Starting phenix.real_space_refine on Mon May 26 16:18:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vut_43539/05_2025/8vut_43539.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vut_43539/05_2025/8vut_43539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vut_43539/05_2025/8vut_43539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vut_43539/05_2025/8vut_43539.map" model { file = "/net/cci-nas-00/data/ceres_data/8vut_43539/05_2025/8vut_43539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vut_43539/05_2025/8vut_43539.cif" } resolution = 3.7 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= 0.017 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 130 5.16 5 C 18356 2.51 5 N 4997 2.21 5 O 5336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 1.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28819 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 5810 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 33, 'TRANS': 755} Chain breaks: 2 Unresolved non-hydrogen bonds: 448 Unresolved non-hydrogen angles: 563 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 21, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 277 Chain: "B" Number of atoms: 5537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 5537 Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 187} Link IDs: {'PTRANS': 30, 'TRANS': 750} Chain breaks: 2 Unresolved non-hydrogen bonds: 666 Unresolved non-hydrogen angles: 845 Unresolved non-hydrogen dihedrals: 551 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 23, 'PHE:plan': 11, 'GLU:plan': 25, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 398 Chain: "C" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 5640 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 33, 'TRANS': 755} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 621 Unresolved non-hydrogen angles: 771 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 11, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 10, 'GLU:plan': 29, 'ASP:plan': 15} Unresolved non-hydrogen planarities: 372 Chain: "D" Number of atoms: 5490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 5490 Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 209} Link IDs: {'PTRANS': 30, 'TRANS': 750} Chain breaks: 2 Unresolved non-hydrogen bonds: 710 Unresolved non-hydrogen angles: 896 Unresolved non-hydrogen dihedrals: 578 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 14, 'TRP:plan': 2, 'ASP:plan': 23, 'PHE:plan': 11, 'GLU:plan': 25, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 409 Chain: "H" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1617 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 209} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1617 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 209} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "L" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1554 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 193} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1554 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 193} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 17.96, per 1000 atoms: 0.62 Number of scatterers: 28819 At special positions: 0 Unit cell: (148.944, 152.368, 225.984, 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 130 16.00 O 5336 8.00 N 4997 7.00 C 18356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, 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 H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 149 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 193 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 91 " distance=2.04 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 193 " 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: 7.80 Conformation dependent library (CDL) restraints added in 4.2 seconds 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7444 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 56 sheets defined 34.0% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 35 through 52 Processing helix chain 'A' and resid 71 through 84 Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.944A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 159 removed outlier: 3.663A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.706A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.716A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.846A pdb=" N GLY A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 526 removed outlier: 4.553A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 581 Processing helix chain 'A' and resid 584 through 596 Processing helix chain 'A' and resid 607 through 638 Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 668 through 677 removed outlier: 3.926A pdb=" N ILE A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 688 removed outlier: 3.640A pdb=" N TYR A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 704 Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 749 through 765 Processing helix chain 'A' and resid 765 through 774 Processing helix chain 'A' and resid 782 through 797 removed outlier: 3.973A pdb=" N GLY A 787 " --> pdb=" O GLU A 783 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL A 788 " --> pdb=" O ASN A 784 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU A 791 " --> pdb=" O GLY A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 812 removed outlier: 3.695A pdb=" N LEU A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 108 through 119 removed outlier: 3.877A pdb=" N MET B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 133 removed outlier: 3.612A pdb=" N SER B 132 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 129 through 133' Processing helix chain 'B' and resid 150 through 165 removed outlier: 3.634A pdb=" N GLN B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 192 removed outlier: 3.668A pdb=" N PHE B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 removed outlier: 3.989A pdb=" N LYS B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 245 Processing helix chain 'B' and resid 258 through 263 removed outlier: 4.080A pdb=" N GLY B 263 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 310 Processing helix chain 'B' and resid 458 through 472 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'B' and resid 516 through 522 Processing helix chain 'B' and resid 555 through 578 Processing helix chain 'B' and resid 580 through 594 Processing helix chain 'B' and resid 605 through 635 Processing helix chain 'B' and resid 652 through 656 Processing helix chain 'B' and resid 669 through 678 Processing helix chain 'B' and resid 678 through 686 removed outlier: 4.214A pdb=" N HIS B 682 " --> pdb=" O TYR B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 702 Processing helix chain 'B' and resid 712 through 721 Processing helix chain 'B' and resid 751 through 765 Processing helix chain 'B' and resid 766 through 776 removed outlier: 3.536A pdb=" N GLU B 770 " --> pdb=" O GLY B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 814 Processing helix chain 'C' and resid 35 through 53 removed outlier: 3.581A pdb=" N LYS C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 84 Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.676A pdb=" N PHE C 102 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.552A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 158 removed outlier: 3.986A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 186 removed outlier: 3.894A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.544A pdb=" N LEU C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 removed outlier: 4.055A pdb=" N MET C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.596A pdb=" N ILE C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.679A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 257 through 262' Processing helix chain 'C' and resid 276 through 296 removed outlier: 3.550A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 removed outlier: 3.527A pdb=" N SER C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 470 Processing helix chain 'C' and resid 500 through 507 removed outlier: 3.703A pdb=" N SER C 507 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 559 through 580 removed outlier: 4.058A pdb=" N TRP C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER C 569 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL C 570 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 595 removed outlier: 3.994A pdb=" N LEU C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 638 Processing helix chain 'C' and resid 650 through 655 Processing helix chain 'C' and resid 669 through 677 removed outlier: 3.604A pdb=" N TYR C 673 " --> pdb=" O SER C 669 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN C 677 " --> pdb=" O TYR C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 689 removed outlier: 3.860A pdb=" N ARG C 685 " --> pdb=" O SER C 681 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N HIS C 686 " --> pdb=" O THR C 682 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N MET C 687 " --> pdb=" O MET C 683 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS C 689 " --> pdb=" O ARG C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 704 removed outlier: 4.164A pdb=" N ILE C 699 " --> pdb=" O ALA C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 724 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 764 through 774 Processing helix chain 'C' and resid 788 through 813 removed outlier: 4.027A pdb=" N ILE C 800 " --> pdb=" O ILE C 796 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE C 801 " --> pdb=" O VAL C 797 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.547A pdb=" N HIS D 119 " --> pdb=" O PHE D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 removed outlier: 3.852A pdb=" N TYR D 165 " --> pdb=" O ILE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 192 removed outlier: 3.535A pdb=" N PHE D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 removed outlier: 3.729A pdb=" N GLN D 216 " --> pdb=" O ASP D 212 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN D 218 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 247 removed outlier: 3.695A pdb=" N SER D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 287 through 310 Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.979A pdb=" N VAL D 339 " --> pdb=" O PRO D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 448 removed outlier: 3.556A pdb=" N ASN D 447 " --> pdb=" O ASN D 444 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU D 448 " --> pdb=" O SER D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 472 Processing helix chain 'D' and resid 496 through 502 Processing helix chain 'D' and resid 517 through 521 removed outlier: 3.535A pdb=" N VAL D 521 " --> pdb=" O ARG D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 578 removed outlier: 3.519A 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 604 through 633 removed outlier: 3.836A pdb=" N MET D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 652 Processing helix chain 'D' and resid 669 through 678 Processing helix chain 'D' and resid 685 through 689 removed outlier: 3.863A pdb=" N ASN D 689 " --> pdb=" O THR D 686 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 702 Processing helix chain 'D' and resid 711 through 721 Processing helix chain 'D' and resid 751 through 765 Processing helix chain 'D' and resid 766 through 776 removed outlier: 4.256A 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 103 through 107 removed outlier: 4.009A pdb=" N ALA H 106 " --> pdb=" O SER H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'I' and resid 87 through 91 removed outlier: 4.026A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 167 No H-bonds generated for 'chain 'I' and resid 165 through 167' Processing helix chain 'I' and resid 196 through 198 No H-bonds generated for 'chain 'I' and resid 196 through 198' Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 181 through 188 Processing helix chain 'M' and resid 121 through 126 Processing helix chain 'M' and resid 181 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 8.061A pdb=" N VAL A 65 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 removed outlier: 6.580A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.691A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 340 through 341 removed outlier: 3.612A pdb=" N ASN A 341 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ASP A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 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 434 through 436 Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 489 removed outlier: 3.523A pdb=" N GLU A 488 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 497 " --> pdb=" O GLU A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 710 through 712 Processing sheet with id=AA9, first strand: chain 'B' and resid 70 through 73 removed outlier: 3.629A pdb=" N LEU B 40 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 203 through 205 removed outlier: 3.571A pdb=" N ILE B 277 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL B 279 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 405 through 410 removed outlier: 3.750A pdb=" N ASP B 476 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 408 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 410 " --> pdb=" O TYR B 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 418 through 420 removed outlier: 3.612A pdb=" N CYS B 455 " --> pdb=" O GLU B 420 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 707 through 710 removed outlier: 4.025A pdb=" N VAL B 728 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.630A pdb=" N ILE C 29 " --> pdb=" O ASN C 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AB7, first strand: chain 'C' and resid 90 through 92 Processing sheet with id=AB8, first strand: chain 'C' and resid 166 through 167 removed outlier: 3.561A pdb=" N VAL C 167 " --> pdb=" O LEU C 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AC1, first strand: chain 'C' and resid 267 through 271 removed outlier: 3.604A pdb=" N MET C 354 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 340 through 341 removed outlier: 3.586A pdb=" N ASN C 341 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ASP C 345 " --> pdb=" O ASN C 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AC4, first strand: chain 'C' and resid 487 through 489 Processing sheet with id=AC5, first strand: chain 'C' and resid 541 through 543 removed outlier: 3.856A pdb=" N VAL C 542 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL C 728 " --> pdb=" O VAL C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 70 through 73 removed outlier: 3.890A pdb=" N LEU D 40 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA D 37 " --> pdb=" O VAL D 99 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 125 through 126 Processing sheet with id=AC8, first strand: chain 'D' and resid 170 through 173 removed outlier: 7.984A pdb=" N PHE D 170 " --> pdb=" O GLN D 201 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL D 203 " --> pdb=" O PHE D 170 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU D 172 " --> pdb=" O VAL D 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 226 through 227 removed outlier: 6.815A pdb=" N TRP D 255 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N VAL D 279 " --> pdb=" O TRP D 255 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL D 257 " --> pdb=" O VAL D 279 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 341 through 342 removed outlier: 3.936A pdb=" N VAL D 341 " --> pdb=" O LEU D 348 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AD3, first strand: chain 'D' and resid 409 through 410 Processing sheet with id=AD4, first strand: chain 'D' and resid 418 through 420 Processing sheet with id=AD5, first strand: chain 'D' and resid 487 through 488 removed outlier: 3.683A pdb=" N LYS D 487 " --> pdb=" O ASN D 494 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN D 494 " --> pdb=" O LYS D 487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 708 through 710 removed outlier: 3.669A pdb=" N VAL D 728 " --> pdb=" O VAL D 537 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.504A pdb=" N SER H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AD9, first strand: chain 'H' and resid 59 through 60 removed outlier: 3.551A pdb=" N GLY H 59 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS H 98 " --> pdb=" O ASP H 110 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 59 through 60 removed outlier: 3.551A pdb=" N GLY H 59 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 129 through 133 removed outlier: 5.350A pdb=" N ALA H 146 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL H 193 " --> pdb=" O ALA H 146 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLY H 148 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL H 191 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU H 150 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N SER H 189 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LYS H 152 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU H 187 " --> pdb=" O LYS H 152 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 129 through 133 removed outlier: 5.350A pdb=" N ALA H 146 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL H 193 " --> pdb=" O ALA H 146 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLY H 148 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL H 191 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU H 150 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N SER H 189 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LYS H 152 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU H 187 " --> pdb=" O LYS H 152 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 160 through 163 Processing sheet with id=AE5, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.560A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AE7, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.452A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 129 through 133 removed outlier: 3.516A pdb=" N VAL I 193 " --> pdb=" O ALA I 145 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU I 147 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP I 153 " --> pdb=" O TYR I 185 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TYR I 185 " --> pdb=" O ASP I 153 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 129 through 133 removed outlier: 3.516A pdb=" N VAL I 193 " --> pdb=" O ALA I 145 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU I 147 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP I 153 " --> pdb=" O TYR I 185 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TYR I 185 " --> pdb=" O ASP I 153 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER I 186 " --> pdb=" O VAL I 178 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 160 through 163 Processing sheet with id=AF2, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.657A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF4, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.648A pdb=" N ASP L 138 " --> pdb=" O TYR L 172 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR L 172 " --> pdb=" O ASP L 138 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.648A pdb=" N ASP L 138 " --> pdb=" O TYR L 172 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR L 172 " --> pdb=" O ASP L 138 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA L 173 " --> pdb=" O SER L 165 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER L 165 " --> pdb=" O ALA L 173 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 154 through 155 removed outlier: 4.064A pdb=" N TRP L 148 " --> pdb=" O VAL L 155 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 4 through 5 Processing sheet with id=AF8, first strand: chain 'M' and resid 9 through 12 removed outlier: 5.920A pdb=" N GLN M 38 " --> pdb=" O THR M 47 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR M 47 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 114 through 118 removed outlier: 3.664A pdb=" N ASP M 138 " --> pdb=" O TYR M 172 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR M 172 " --> pdb=" O ASP M 138 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 114 through 118 removed outlier: 3.664A pdb=" N ASP M 138 " --> pdb=" O TYR M 172 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR M 172 " --> pdb=" O ASP M 138 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA M 173 " --> pdb=" O SER M 165 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER M 165 " --> pdb=" O ALA M 173 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 154 through 155 removed outlier: 4.498A pdb=" N TRP M 148 " --> pdb=" O VAL M 155 " (cutoff:3.500A) 1232 hydrogen bonds defined for protein. 3462 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: 11.55 Time building geometry restraints manager: 9.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7780 1.33 - 1.46: 6403 1.46 - 1.58: 15077 1.58 - 1.70: 2 1.70 - 1.83: 207 Bond restraints: 29469 Sorted by residual: bond pdb=" CG PRO C 447 " pdb=" CD PRO C 447 " ideal model delta sigma weight residual 1.503 1.209 0.294 3.40e-02 8.65e+02 7.48e+01 bond pdb=" N PRO C 447 " pdb=" CD PRO C 447 " ideal model delta sigma weight residual 1.473 1.540 -0.067 1.40e-02 5.10e+03 2.28e+01 bond pdb=" CB PRO C 447 " pdb=" CG PRO C 447 " ideal model delta sigma weight residual 1.492 1.644 -0.152 5.00e-02 4.00e+02 9.26e+00 bond pdb=" N PRO C 447 " pdb=" CA PRO C 447 " ideal model delta sigma weight residual 1.469 1.432 0.037 1.28e-02 6.10e+03 8.27e+00 bond pdb=" CB PRO A 304 " pdb=" CG PRO A 304 " ideal model delta sigma weight residual 1.492 1.598 -0.106 5.00e-02 4.00e+02 4.51e+00 ... (remaining 29464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 40128 3.69 - 7.39: 122 7.39 - 11.08: 9 11.08 - 14.77: 1 14.77 - 18.46: 2 Bond angle restraints: 40262 Sorted by residual: angle pdb=" CA PRO C 447 " pdb=" N PRO C 447 " pdb=" CD PRO C 447 " ideal model delta sigma weight residual 112.00 93.54 18.46 1.40e+00 5.10e-01 1.74e+02 angle pdb=" N PRO C 447 " pdb=" CD PRO C 447 " pdb=" CG PRO C 447 " ideal model delta sigma weight residual 103.20 85.95 17.25 1.50e+00 4.44e-01 1.32e+02 angle pdb=" CA PRO C 447 " pdb=" CB PRO C 447 " pdb=" CG PRO C 447 " ideal model delta sigma weight residual 104.50 91.58 12.92 1.90e+00 2.77e-01 4.62e+01 angle pdb=" N VAL B 357 " pdb=" CA VAL B 357 " pdb=" C VAL B 357 " ideal model delta sigma weight residual 113.71 108.20 5.51 9.50e-01 1.11e+00 3.36e+01 angle pdb=" CA PRO A 304 " pdb=" N PRO A 304 " pdb=" CD PRO A 304 " ideal model delta sigma weight residual 112.00 104.36 7.64 1.40e+00 5.10e-01 2.98e+01 ... (remaining 40257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 15009 17.69 - 35.39: 1831 35.39 - 53.08: 444 53.08 - 70.78: 82 70.78 - 88.47: 21 Dihedral angle restraints: 17387 sinusoidal: 5837 harmonic: 11550 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 -86.00 -170.40 84.40 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS B 436 " pdb=" SG CYS B 436 " pdb=" SG CYS B 456 " pdb=" CB CYS B 456 " ideal model delta sinusoidal sigma weight residual -86.00 -158.90 72.90 1 1.00e+01 1.00e-02 6.78e+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 93.00 164.96 -71.96 1 1.00e+01 1.00e-02 6.63e+01 ... (remaining 17384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3307 0.040 - 0.081: 1021 0.081 - 0.121: 339 0.121 - 0.161: 37 0.161 - 0.202: 2 Chirality restraints: 4706 Sorted by residual: chirality pdb=" CA PRO C 447 " pdb=" N PRO C 447 " pdb=" C PRO C 447 " pdb=" CB PRO C 447 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB THR D 205 " pdb=" CA THR D 205 " pdb=" OG1 THR D 205 " pdb=" CG2 THR D 205 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CA ILE A 527 " pdb=" N ILE A 527 " pdb=" C ILE A 527 " pdb=" CB ILE A 527 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 4703 not shown) Planarity restraints: 5169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 446 " 0.088 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO C 447 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO C 447 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 447 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 303 " -0.077 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO A 304 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 761 " 0.020 2.00e-02 2.50e+03 4.17e-02 1.74e+01 pdb=" C HIS A 761 " -0.072 2.00e-02 2.50e+03 pdb=" O HIS A 761 " 0.028 2.00e-02 2.50e+03 pdb=" N GLU A 762 " 0.024 2.00e-02 2.50e+03 ... (remaining 5166 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 408 2.65 - 3.21: 26829 3.21 - 3.77: 41840 3.77 - 4.34: 51480 4.34 - 4.90: 88642 Nonbonded interactions: 209199 Sorted by model distance: nonbonded pdb=" OG1 THR C 312 " pdb=" O THR D 77 " model vdw 2.087 3.040 nonbonded pdb=" OD2 ASP B 523 " pdb=" NZ LYS B 752 " model vdw 2.183 3.120 nonbonded pdb=" O MET M 3 " pdb=" OG SER M 25 " model vdw 2.200 3.040 nonbonded pdb=" NZ LYS A 131 " pdb=" O PHE A 137 " model vdw 2.202 3.120 nonbonded pdb=" NZ LYS C 483 " pdb=" O LYS C 666 " model vdw 2.210 3.120 ... (remaining 209194 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 25 through 43 or (resid 44 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 100 or (resid 101 throu \ gh 102 and (name N or name CA or name C or name O or name CB )) or resid 103 thr \ ough 184 or (resid 185 through 186 and (name N or name CA or name C or name O or \ name CB )) or resid 187 through 387 or (resid 388 and (name N or name CA or nam \ e C or name O or name CB )) or resid 389 through 391 or (resid 392 and (name N o \ r name CA or name C or name O or name CB )) or resid 393 or (resid 394 and (name \ N or name CA or name C or name O or name CB )) or resid 395 through 398 or (res \ id 399 and (name N or name CA or name C or name O or name CB )) or resid 400 thr \ ough 415 or (resid 416 through 417 and (name N or name CA or name C or name O or \ name CB )) or resid 418 or (resid 419 and (name N or name CA or name C or name \ O or name CB )) or resid 420 or (resid 421 through 424 and (name N or name CA or \ name C or name O or name CB )) or resid 425 through 426 or (resid 427 and (name \ N or name CA or name C or name O or name CB )) or resid 428 or (resid 429 and ( \ name N or name CA or name C or name O or name CB )) or resid 430 through 445 or \ (resid 446 and (name N or name CA or name C or name O or name CB )) or resid 447 \ through 450 or (resid 451 and (name N or name CA or name C or name O or name CB \ )) or resid 452 through 469 or (resid 470 and (name N or name CA or name C or n \ ame O or name CB )) or resid 471 through 488 or (resid 489 and (name N or name C \ A or name C or name 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 or (resid 494 a \ nd (name N or name CA or name C or name O or name CB )) or resid 495 through 510 \ or (resid 511 and (name N or name CA or name C or name O or name CB )) or resid \ 512 through 542 or (resid 543 through 546 and (name N or name CA or name C or n \ ame O or name CB )) or resid 547 through 550 or (resid 551 through 556 and (name \ N or name CA or name C or name O or name CB )) or resid 557 through 572 or (res \ id 573 through 577 and (name N or name CA or name C or name O or name CB )) or r \ esid 578 or (resid 579 through 582 and (name N or name CA or name C or name O or \ name CB )) or resid 583 or (resid 584 through 588 and (name N or name CA or nam \ e C or name O or name CB )) or resid 589 through 606 or (resid 607 through 613 a \ nd (name N or name CA or name C or name O or name CB )) or resid 614 through 634 \ or (resid 635 through 640 and (name N or name CA or name C or name O or name CB \ )) or resid 641 through 642 or (resid 643 and (name N or name CA or name C or n \ ame O or name CB )) or resid 644 or (resid 645 and (name N or name CA or name C \ or name O or name CB )) or resid 646 through 650 or (resid 651 and (name N or na \ me CA or name C or name O or name CB )) or resid 652 or (resid 653 through 655 a \ nd (name N or name CA or name C or name O or name CB )) or resid 656 or (resid 6 \ 57 through 659 and (name N or name CA or name 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 n \ ame O or name CB )) or resid 668 through 675 or (resid 676 and (name N or name C \ A or name C or name O or name CB )) or resid 677 through 679 or (resid 680 and ( \ name N or name CA or name C or name O or name CB )) or resid 681 through 684 or \ (resid 685 and (name N or name CA or name C or name O or name CB )) or resid 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 692 or (resid 693 and (name N or name CA or name C or n \ ame O or name CB )) or resid 694 through 696 or (resid 697 through 698 and (name \ N or name CA or name C or name O or name CB )) or resid 699 through 703 or (res \ id 704 and (name N or name CA or name C or name O or name CB )) or resid 705 thr \ ough 723 or (resid 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 o \ r name CA or name C or name O or name CB )) or resid 747 through 750 or (resid 7 \ 51 and (name N or name CA or name C or name O or name CB )) or resid 752 through \ 761 or (resid 762 and (name N or name CA or name C or name O or name CB )) or r \ esid 763 through 769 or (resid 770 through 771 and (name N or name CA or name C \ or name O or name CB )) or resid 772 through 775 or (resid 776 through 778 and ( \ name N or name CA or name C or name O or name CB )) or resid 779 through 789 or \ (resid 790 through 793 and (name N or name CA or name C or name O or name CB )) \ or (resid 794 through 801 and (name N or name CA or name C or name O or name CB \ )) or resid 802 or (resid 803 through 813 and (name N or name CA or name C or na \ me O or name CB )))) selection = (chain 'C' and (resid 25 through 447 or (resid 448 through 449 and (name N or na \ me CA or name C or name O or name CB )) or resid 450 through 482 or (resid 483 a \ nd (name N or name CA or name C or name O or name CB )) or resid 484 through 485 \ or (resid 486 and (name N or name CA or name C or name O or name CB )) or resid \ 487 through 501 or (resid 502 and (name N or name CA or name C or name O or nam \ e CB )) or resid 503 through 561 or (resid 562 and (name N or name CA or name C \ or name O or name CB )) or resid 563 through 565 or (resid 566 and (name N or na \ me CA or name C or name O or name CB )) or resid 567 or (resid 568 through 569 a \ nd (name N or name CA or name C or name O or name CB )) or resid 570 through 584 \ or (resid 585 through 588 and (name N or name CA or name C or name O or name CB \ )) or resid 589 through 591 or (resid 592 and (name N or name CA or name C or n \ ame O or name CB )) or resid 593 through 611 or (resid 612 through 613 and (name \ N or name CA or name C or name O or name CB )) or resid 614 through 619 or (res \ id 620 through 624 and (name N or name CA or name C or name O or name CB )) or r \ esid 625 through 677 or (resid 678 through 680 and (name N or name CA or name C \ or name O or name CB )) or resid 681 through 683 or (resid 684 through 685 and ( \ name N or name CA or name C or name O or name CB )) or resid 686 through 690 or \ (resid 691 and (name N or name CA or name C or name O or name CB )) or resid 692 \ through 726 or (resid 727 and (name N or name CA or name C or name O or name CB \ )) or resid 728 through 766 or (resid 767 and (name N or name CA or name C or n \ ame O or name CB )) or resid 768 through 774 or (resid 775 through 778 and (name \ N or name CA or name C or name O or name CB )) or resid 779 through 784 or (res \ id 785 through 786 and (name N or name CA or name C or name O or name CB )) or r \ esid 787 through 813)) } ncs_group { reference = (chain 'B' and (resid 34 through 241 or (resid 242 through 243 and (name N or na \ me CA or name C or name O or name CB )) or resid 244 through 288 or (resid 289 t \ hrough 290 and (name N or name CA or name C or name O or name CB )) or resid 291 \ through 314 or (resid 315 through 318 and (name N or name CA or name C or name \ O or name CB )) or resid 319 through 351 or (resid 352 through 353 and (name N o \ r name CA or name C or name O or name CB )) or resid 354 through 396 or (resid 3 \ 97 through 400 and (name N or name CA or name C or name O or name CB )) or resid \ 401 through 402 or (resid 403 and (name N or name CA or name C or name O or nam \ e CB )) or resid 404 through 419 or (resid 420 through 421 and (name N or name C \ A or name C or name O or name CB )) or resid 422 or (resid 423 and (name N or na \ me CA or name C or name O or name CB )) or resid 424 or (resid 425 and (name N o \ r name CA or name C or name O or name CB )) or resid 426 or (resid 427 through 4 \ 28 and (name N or name CA or name C or name O or name CB )) or resid 429 through \ 437 or (resid 438 and (name N or name CA or name C or name O or name CB )) or r \ esid 439 or (resid 440 through 448 and (name N or name CA or name C or name O or \ name CB )) or resid 449 through 471 or (resid 472 and (name N or name CA or nam \ e 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 480 or (resid 481 through 4 \ 82 and (name N or name CA or name C or name O or name CB )) or resid 483 or (res \ id 484 and (name N or name CA or name C or name O or name CB )) or resid 485 thr \ ough 487 or (resid 488 through 491 and (name N or name CA or name C or name O or \ name CB )) or resid 492 through 493 or (resid 494 and (name N or name CA or nam \ e C or name O or name CB )) or resid 495 through 502 or (resid 503 and (name N o \ r name CA or name C or name O or name CB )) or resid 504 through 510 or (resid 5 \ 11 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 r \ esid 517 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 name \ O or name CB )) or resid 526 through 535 or (resid 536 and (name N or name CA or \ name C or name O or name CB )) or resid 537 or (resid 538 and (name N or name C \ A or name C or name O or name CB )) or resid 539 through 540 or (resid 541 and ( \ name N or name CA or name C or name O or name CB )) or resid 542 through 590 or \ (resid 591 through 593 and (name N or name CA or name C or name O or name CB )) \ or resid 594 through 606 or (resid 607 through 609 and (name N or name CA or nam \ e C or name O or name CB )) or resid 610 through 618 or (resid 619 through 621 a \ nd (name N or name CA or name C or name O or name CB )) or resid 622 through 627 \ or (resid 628 through 631 and (name N or name CA or name C or name O or name CB \ )) or resid 632 through 640 or (resid 641 through 643 and (name N or name CA or \ name C or name O or name CB )) or resid 644 through 646 or (resid 647 and (name \ N or name CA or name C or name O or name CB )) or resid 648 through 663 or (res \ id 664 through 665 and (name N or name CA or name C or name O or name CB )) or r \ esid 666 through 669 or (resid 670 and (name N or name CA or name C or name O or \ name CB )) or resid 671 through 676 or (resid 677 and (name N or name CA or nam \ e C or name O or name CB )) or resid 678 through 682 or (resid 683 and (name N o \ r name CA or name C or name O or name CB )) or resid 684 through 685 or (resid 6 \ 86 through 687 and (name N or name CA or name C or name O or name CB )) or resid \ 688 or (resid 689 and (name N or name CA or name C or name O or name CB )) or r \ esid 690 through 696 or (resid 697 through 698 and (name N or name CA or name C \ or name O or name CB )) or resid 699 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 707 an \ d (name N or name CA or name C or name O or name CB )) or resid 708 through 720 \ or (resid 721 through 723 and (name N or name CA or name C or name O or name CB \ )) or resid 724 through 733 or (resid 734 through 737 and (name N or name CA or \ name C or name O or name CB )) or resid 738 through 766 or (resid 767 and (name \ N or name CA or name C or name O or name CB )) or resid 768 through 780 or (resi \ d 781 through 791 and (name N or name CA or name C or name O or name CB )) or re \ sid 792 through 793 or (resid 794 through 814 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'D' and (resid 34 through 49 or (resid 50 through 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 65 or (resid 66 and (na \ me N or name CA or name C or name O or name CB )) or resid 67 through 75 or (res \ id 76 and (name N or name CA or name C or name O or name CB )) or resid 77 throu \ gh 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) or \ resid 193 through 234 or (resid 235 through 236 and (name N or name CA or name \ C or name O or name CB )) or resid 237 through 263 or (resid 264 and (name N or \ name CA or name C or name O or name CB )) or resid 265 through 269 or (resid 270 \ and (name N or name CA or name C or name O or name CB )) or resid 271 through 2 \ 84 or (resid 285 and (name N or name CA or name C or name O or name CB )) or res \ id 286 through 293 or (resid 294 and (name N or name CA or name C or name O or n \ ame CB )) or resid 295 through 399 or (resid 400 and (name N or name CA or name \ C or name O or name CB )) or resid 401 through 411 or (resid 412 and (name N or \ name CA or name C or name O or name CB )) or resid 413 through 519 or (resid 520 \ and (name N or name CA or name C or name O or name CB )) or resid 521 through 5 \ 53 or (resid 554 through 557 and (name N or name CA or name C or name O or name \ CB )) or resid 558 through 563 or (resid 564 and (name N or name CA or name C or \ name O or name CB )) or resid 565 through 566 or (resid 567 and (name N or name \ CA or name C or name O or name CB )) or resid 568 through 575 or (resid 576 thr \ ough 579 and (name N or name CA or name C or name O or name CB )) or resid 580 o \ r (resid 581 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 82 through 591 or (resid 592 through 593 and (name N or name CA or name C or nam \ e O or name CB )) or resid 594 through 619 or (resid 620 through 621 and (name N \ or name CA or name C or name O or name CB )) or resid 622 through 641 or (resid \ 642 through 643 and (name N or name CA or name C or name O or name CB )) or res \ id 644 through 655 or (resid 656 through 657 and (name N or name CA or name C or \ name O or name CB )) or resid 658 through 694 or (resid 695 through 698 and (na \ me N or name CA or name C or name O or name CB )) or resid 699 through 746 or (r \ esid 747 and (name N or name CA or name C or name O or name CB )) or resid 748 t \ hrough 768 or (resid 769 through 770 and (name N or name CA or name C or name O \ or name CB )) or resid 771 through 773 or (resid 774 and (name N or name CA or n \ ame C or name O or name CB )) or resid 775 through 778 or (resid 779 and (name N \ or name CA or name C or name O or name CB )) or resid 780 through 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' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } 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: 5.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.310 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 67.790 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 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 : 0.004 0.294 29493 Z= 0.172 Angle : 0.631 18.463 40310 Z= 0.337 Chirality : 0.043 0.202 4706 Planarity : 0.005 0.117 5169 Dihedral : 16.555 88.474 9871 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.50 % Allowed : 12.15 % Favored : 87.34 % Rotamer: Outliers : 0.40 % Allowed : 34.53 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3966 helix: 1.80 (0.15), residues: 1253 sheet: -1.03 (0.20), residues: 790 loop : -2.35 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 284 HIS 0.005 0.001 HIS C 761 PHE 0.022 0.001 PHE A 472 TYR 0.015 0.001 TYR A 526 ARG 0.007 0.000 ARG M 62 Details of bonding type rmsd hydrogen bonds : bond 0.16370 ( 1174) hydrogen bonds : angle 6.16788 ( 3462) SS BOND : bond 0.00268 ( 24) SS BOND : angle 1.12517 ( 48) covalent geometry : bond 0.00433 (29469) covalent geometry : angle 0.62978 (40262) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 280 time to evaluate : 3.042 Fit side-chains revert: symmetry clash REVERT: A 685 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6727 (mmt180) REVERT: A 770 ASP cc_start: 0.8032 (t70) cc_final: 0.7777 (t0) REVERT: C 41 MET cc_start: 0.6506 (tpt) cc_final: 0.6058 (tpt) REVERT: D 135 MET cc_start: 0.7822 (pmm) cc_final: 0.6158 (ttp) outliers start: 11 outliers final: 5 residues processed: 290 average time/residue: 0.3647 time to fit residues: 175.2549 Evaluate side-chains 283 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 277 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 685 ARG Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain H residue 30 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 20.0000 chunk 300 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 102 optimal weight: 0.2980 chunk 202 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 310 optimal weight: 9.9990 chunk 120 optimal weight: 0.7980 chunk 188 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 359 optimal weight: 0.9980 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.187600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.153388 restraints weight = 53458.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.143121 restraints weight = 87292.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138826 restraints weight = 90620.813| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 29493 Z= 0.218 Angle : 0.648 14.912 40310 Z= 0.337 Chirality : 0.045 0.172 4706 Planarity : 0.004 0.071 5169 Dihedral : 4.849 58.527 4244 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.96 % Favored : 86.56 % Rotamer: Outliers : 5.66 % Allowed : 31.37 % Favored : 62.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3966 helix: 1.84 (0.15), residues: 1271 sheet: -1.05 (0.20), residues: 780 loop : -2.43 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 151 HIS 0.006 0.001 HIS C 761 PHE 0.028 0.002 PHE A 472 TYR 0.031 0.001 TYR D 478 ARG 0.004 0.000 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.04721 ( 1174) hydrogen bonds : angle 4.92027 ( 3462) SS BOND : bond 0.00292 ( 24) SS BOND : angle 1.02175 ( 48) covalent geometry : bond 0.00532 (29469) covalent geometry : angle 0.64762 (40262) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 290 time to evaluate : 3.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8795 (tt) REVERT: A 526 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7693 (p90) REVERT: A 770 ASP cc_start: 0.8215 (t70) cc_final: 0.7947 (t0) REVERT: B 228 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8554 (mp) REVERT: C 83 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8440 (mt) REVERT: C 184 LEU cc_start: 0.7741 (pt) cc_final: 0.7244 (mt) REVERT: C 209 MET cc_start: 0.7817 (tpt) cc_final: 0.7597 (ptp) REVERT: C 661 ILE cc_start: 0.4983 (OUTLIER) cc_final: 0.4513 (pp) REVERT: C 779 CYS cc_start: 0.3784 (OUTLIER) cc_final: 0.2394 (t) REVERT: D 73 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8083 (tm) REVERT: D 135 MET cc_start: 0.8161 (pmm) cc_final: 0.6635 (ttp) REVERT: D 159 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8636 (mm) REVERT: D 457 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8528 (pmtt) REVERT: L 76 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7674 (pp) REVERT: M 69 SER cc_start: 0.6947 (OUTLIER) cc_final: 0.6319 (m) outliers start: 156 outliers final: 94 residues processed: 420 average time/residue: 0.3667 time to fit residues: 258.2717 Evaluate side-chains 383 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 278 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 779 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 457 LYS Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 94 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 51 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 77 optimal weight: 30.0000 chunk 225 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 303 optimal weight: 5.9990 chunk 377 optimal weight: 0.9980 chunk 328 optimal weight: 30.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 GLN C 363 GLN L 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.185864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132393 restraints weight = 53166.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127121 restraints weight = 66809.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.128649 restraints weight = 55626.912| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29493 Z= 0.136 Angle : 0.575 8.874 40310 Z= 0.299 Chirality : 0.043 0.153 4706 Planarity : 0.004 0.057 5169 Dihedral : 4.565 54.519 4236 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.97 % Favored : 88.55 % Rotamer: Outliers : 6.35 % Allowed : 30.90 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3966 helix: 1.94 (0.15), residues: 1273 sheet: -1.05 (0.20), residues: 773 loop : -2.34 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 151 HIS 0.004 0.001 HIS D 332 PHE 0.020 0.001 PHE A 472 TYR 0.018 0.001 TYR D 478 ARG 0.007 0.000 ARG L 40 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 1174) hydrogen bonds : angle 4.53906 ( 3462) SS BOND : bond 0.00274 ( 24) SS BOND : angle 0.93898 ( 48) covalent geometry : bond 0.00323 (29469) covalent geometry : angle 0.57424 (40262) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 287 time to evaluate : 3.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: A 526 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.7562 (p90) REVERT: A 755 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8590 (tt) REVERT: A 770 ASP cc_start: 0.8065 (t70) cc_final: 0.7779 (t0) REVERT: A 790 MET cc_start: 0.0665 (tpt) cc_final: -0.1656 (ptp) REVERT: B 378 TRP cc_start: 0.8829 (OUTLIER) cc_final: 0.8473 (t60) REVERT: B 427 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6967 (tm-30) REVERT: C 466 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8109 (tt) REVERT: C 512 MET cc_start: 0.7742 (tmm) cc_final: 0.7416 (tmm) REVERT: C 661 ILE cc_start: 0.4841 (OUTLIER) cc_final: 0.4352 (pp) REVERT: D 73 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7944 (tm) REVERT: D 135 MET cc_start: 0.8094 (pmm) cc_final: 0.6675 (ttp) REVERT: D 159 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8472 (mm) REVERT: D 348 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7837 (pp) REVERT: D 378 TRP cc_start: 0.7884 (OUTLIER) cc_final: 0.6830 (t60) REVERT: D 457 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8576 (pmtt) REVERT: D 564 MET cc_start: -0.0660 (ppp) cc_final: -0.0891 (ppp) REVERT: I 105 TYR cc_start: 0.8911 (m-80) cc_final: 0.8479 (m-80) outliers start: 175 outliers final: 112 residues processed: 436 average time/residue: 0.3518 time to fit residues: 256.9100 Evaluate side-chains 399 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 275 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 378 TRP Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 457 LYS Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 94 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 252 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 353 optimal weight: 0.5980 chunk 225 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 382 optimal weight: 6.9990 chunk 355 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 307 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN I 208 ASN L 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.185294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.126768 restraints weight = 53768.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.118153 restraints weight = 45872.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118505 restraints weight = 47247.049| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29493 Z= 0.106 Angle : 0.557 13.820 40310 Z= 0.285 Chirality : 0.042 0.154 4706 Planarity : 0.004 0.058 5169 Dihedral : 4.335 57.545 4236 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.94 % Favored : 88.58 % Rotamer: Outliers : 5.99 % Allowed : 30.97 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3966 helix: 2.06 (0.15), residues: 1272 sheet: -0.91 (0.20), residues: 781 loop : -2.32 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 151 HIS 0.004 0.001 HIS D 332 PHE 0.013 0.001 PHE A 472 TYR 0.014 0.001 TYR B 321 ARG 0.007 0.000 ARG M 40 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 1174) hydrogen bonds : angle 4.27490 ( 3462) SS BOND : bond 0.00262 ( 24) SS BOND : angle 1.13388 ( 48) covalent geometry : bond 0.00241 (29469) covalent geometry : angle 0.55547 (40262) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 287 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: A 489 ARG cc_start: 0.8499 (ttm170) cc_final: 0.7952 (ptm160) REVERT: A 526 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7415 (p90) REVERT: A 770 ASP cc_start: 0.8146 (t70) cc_final: 0.7848 (t0) REVERT: A 790 MET cc_start: 0.0006 (tpt) cc_final: -0.1725 (mtt) REVERT: B 378 TRP cc_start: 0.8766 (OUTLIER) cc_final: 0.8394 (t60) REVERT: B 427 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6991 (tm-30) REVERT: C 184 LEU cc_start: 0.7559 (pt) cc_final: 0.7161 (mt) REVERT: C 209 MET cc_start: 0.8239 (mmm) cc_final: 0.7877 (ptp) REVERT: C 435 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7737 (tp) REVERT: C 661 ILE cc_start: 0.5173 (OUTLIER) cc_final: 0.4764 (pp) REVERT: D 73 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7765 (tm) REVERT: D 135 MET cc_start: 0.8104 (pmm) cc_final: 0.6743 (ttp) REVERT: D 159 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8439 (mm) REVERT: D 348 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7581 (pp) REVERT: D 378 TRP cc_start: 0.7865 (OUTLIER) cc_final: 0.6751 (t60) REVERT: D 457 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8519 (pmtt) REVERT: D 561 MET cc_start: -0.1010 (mmt) cc_final: -0.2563 (ttm) REVERT: L 37 TYR cc_start: 0.7260 (m-80) cc_final: 0.7051 (m-80) REVERT: M 69 SER cc_start: 0.7733 (OUTLIER) cc_final: 0.7055 (m) outliers start: 165 outliers final: 104 residues processed: 427 average time/residue: 0.3312 time to fit residues: 239.4925 Evaluate side-chains 389 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 273 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 761 HIS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 378 TRP Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 457 LYS Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 812 HIS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 279 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 389 optimal weight: 3.9990 chunk 361 optimal weight: 4.9990 chunk 366 optimal weight: 40.0000 chunk 26 optimal weight: 0.8980 chunk 273 optimal weight: 3.9990 chunk 295 optimal weight: 4.9990 chunk 308 optimal weight: 0.5980 chunk 236 optimal weight: 8.9990 chunk 165 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN C 499 ASN L 61 ASN ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.181356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3672 r_free = 0.3672 target = 0.127809 restraints weight = 53440.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121848 restraints weight = 72550.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.124109 restraints weight = 60598.664| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 29493 Z= 0.209 Angle : 0.630 10.195 40310 Z= 0.327 Chirality : 0.044 0.169 4706 Planarity : 0.004 0.070 5169 Dihedral : 4.639 53.701 4236 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.58 % Favored : 86.94 % Rotamer: Outliers : 8.13 % Allowed : 29.38 % Favored : 62.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3966 helix: 2.00 (0.15), residues: 1264 sheet: -0.99 (0.19), residues: 800 loop : -2.34 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 151 HIS 0.006 0.001 HIS A 477 PHE 0.029 0.002 PHE A 472 TYR 0.029 0.001 TYR D 478 ARG 0.005 0.000 ARG M 62 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 1174) hydrogen bonds : angle 4.39630 ( 3462) SS BOND : bond 0.00284 ( 24) SS BOND : angle 1.14238 ( 48) covalent geometry : bond 0.00513 (29469) covalent geometry : angle 0.62864 (40262) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 279 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: A 526 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.7827 (p90) REVERT: A 755 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8710 (tt) REVERT: A 770 ASP cc_start: 0.8071 (t70) cc_final: 0.7755 (t0) REVERT: A 790 MET cc_start: 0.0499 (tpt) cc_final: -0.1576 (mtt) REVERT: B 72 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8091 (tt) REVERT: B 228 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8931 (mp) REVERT: B 238 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7149 (mp) REVERT: B 378 TRP cc_start: 0.8852 (OUTLIER) cc_final: 0.8485 (t60) REVERT: B 734 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.8188 (t80) REVERT: C 41 MET cc_start: 0.8127 (tpt) cc_final: 0.7599 (tpt) REVERT: C 184 LEU cc_start: 0.7574 (pt) cc_final: 0.6889 (mt) REVERT: C 499 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8353 (p0) REVERT: C 512 MET cc_start: 0.8064 (tmm) cc_final: 0.7574 (tmm) REVERT: C 661 ILE cc_start: 0.5101 (OUTLIER) cc_final: 0.4556 (pp) REVERT: C 761 HIS cc_start: 0.9275 (OUTLIER) cc_final: 0.8973 (m-70) REVERT: D 73 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7886 (tm) REVERT: D 113 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7626 (mp) REVERT: D 135 MET cc_start: 0.8138 (pmm) cc_final: 0.6770 (ttp) REVERT: D 159 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8646 (mm) REVERT: D 240 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8489 (mt) REVERT: D 348 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7900 (pp) REVERT: D 378 TRP cc_start: 0.8011 (OUTLIER) cc_final: 0.6828 (t60) REVERT: D 457 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8506 (pmtt) REVERT: D 496 MET cc_start: 0.8034 (mtt) cc_final: 0.7488 (mtt) REVERT: M 69 SER cc_start: 0.7206 (OUTLIER) cc_final: 0.6534 (m) outliers start: 224 outliers final: 162 residues processed: 472 average time/residue: 0.3405 time to fit residues: 268.5185 Evaluate side-chains 450 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 269 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 746 ASP Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 734 TYR Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 761 HIS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 378 TRP Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 457 LYS Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 660 PHE Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 812 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 121 optimal weight: 1.9990 chunk 379 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 295 optimal weight: 5.9990 chunk 274 optimal weight: 0.9980 chunk 212 optimal weight: 40.0000 chunk 326 optimal weight: 30.0000 chunk 357 optimal weight: 0.0060 chunk 258 optimal weight: 0.3980 chunk 238 optimal weight: 0.0570 chunk 139 optimal weight: 4.9990 overall best weight: 0.6916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN L 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.183043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.130765 restraints weight = 53828.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127228 restraints weight = 65736.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.127916 restraints weight = 56518.339| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29493 Z= 0.105 Angle : 0.555 9.312 40310 Z= 0.287 Chirality : 0.042 0.169 4706 Planarity : 0.004 0.067 5169 Dihedral : 4.377 56.476 4236 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.67 % Favored : 88.86 % Rotamer: Outliers : 6.10 % Allowed : 31.23 % Favored : 62.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3966 helix: 2.11 (0.15), residues: 1263 sheet: -0.77 (0.20), residues: 756 loop : -2.28 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 151 HIS 0.004 0.001 HIS D 332 PHE 0.014 0.001 PHE A 472 TYR 0.014 0.001 TYR B 321 ARG 0.006 0.000 ARG M 62 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 1174) hydrogen bonds : angle 4.15682 ( 3462) SS BOND : bond 0.00252 ( 24) SS BOND : angle 0.98947 ( 48) covalent geometry : bond 0.00239 (29469) covalent geometry : angle 0.55447 (40262) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 285 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: A 526 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.7503 (p90) REVERT: A 755 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8378 (tt) REVERT: A 770 ASP cc_start: 0.8026 (t70) cc_final: 0.7797 (t0) REVERT: A 790 MET cc_start: 0.0681 (tpt) cc_final: -0.1404 (mtt) REVERT: B 72 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7861 (tt) REVERT: B 378 TRP cc_start: 0.8775 (OUTLIER) cc_final: 0.8430 (t60) REVERT: C 435 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7811 (tp) REVERT: C 512 MET cc_start: 0.7983 (tmm) cc_final: 0.7223 (tmm) REVERT: C 661 ILE cc_start: 0.4859 (OUTLIER) cc_final: 0.4318 (pp) REVERT: D 73 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7834 (tm) REVERT: D 135 MET cc_start: 0.7968 (pmm) cc_final: 0.6790 (ttp) REVERT: D 159 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8465 (mm) REVERT: D 348 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7828 (pp) REVERT: D 378 TRP cc_start: 0.7924 (OUTLIER) cc_final: 0.6721 (t60) REVERT: D 457 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8565 (pmtt) REVERT: D 561 MET cc_start: -0.1235 (mmt) cc_final: -0.2676 (ttm) REVERT: H 3 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7446 (mm-40) REVERT: M 69 SER cc_start: 0.7202 (OUTLIER) cc_final: 0.6516 (m) outliers start: 168 outliers final: 131 residues processed: 429 average time/residue: 0.3497 time to fit residues: 251.1963 Evaluate side-chains 422 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 278 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 771 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 378 TRP 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 411 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 457 LYS Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 660 PHE Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 812 HIS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 77 optimal weight: 6.9990 chunk 316 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 310 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 314 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN C 363 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.184160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123046 restraints weight = 53199.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.115939 restraints weight = 44375.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115810 restraints weight = 44802.967| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 29493 Z= 0.199 Angle : 0.622 15.107 40310 Z= 0.321 Chirality : 0.044 0.168 4706 Planarity : 0.004 0.071 5169 Dihedral : 4.570 53.898 4236 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.50 % Allowed : 12.41 % Favored : 87.09 % Rotamer: Outliers : 7.19 % Allowed : 30.46 % Favored : 62.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.14), residues: 3966 helix: 2.00 (0.15), residues: 1275 sheet: -0.80 (0.20), residues: 766 loop : -2.35 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 151 HIS 0.006 0.001 HIS A 477 PHE 0.028 0.002 PHE A 472 TYR 0.026 0.001 TYR D 478 ARG 0.012 0.000 ARG L 189 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 1174) hydrogen bonds : angle 4.27496 ( 3462) SS BOND : bond 0.00363 ( 24) SS BOND : angle 1.15489 ( 48) covalent geometry : bond 0.00489 (29469) covalent geometry : angle 0.62109 (40262) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 278 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: A 397 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7705 (tmm160) REVERT: A 526 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7837 (p90) REVERT: A 755 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8447 (tt) REVERT: A 770 ASP cc_start: 0.8209 (t70) cc_final: 0.7908 (t0) REVERT: A 790 MET cc_start: 0.0046 (tpt) cc_final: -0.1624 (mtt) REVERT: B 72 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8049 (tt) REVERT: B 238 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7215 (mp) REVERT: B 378 TRP cc_start: 0.8858 (OUTLIER) cc_final: 0.8468 (t60) REVERT: C 41 MET cc_start: 0.8419 (tpt) cc_final: 0.7951 (tpt) REVERT: C 184 LEU cc_start: 0.7516 (pt) cc_final: 0.7155 (mt) REVERT: C 435 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7763 (tp) REVERT: C 483 LYS cc_start: 0.7272 (mmmt) cc_final: 0.7066 (mmmt) REVERT: C 512 MET cc_start: 0.8041 (tmm) cc_final: 0.7317 (tmm) REVERT: C 661 ILE cc_start: 0.5378 (OUTLIER) cc_final: 0.4929 (pp) REVERT: D 73 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7804 (tm) REVERT: D 135 MET cc_start: 0.8093 (pmm) cc_final: 0.6874 (ttp) REVERT: D 159 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8673 (mm) REVERT: D 221 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8825 (ptpp) REVERT: D 348 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7523 (pp) REVERT: D 378 TRP cc_start: 0.8041 (OUTLIER) cc_final: 0.6804 (t60) REVERT: D 457 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8464 (pmtt) REVERT: D 561 MET cc_start: -0.1085 (mmt) cc_final: -0.2459 (ttm) REVERT: I 180 GLN cc_start: 0.2289 (OUTLIER) cc_final: 0.2012 (tt0) REVERT: M 69 SER cc_start: 0.7754 (OUTLIER) cc_final: 0.7073 (m) outliers start: 198 outliers final: 157 residues processed: 449 average time/residue: 0.3412 time to fit residues: 257.2695 Evaluate side-chains 449 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 275 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 771 LYS Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 585 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 779 CYS Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 378 TRP 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 411 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 457 LYS Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 660 PHE Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 812 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 180 GLN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 60 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 222 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 192 optimal weight: 50.0000 chunk 327 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.181426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119833 restraints weight = 53240.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113169 restraints weight = 43185.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113269 restraints weight = 40469.217| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29493 Z= 0.130 Angle : 0.576 12.785 40310 Z= 0.296 Chirality : 0.042 0.175 4706 Planarity : 0.004 0.090 5169 Dihedral : 4.457 55.557 4236 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.04 % Favored : 88.48 % Rotamer: Outliers : 6.75 % Allowed : 31.01 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3966 helix: 2.05 (0.15), residues: 1278 sheet: -0.78 (0.20), residues: 762 loop : -2.30 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 36 HIS 0.004 0.001 HIS D 332 PHE 0.019 0.001 PHE A 472 TYR 0.016 0.001 TYR D 478 ARG 0.012 0.000 ARG L 55 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 1174) hydrogen bonds : angle 4.14006 ( 3462) SS BOND : bond 0.00254 ( 24) SS BOND : angle 1.03058 ( 48) covalent geometry : bond 0.00311 (29469) covalent geometry : angle 0.57561 (40262) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 278 time to evaluate : 3.281 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8899 (tt) REVERT: A 181 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: A 526 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7703 (p90) REVERT: A 667 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7277 (mm-40) REVERT: A 755 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8415 (tt) REVERT: A 770 ASP cc_start: 0.8202 (t70) cc_final: 0.7915 (t0) REVERT: A 790 MET cc_start: 0.0262 (tpt) cc_final: -0.1470 (mtt) REVERT: B 72 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7906 (tt) REVERT: B 238 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7123 (mp) REVERT: B 378 TRP cc_start: 0.8877 (OUTLIER) cc_final: 0.8553 (t60) REVERT: B 427 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7011 (tm-30) REVERT: B 734 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.8346 (t80) REVERT: C 41 MET cc_start: 0.8413 (tpt) cc_final: 0.7968 (tpt) REVERT: C 43 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8377 (mtm-85) REVERT: C 184 LEU cc_start: 0.7578 (pt) cc_final: 0.7122 (mt) REVERT: C 435 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7699 (tp) REVERT: C 483 LYS cc_start: 0.7221 (mmmt) cc_final: 0.6990 (mmmt) REVERT: C 512 MET cc_start: 0.7976 (tmm) cc_final: 0.7202 (tmm) REVERT: C 661 ILE cc_start: 0.5215 (OUTLIER) cc_final: 0.4783 (pp) REVERT: D 73 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7725 (tm) REVERT: D 135 MET cc_start: 0.8104 (pmm) cc_final: 0.6871 (ttp) REVERT: D 159 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8523 (mm) REVERT: D 348 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7567 (pp) REVERT: D 378 TRP cc_start: 0.8029 (OUTLIER) cc_final: 0.6751 (t60) REVERT: D 457 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8458 (pmtt) REVERT: D 561 MET cc_start: -0.1015 (mmt) cc_final: -0.2473 (ttm) REVERT: I 180 GLN cc_start: 0.2238 (OUTLIER) cc_final: 0.1967 (tt0) REVERT: L 55 ARG cc_start: 0.7862 (mtt-85) cc_final: 0.7581 (mtt180) REVERT: M 69 SER cc_start: 0.7781 (OUTLIER) cc_final: 0.7108 (m) outliers start: 186 outliers final: 147 residues processed: 441 average time/residue: 0.3340 time to fit residues: 248.5587 Evaluate side-chains 438 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 271 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 667 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 771 LYS Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 517 GLU Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 734 TYR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 585 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 378 TRP 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 411 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 457 LYS Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 660 PHE Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 812 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 180 GLN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 27 optimal weight: 0.7980 chunk 384 optimal weight: 20.0000 chunk 360 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 304 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 363 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.184478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129960 restraints weight = 53621.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.125731 restraints weight = 58929.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.126332 restraints weight = 52906.769| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29493 Z= 0.118 Angle : 0.567 11.521 40310 Z= 0.291 Chirality : 0.042 0.159 4706 Planarity : 0.004 0.074 5169 Dihedral : 4.328 55.782 4236 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.37 % Favored : 88.15 % Rotamer: Outliers : 6.75 % Allowed : 30.76 % Favored : 62.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3966 helix: 2.15 (0.15), residues: 1266 sheet: -0.72 (0.20), residues: 764 loop : -2.28 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP M 36 HIS 0.004 0.001 HIS D 332 PHE 0.016 0.001 PHE A 472 TYR 0.015 0.001 TYR B 321 ARG 0.009 0.000 ARG M 62 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 1174) hydrogen bonds : angle 4.06149 ( 3462) SS BOND : bond 0.00242 ( 24) SS BOND : angle 0.99077 ( 48) covalent geometry : bond 0.00280 (29469) covalent geometry : angle 0.56631 (40262) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 282 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8607 (tpp) cc_final: 0.8382 (tpp) REVERT: A 165 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8842 (tt) REVERT: A 181 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: A 526 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7660 (p90) REVERT: A 667 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7310 (mm-40) REVERT: A 755 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8340 (tt) REVERT: A 770 ASP cc_start: 0.8083 (t70) cc_final: 0.7818 (t0) REVERT: A 790 MET cc_start: 0.0193 (tpt) cc_final: -0.1494 (mtt) REVERT: B 238 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7546 (mp) REVERT: B 378 TRP cc_start: 0.8807 (OUTLIER) cc_final: 0.8477 (t60) REVERT: B 734 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.8245 (t80) REVERT: C 41 MET cc_start: 0.7984 (tpt) cc_final: 0.7478 (tpt) REVERT: C 184 LEU cc_start: 0.7627 (pt) cc_final: 0.7026 (mt) REVERT: C 435 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7756 (tp) REVERT: C 512 MET cc_start: 0.8006 (tmm) cc_final: 0.7172 (tmm) REVERT: C 661 ILE cc_start: 0.5042 (OUTLIER) cc_final: 0.4507 (pp) REVERT: D 73 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7735 (tm) REVERT: D 135 MET cc_start: 0.7958 (pmm) cc_final: 0.6821 (ttp) REVERT: D 159 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8544 (mm) REVERT: D 221 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8843 (ptpp) REVERT: D 348 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7855 (pp) REVERT: D 378 TRP cc_start: 0.7976 (OUTLIER) cc_final: 0.6719 (t60) REVERT: D 457 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8506 (pmtt) REVERT: D 561 MET cc_start: -0.1418 (mmt) cc_final: -0.2563 (ttm) REVERT: I 180 GLN cc_start: 0.2577 (OUTLIER) cc_final: 0.2149 (tt0) REVERT: M 69 SER cc_start: 0.7263 (OUTLIER) cc_final: 0.6540 (m) outliers start: 186 outliers final: 154 residues processed: 448 average time/residue: 0.3354 time to fit residues: 252.4569 Evaluate side-chains 447 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 275 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 667 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 771 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 715 LEU 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 759 LEU Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 585 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 779 CYS Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 378 TRP Chi-restraints excluded: chain D residue 382 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 411 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 457 LYS Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 660 PHE Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 812 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 180 GLN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 254 optimal weight: 0.8980 chunk 232 optimal weight: 10.0000 chunk 341 optimal weight: 2.9990 chunk 361 optimal weight: 0.0570 chunk 367 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 340 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 GLN A 761 HIS ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN H 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.184208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122637 restraints weight = 53113.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116808 restraints weight = 41810.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.116838 restraints weight = 41560.599| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29493 Z= 0.101 Angle : 0.557 11.172 40310 Z= 0.284 Chirality : 0.042 0.161 4706 Planarity : 0.004 0.082 5169 Dihedral : 4.163 57.145 4234 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.51 % Favored : 88.98 % Rotamer: Outliers : 5.70 % Allowed : 32.06 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3966 helix: 2.24 (0.15), residues: 1267 sheet: -0.62 (0.20), residues: 755 loop : -2.22 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 36 HIS 0.004 0.001 HIS A 761 PHE 0.012 0.001 PHE A 472 TYR 0.018 0.001 TYR L 50 ARG 0.010 0.000 ARG M 62 Details of bonding type rmsd hydrogen bonds : bond 0.02872 ( 1174) hydrogen bonds : angle 3.94692 ( 3462) SS BOND : bond 0.00269 ( 24) SS BOND : angle 0.92027 ( 48) covalent geometry : bond 0.00231 (29469) covalent geometry : angle 0.55665 (40262) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 297 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8672 (tpp) cc_final: 0.8430 (tpp) REVERT: A 165 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8740 (tt) REVERT: A 181 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: A 526 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7453 (p90) REVERT: A 755 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8418 (tt) REVERT: A 770 ASP cc_start: 0.8185 (t70) cc_final: 0.7868 (t0) REVERT: A 790 MET cc_start: -0.0061 (tpt) cc_final: -0.1501 (mtt) REVERT: B 238 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7324 (mp) REVERT: B 378 TRP cc_start: 0.8775 (OUTLIER) cc_final: 0.8435 (t60) REVERT: B 734 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.8299 (t80) REVERT: C 41 MET cc_start: 0.8405 (tpt) cc_final: 0.7903 (tpt) REVERT: C 184 LEU cc_start: 0.7515 (pt) cc_final: 0.7047 (mt) REVERT: C 190 LYS cc_start: 0.7520 (tptp) cc_final: 0.7146 (tptp) REVERT: C 435 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7634 (tp) REVERT: C 512 MET cc_start: 0.8012 (tmm) cc_final: 0.7262 (tmm) REVERT: C 661 ILE cc_start: 0.5364 (OUTLIER) cc_final: 0.4943 (pp) REVERT: D 73 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7629 (tm) REVERT: D 135 MET cc_start: 0.7958 (pmm) cc_final: 0.6856 (ttp) REVERT: D 159 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8482 (mm) REVERT: D 176 ILE cc_start: 0.9053 (tp) cc_final: 0.8786 (tt) REVERT: D 221 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8835 (ptpp) REVERT: D 348 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7534 (pp) REVERT: D 378 TRP cc_start: 0.7892 (OUTLIER) cc_final: 0.6596 (t60) REVERT: D 450 MET cc_start: 0.7075 (pmm) cc_final: 0.6146 (mpp) REVERT: D 457 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8442 (pmtt) REVERT: D 561 MET cc_start: -0.1239 (mmt) cc_final: -0.2406 (ttm) REVERT: I 180 GLN cc_start: 0.2210 (OUTLIER) cc_final: 0.1933 (tt0) REVERT: L 55 ARG cc_start: 0.7891 (mtt180) cc_final: 0.7620 (mtt180) REVERT: M 69 SER cc_start: 0.7732 (OUTLIER) cc_final: 0.7021 (m) outliers start: 157 outliers final: 130 residues processed: 434 average time/residue: 0.3579 time to fit residues: 261.1894 Evaluate side-chains 428 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 281 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 771 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 678 TYR Chi-restraints excluded: chain B residue 715 LEU 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 759 LEU Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 362 VAL 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 435 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 585 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 779 CYS Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 284 TRP Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 378 TRP 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 411 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 457 LYS Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 660 PHE Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 812 HIS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 180 GLN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 372 optimal weight: 20.0000 chunk 144 optimal weight: 9.9990 chunk 295 optimal weight: 0.0020 chunk 110 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 301 optimal weight: 0.8980 chunk 374 optimal weight: 0.9980 chunk 259 optimal weight: 0.4980 chunk 128 optimal weight: 4.9990 chunk 206 optimal weight: 0.0970 chunk 354 optimal weight: 20.0000 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN B 676 ASN C 363 GLN M 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.184985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123657 restraints weight = 53190.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118480 restraints weight = 41384.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.118738 restraints weight = 39300.248| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29493 Z= 0.098 Angle : 0.556 10.719 40310 Z= 0.282 Chirality : 0.042 0.173 4706 Planarity : 0.004 0.065 5169 Dihedral : 4.042 56.962 4234 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.11 % Favored : 89.38 % Rotamer: Outliers : 5.16 % Allowed : 32.86 % Favored : 61.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3966 helix: 2.32 (0.15), residues: 1266 sheet: -0.60 (0.20), residues: 764 loop : -2.18 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 36 HIS 0.004 0.001 HIS D 332 PHE 0.011 0.001 PHE A 472 TYR 0.018 0.001 TYR H 80 ARG 0.011 0.000 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.02764 ( 1174) hydrogen bonds : angle 3.87206 ( 3462) SS BOND : bond 0.00243 ( 24) SS BOND : angle 0.90134 ( 48) covalent geometry : bond 0.00219 (29469) covalent geometry : angle 0.55522 (40262) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10037.46 seconds wall clock time: 176 minutes 10.81 seconds (10570.81 seconds total)