Starting phenix.real_space_refine on Mon Sep 30 10:38:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuj_43531/09_2024/8vuj_43531.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuj_43531/09_2024/8vuj_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuj_43531/09_2024/8vuj_43531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuj_43531/09_2024/8vuj_43531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuj_43531/09_2024/8vuj_43531.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vuj_43531/09_2024/8vuj_43531.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 9, 'TRP:plan': 4, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 24, 'ARG:plan': 9} 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: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 11, 'TRP:plan': 5, 'ASP:plan': 22, 'PHE:plan': 13, 'GLU:plan': 26, 'ARG:plan': 6} 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: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 5, 'ASP:plan': 17, 'PHE:plan': 9, 'GLU:plan': 35, 'ARG:plan': 14} 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: {'GLN:plan1': 8, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 18, 'TRP:plan': 4, 'ASP:plan': 28, 'PHE:plan': 13, 'GLU:plan': 25, 'ARG:plan': 7} 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: {'GLN:plan1': 1, 'GLU:plan': 3, '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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} 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, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 53 Time building chain proxies: 15.51, per 1000 atoms: 0.62 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: 6.03 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 2.90 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: 8.94 Time building geometry restraints manager: 7.09 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: 4.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 55.740 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.020 ------------------------------------------------------------------------------- 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 25735 Z= 0.160 Angle : 0.584 10.947 35211 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 : 8.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (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 TRP 0.036 0.001 TRP M 265 HIS 0.002 0.000 HIS C 94 PHE 0.052 0.001 PHE B 310 TYR 0.015 0.001 TYR B 321 ARG 0.002 0.000 ARG C 36 *********************** 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 fitting. rotamer outliers: 9 poor density : 239 time to evaluate : 2.544 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 245 average time/residue: 0.2826 time to fit residues: 118.6078 Evaluate side-chains 242 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 235 time to evaluate : 2.596 ------------------------------------------------------------------------------- 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 298 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 321 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25735 Z= 0.324 Angle : 0.623 10.155 35211 Z= 0.324 Chirality : 0.044 0.194 4156 Planarity : 0.004 0.051 4547 Dihedral : 4.833 58.275 3798 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.19 % Favored : 86.47 % Rotamer: Outliers : 6.42 % Allowed : 35.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.15), residues: 3556 helix: 2.16 (0.16), residues: 1171 sheet: -2.01 (0.23), residues: 529 loop : -2.51 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 378 HIS 0.005 0.001 HIS A 162 PHE 0.017 0.001 PHE A 472 TYR 0.017 0.001 TYR A 367 ARG 0.004 0.000 ARG B 518 *********************** 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 378 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 235 time to evaluate : 2.807 Fit side-chains REVERT: C 226 ASP cc_start: 0.8553 (m-30) cc_final: 0.8009 (t0) REVERT: C 495 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6942 (mtmm) REVERT: C 761 HIS cc_start: 0.8994 (OUTLIER) cc_final: 0.8480 (t70) REVERT: D 396 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.6892 (m-80) REVERT: H 2 LEU cc_start: 0.8395 (pt) cc_final: 0.7837 (pp) REVERT: H 73 ASP cc_start: 0.8330 (t0) cc_final: 0.8127 (t0) REVERT: L 33 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6662 (p90) outliers start: 143 outliers final: 82 residues processed: 360 average time/residue: 0.3017 time to fit residues: 184.2611 Evaluate side-chains 314 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 228 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 HIS 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 204 VAL 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 315 TRP Chi-restraints excluded: chain A residue 317 THR 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 526 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain B residue 67 VAL 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 191 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 321 TYR 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 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 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 163 ILE Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 278 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 495 LYS 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 C residue 757 ILE Chi-restraints excluded: chain C residue 761 HIS 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 172 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 396 PHE 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 296 ILE 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 178 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 chunk 218 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 322 optimal weight: 1.9990 chunk 347 optimal weight: 6.9990 chunk 286 optimal weight: 0.8980 chunk 319 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 258 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 631 ASN C 357 GLN I 286 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25735 Z= 0.180 Angle : 0.569 12.397 35211 Z= 0.290 Chirality : 0.042 0.183 4156 Planarity : 0.003 0.050 4547 Dihedral : 4.644 54.302 3795 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.60 % Favored : 89.03 % Rotamer: Outliers : 5.66 % Allowed : 35.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3556 helix: 2.27 (0.16), residues: 1170 sheet: -2.02 (0.23), residues: 508 loop : -2.45 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 315 HIS 0.004 0.001 HIS A 477 PHE 0.017 0.001 PHE A 152 TYR 0.016 0.001 TYR B 684 ARG 0.002 0.000 ARG C 654 *********************** 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 373 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 247 time to evaluate : 2.854 Fit side-chains REVERT: B 221 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8199 (pttm) REVERT: C 226 ASP cc_start: 0.8587 (m-30) cc_final: 0.8045 (t0) REVERT: C 743 MET cc_start: 0.7991 (tpp) cc_final: 0.7709 (mmm) REVERT: C 761 HIS cc_start: 0.8952 (OUTLIER) cc_final: 0.8465 (t70) REVERT: H 2 LEU cc_start: 0.8376 (pt) cc_final: 0.7859 (pp) REVERT: H 73 ASP cc_start: 0.8240 (t0) cc_final: 0.7961 (t0) REVERT: H 76 LYS cc_start: 0.8823 (mtpt) cc_final: 0.8618 (mtpt) REVERT: L 33 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6618 (p90) outliers start: 126 outliers final: 82 residues processed: 357 average time/residue: 0.2953 time to fit residues: 179.9553 Evaluate side-chains 320 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 235 time to evaluate : 2.964 ------------------------------------------------------------------------------- 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 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 221 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 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 435 ILE Chi-restraints excluded: chain A residue 451 VAL 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 638 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 B residue 195 PHE 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 279 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 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 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 224 SER Chi-restraints excluded: chain C residue 238 LEU 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 451 VAL Chi-restraints excluded: chain C residue 455 CYS Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 761 HIS 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 257 VAL Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 492 VAL 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 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 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 337 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 0.9990 chunk 242 optimal weight: 0.0970 chunk 167 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 153 optimal weight: 30.0000 chunk 216 optimal weight: 20.0000 chunk 323 optimal weight: 30.0000 chunk 342 optimal weight: 0.3980 chunk 168 optimal weight: 1.9990 chunk 306 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25735 Z= 0.158 Angle : 0.559 10.191 35211 Z= 0.285 Chirality : 0.042 0.186 4156 Planarity : 0.003 0.051 4547 Dihedral : 4.552 57.378 3795 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.97 % Favored : 88.72 % Rotamer: Outliers : 6.06 % Allowed : 35.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 3556 helix: 2.30 (0.16), residues: 1171 sheet: -1.94 (0.23), residues: 518 loop : -2.42 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 265 HIS 0.003 0.001 HIS A 477 PHE 0.010 0.001 PHE C 533 TYR 0.016 0.001 TYR B 684 ARG 0.002 0.000 ARG C 358 *********************** 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 376 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 241 time to evaluate : 2.653 Fit side-chains REVERT: A 208 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8252 (mp) REVERT: B 228 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8519 (tt) REVERT: C 226 ASP cc_start: 0.8608 (m-30) cc_final: 0.8074 (t0) REVERT: C 315 TRP cc_start: 0.7783 (OUTLIER) cc_final: 0.7204 (p-90) REVERT: C 743 MET cc_start: 0.7984 (tpp) cc_final: 0.7691 (mmm) REVERT: C 761 HIS cc_start: 0.8907 (OUTLIER) cc_final: 0.8423 (t70) REVERT: H 2 LEU cc_start: 0.8309 (pt) cc_final: 0.7788 (pp) REVERT: H 39 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7126 (ttm-80) REVERT: H 73 ASP cc_start: 0.8264 (t0) cc_final: 0.7940 (t0) REVERT: H 76 LYS cc_start: 0.8812 (mtpt) cc_final: 0.8576 (mtpt) REVERT: L 33 TYR cc_start: 0.7048 (OUTLIER) cc_final: 0.6659 (p90) REVERT: M 264 GLN cc_start: 0.8542 (pm20) cc_final: 0.8318 (pm20) outliers start: 135 outliers final: 88 residues processed: 364 average time/residue: 0.2886 time to fit residues: 179.0543 Evaluate side-chains 329 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 235 time to evaluate : 3.476 ------------------------------------------------------------------------------- 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 208 LEU Chi-restraints excluded: chain A residue 221 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 315 TRP 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 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 161 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 365 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 535 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 715 LEU 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 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 401 VAL Chi-restraints excluded: chain C residue 402 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 C residue 761 HIS 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 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 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 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 284 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 254 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 291 optimal weight: 6.9990 chunk 236 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 307 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25735 Z= 0.307 Angle : 0.621 10.167 35211 Z= 0.317 Chirality : 0.043 0.199 4156 Planarity : 0.004 0.068 4547 Dihedral : 4.787 54.548 3795 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.85 % Favored : 86.78 % Rotamer: Outliers : 7.63 % Allowed : 34.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.15), residues: 3556 helix: 2.29 (0.16), residues: 1170 sheet: -2.16 (0.23), residues: 518 loop : -2.49 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 315 HIS 0.005 0.001 HIS C 477 PHE 0.021 0.001 PHE A 152 TYR 0.017 0.001 TYR B 684 ARG 0.003 0.000 ARG A 346 *********************** 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 400 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 230 time to evaluate : 2.682 Fit side-chains REVERT: A 208 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8291 (mp) REVERT: A 240 MET cc_start: 0.8649 (mmm) cc_final: 0.8181 (tpp) REVERT: A 761 HIS cc_start: 0.9244 (OUTLIER) cc_final: 0.8947 (t-170) REVERT: C 226 ASP cc_start: 0.8591 (m-30) cc_final: 0.8066 (t0) REVERT: C 315 TRP cc_start: 0.7870 (OUTLIER) cc_final: 0.7307 (p-90) REVERT: C 495 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7006 (mtmm) REVERT: C 761 HIS cc_start: 0.9132 (OUTLIER) cc_final: 0.8617 (t70) REVERT: D 251 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.8813 (t80) REVERT: D 768 MET cc_start: 0.8444 (mpp) cc_final: 0.8212 (mpp) REVERT: H 2 LEU cc_start: 0.8412 (pt) cc_final: 0.7901 (pp) REVERT: H 73 ASP cc_start: 0.8247 (t0) cc_final: 0.7965 (t0) REVERT: L 33 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.6460 (p90) outliers start: 170 outliers final: 126 residues processed: 386 average time/residue: 0.3189 time to fit residues: 212.7505 Evaluate side-chains 354 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 221 time to evaluate : 2.730 ------------------------------------------------------------------------------- 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 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 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 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 435 ILE 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 661 ILE Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 761 HIS 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 187 VAL 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 279 VAL 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 463 ILE 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 715 LEU Chi-restraints excluded: chain B residue 729 THR 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 163 ILE 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 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 753 VAL Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 761 HIS 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 251 TYR 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 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 115 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 342 optimal weight: 4.9990 chunk 284 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 chunk 28 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN I 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25735 Z= 0.204 Angle : 0.580 10.082 35211 Z= 0.295 Chirality : 0.042 0.188 4156 Planarity : 0.003 0.056 4547 Dihedral : 4.717 53.133 3795 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.42 % Favored : 88.22 % Rotamer: Outliers : 6.87 % Allowed : 35.68 % Favored : 57.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 3556 helix: 2.33 (0.16), residues: 1169 sheet: -2.18 (0.23), residues: 501 loop : -2.44 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 265 HIS 0.004 0.001 HIS A 477 PHE 0.013 0.001 PHE C 533 TYR 0.015 0.001 TYR B 684 ARG 0.002 0.000 ARG B 518 *********************** 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 384 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 231 time to evaluate : 3.005 Fit side-chains REVERT: A 208 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8204 (mp) REVERT: C 226 ASP cc_start: 0.8599 (m-30) cc_final: 0.8078 (t0) REVERT: C 315 TRP cc_start: 0.7781 (OUTLIER) cc_final: 0.7218 (p-90) REVERT: C 495 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7028 (mtmm) REVERT: C 761 HIS cc_start: 0.9049 (OUTLIER) cc_final: 0.8477 (t70) REVERT: D 251 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.8784 (t80) REVERT: H 2 LEU cc_start: 0.8392 (pt) cc_final: 0.7900 (pp) REVERT: H 73 ASP cc_start: 0.8251 (t0) cc_final: 0.7912 (t0) REVERT: L 33 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6624 (p90) outliers start: 153 outliers final: 125 residues processed: 367 average time/residue: 0.2837 time to fit residues: 178.9146 Evaluate side-chains 359 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 228 time to evaluate : 2.730 ------------------------------------------------------------------------------- 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 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 278 SER 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 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 661 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 125 LEU Chi-restraints excluded: chain B residue 133 MET 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 279 VAL Chi-restraints excluded: chain B residue 321 TYR 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 463 ILE 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 537 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 715 LEU 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 392 TYR 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 754 SER Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 761 HIS 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 251 TYR 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 409 VAL 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 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 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 239 VAL Chi-restraints excluded: chain M residue 248 THR 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 330 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 195 optimal weight: 9.9990 chunk 250 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 288 optimal weight: 7.9990 chunk 191 optimal weight: 0.9990 chunk 341 optimal weight: 8.9990 chunk 213 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 25735 Z= 0.444 Angle : 0.696 10.154 35211 Z= 0.359 Chirality : 0.045 0.208 4156 Planarity : 0.004 0.064 4547 Dihedral : 5.172 54.438 3795 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.37 % Allowed : 14.45 % Favored : 85.18 % Rotamer: Outliers : 8.21 % Allowed : 34.47 % Favored : 57.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.15), residues: 3556 helix: 2.11 (0.16), residues: 1178 sheet: -2.44 (0.22), residues: 523 loop : -2.61 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 378 HIS 0.007 0.001 HIS C 477 PHE 0.023 0.002 PHE A 472 TYR 0.021 0.002 TYR A 392 ARG 0.003 0.000 ARG H 98 *********************** 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 403 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 220 time to evaluate : 2.817 Fit side-chains REVERT: A 761 HIS cc_start: 0.9215 (OUTLIER) cc_final: 0.8930 (t-170) REVERT: C 495 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6976 (mtmm) REVERT: C 761 HIS cc_start: 0.9233 (OUTLIER) cc_final: 0.8663 (t70) REVERT: D 229 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.8911 (pt) REVERT: D 251 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.8738 (t80) REVERT: H 2 LEU cc_start: 0.8443 (pt) cc_final: 0.7914 (pp) REVERT: H 73 ASP cc_start: 0.8199 (t0) cc_final: 0.7901 (t0) REVERT: L 33 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.6349 (p90) REVERT: L 67 ILE cc_start: 0.8979 (mp) cc_final: 0.8715 (mt) outliers start: 183 outliers final: 142 residues processed: 387 average time/residue: 0.2917 time to fit residues: 194.2482 Evaluate side-chains 368 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 220 time to evaluate : 3.033 ------------------------------------------------------------------------------- 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 246 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 288 VAL 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 388 LYS Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 435 ILE 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 657 SER Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 67 VAL 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 191 VAL 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 321 TYR 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 463 ILE 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 519 SER 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 686 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 739 THR 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 97 THR Chi-restraints excluded: chain C residue 110 THR 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 325 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 380 ILE 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 411 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 712 TRP 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 C residue 761 HIS 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 187 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 251 TYR 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 407 SER Chi-restraints excluded: chain D residue 409 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 533 ILE 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 I residue 301 VAL 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 248 THR 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 211 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 232 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 25735 Z= 0.356 Angle : 0.663 10.404 35211 Z= 0.340 Chirality : 0.044 0.206 4156 Planarity : 0.004 0.062 4547 Dihedral : 5.174 59.783 3795 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.10 % Favored : 86.50 % Rotamer: Outliers : 7.32 % Allowed : 35.32 % Favored : 57.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.15), residues: 3556 helix: 2.13 (0.16), residues: 1175 sheet: -2.40 (0.22), residues: 517 loop : -2.64 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 265 HIS 0.006 0.001 HIS C 477 PHE 0.037 0.002 PHE D 617 TYR 0.021 0.001 TYR B 684 ARG 0.003 0.000 ARG B 518 *********************** 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 387 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 224 time to evaluate : 2.964 Fit side-chains REVERT: A 343 ASP cc_start: 0.7822 (p0) cc_final: 0.7573 (p0) REVERT: C 495 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7015 (mtmm) REVERT: C 761 HIS cc_start: 0.9196 (OUTLIER) cc_final: 0.8571 (t70) REVERT: D 251 TYR cc_start: 0.9016 (OUTLIER) cc_final: 0.8623 (t80) REVERT: H 2 LEU cc_start: 0.8505 (pt) cc_final: 0.7961 (pp) REVERT: H 73 ASP cc_start: 0.8191 (t0) cc_final: 0.7885 (t0) REVERT: L 33 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.6387 (p90) REVERT: L 67 ILE cc_start: 0.8990 (mp) cc_final: 0.8690 (mt) outliers start: 163 outliers final: 144 residues processed: 372 average time/residue: 0.2888 time to fit residues: 183.8349 Evaluate side-chains 367 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 219 time to evaluate : 2.695 ------------------------------------------------------------------------------- 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 246 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL 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 388 LYS Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 435 ILE 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 661 ILE Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 67 VAL 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 191 VAL 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 321 TYR 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 463 ILE 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 514 ILE Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 522 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 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 97 THR Chi-restraints excluded: chain C residue 110 THR 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 325 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 380 ILE 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 459 CYS Chi-restraints excluded: chain C residue 495 LYS Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 519 ILE 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 C residue 761 HIS 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 187 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 251 TYR 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 407 SER Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 468 SER 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 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 I residue 301 VAL 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 248 THR Chi-restraints excluded: chain M residue 252 THR Chi-restraints excluded: chain M residue 296 ILE Chi-restraints excluded: chain M residue 327 THR 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 310 optimal weight: 30.0000 chunk 326 optimal weight: 6.9990 chunk 298 optimal weight: 0.5980 chunk 317 optimal weight: 0.3980 chunk 191 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 249 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 287 optimal weight: 10.0000 chunk 300 optimal weight: 7.9990 chunk 316 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS I 286 ASN ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25735 Z= 0.169 Angle : 0.601 11.404 35211 Z= 0.303 Chirality : 0.042 0.192 4156 Planarity : 0.004 0.061 4547 Dihedral : 4.846 56.864 3795 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.36 % Favored : 88.22 % Rotamer: Outliers : 5.70 % Allowed : 36.58 % Favored : 57.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 3556 helix: 2.29 (0.16), residues: 1167 sheet: -2.22 (0.24), residues: 484 loop : -2.49 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP M 265 HIS 0.003 0.001 HIS A 477 PHE 0.030 0.001 PHE D 617 TYR 0.013 0.001 TYR B 684 ARG 0.002 0.000 ARG B 518 *********************** 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 366 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 239 time to evaluate : 2.750 Fit side-chains REVERT: A 125 MET cc_start: 0.7589 (mmm) cc_final: 0.7324 (mmm) REVERT: C 743 MET cc_start: 0.7854 (tpp) cc_final: 0.7612 (mmm) REVERT: C 761 HIS cc_start: 0.9028 (OUTLIER) cc_final: 0.8456 (t70) REVERT: D 507 MET cc_start: 0.8295 (tpp) cc_final: 0.8074 (tpp) REVERT: H 2 LEU cc_start: 0.8345 (pt) cc_final: 0.7797 (pp) REVERT: H 73 ASP cc_start: 0.8128 (t0) cc_final: 0.7802 (t0) REVERT: L 33 TYR cc_start: 0.7057 (OUTLIER) cc_final: 0.6691 (p90) REVERT: L 67 ILE cc_start: 0.8962 (mp) cc_final: 0.8711 (mt) outliers start: 127 outliers final: 112 residues processed: 357 average time/residue: 0.2917 time to fit residues: 177.5831 Evaluate side-chains 341 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 227 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 93 SER 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 278 SER Chi-restraints excluded: chain A residue 315 TRP 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 388 LYS 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 526 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 657 SER 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 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 217 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 279 VAL 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 477 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 519 SER 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 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 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 224 SER Chi-restraints excluded: chain C residue 238 LEU 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 392 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 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 754 SER Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 761 HIS 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 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 407 SER Chi-restraints excluded: chain D residue 409 VAL 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 I residue 301 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 40.0000 chunk 336 optimal weight: 0.0010 chunk 205 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 233 optimal weight: 40.0000 chunk 352 optimal weight: 0.3980 chunk 324 optimal weight: 0.0980 chunk 280 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 172 optimal weight: 3.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25735 Z= 0.155 Angle : 0.593 10.684 35211 Z= 0.299 Chirality : 0.042 0.186 4156 Planarity : 0.004 0.060 4547 Dihedral : 4.672 55.284 3795 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.66 % Favored : 89.00 % Rotamer: Outliers : 4.67 % Allowed : 37.75 % Favored : 57.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 3556 helix: 2.39 (0.16), residues: 1167 sheet: -2.03 (0.23), residues: 509 loop : -2.44 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP M 265 HIS 0.007 0.001 HIS A 67 PHE 0.031 0.001 PHE D 617 TYR 0.010 0.001 TYR B 684 ARG 0.007 0.000 ARG A 652 ********************** 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 351 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 247 time to evaluate : 2.967 Fit side-chains REVERT: B 425 LEU cc_start: 0.7785 (tp) cc_final: 0.7502 (tt) REVERT: C 743 MET cc_start: 0.7861 (tpp) cc_final: 0.7616 (mmm) REVERT: C 761 HIS cc_start: 0.8948 (OUTLIER) cc_final: 0.8392 (t70) REVERT: H 2 LEU cc_start: 0.8373 (pt) cc_final: 0.7869 (pp) REVERT: H 73 ASP cc_start: 0.8188 (t0) cc_final: 0.7853 (t0) REVERT: L 33 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6732 (p90) outliers start: 104 outliers final: 94 residues processed: 342 average time/residue: 0.2872 time to fit residues: 167.1559 Evaluate side-chains 330 residues out of total 3120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 234 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR 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 315 TRP 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 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 661 ILE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 279 VAL 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 480 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 535 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 325 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 380 ILE 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 451 VAL Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 761 HIS 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 215 THR 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 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 I residue 325 CYS 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 296 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 6.9990 chunk 299 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 258 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 281 optimal weight: 0.3980 chunk 117 optimal weight: 0.3980 chunk 288 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 686 HIS ** 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 = 0.3992 r_free = 0.3992 target = 0.133138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097678 restraints weight = 59141.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.093913 restraints weight = 51121.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.094711 restraints weight = 52497.647| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25735 Z= 0.173 Angle : 0.592 11.122 35211 Z= 0.297 Chirality : 0.042 0.185 4156 Planarity : 0.004 0.061 4547 Dihedral : 4.614 56.819 3795 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.19 % Favored : 88.44 % Rotamer: Outliers : 4.80 % Allowed : 37.52 % Favored : 57.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3556 helix: 2.45 (0.16), residues: 1165 sheet: -1.87 (0.24), residues: 492 loop : -2.43 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP M 265 HIS 0.002 0.000 HIS A 477 PHE 0.031 0.001 PHE D 617 TYR 0.013 0.001 TYR B 321 ARG 0.007 0.000 ARG A 652 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4750.56 seconds wall clock time: 85 minutes 21.51 seconds (5121.51 seconds total)