16 seconds total)