Starting phenix.real_space_refine on Mon May 19 09:12:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e99_27961/05_2025/8e99_27961.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e99_27961/05_2025/8e99_27961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e99_27961/05_2025/8e99_27961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e99_27961/05_2025/8e99_27961.map" model { file = "/net/cci-nas-00/data/ceres_data/8e99_27961/05_2025/8e99_27961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e99_27961/05_2025/8e99_27961.cif" } resolution = 4.24 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= 0.031 sd= 0.707 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 534 atoms to isotropic. 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 48 5.16 5 C 11316 2.51 5 N 2958 2.21 5 O 3261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17583 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 4134 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 268} Link IDs: {'PTRANS': 29, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 1096 Unresolved non-hydrogen angles: 1342 Unresolved non-hydrogen dihedrals: 915 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 22, 'ASP:plan': 26, 'TYR:plan': 6, 'ASN:plan1': 25, 'TRP:plan': 1, 'HIS:plan': 13, 'PHE:plan': 7, 'GLU:plan': 42, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 727 Chain: "B" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 4283 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'PTRANS': 26, 'TRANS': 621} Chain breaks: 1 Unresolved non-hydrogen bonds: 863 Unresolved non-hydrogen angles: 1054 Unresolved non-hydrogen dihedrals: 723 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 9, 'TYR:plan': 3, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 32, 'PHE:plan': 5, 'GLU:plan': 37, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 564 Chain: "C" Number of atoms: 4197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 4197 Classifications: {'peptide': 653} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 29, 'TRANS': 623} Chain breaks: 1 Unresolved non-hydrogen bonds: 1007 Unresolved non-hydrogen angles: 1226 Unresolved non-hydrogen dihedrals: 837 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 26, 'TYR:plan': 6, 'ASN:plan1': 25, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 7, 'GLU:plan': 40, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 656 Chain: "D" Number of atoms: 4135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4135 Classifications: {'peptide': 637} Incomplete info: {'truncation_to_alanine': 195} Link IDs: {'PTRANS': 39, 'TRANS': 597} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 825 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 686 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 24, 'HIS:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 27, 'PHE:plan': 5, 'GLU:plan': 30, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 594 Chain: "E" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 694 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 79 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.76, per 1000 atoms: 0.61 Number of scatterers: 17583 At special positions: 0 Unit cell: (130.112, 147.232, 138.672, 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 48 16.00 O 3261 8.00 N 2958 7.00 C 11316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 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 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=2.04 Simple disulfide: pdb=" SG CYS B 745 " - pdb=" SG CYS B 800 " distance=2.03 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 D 82 " - pdb=" SG CYS D 317 " distance=2.05 Simple disulfide: pdb=" SG CYS D 426 " - pdb=" SG CYS D 453 " distance=2.03 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 454 " distance=2.04 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 798 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 901 " - " ASN A 771 " " NAG B 901 " - " ASN B 687 " " NAG F 1 " - " ASN C 61 " " NAG G 1 " - " ASN C 771 " " NAG H 1 " - " ASN D 685 " " NAG I 1 " - " ASN D 337 " Time building additional restraints: 4.49 Conformation dependent library (CDL) restraints added in 2.5 seconds 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5036 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 34 sheets defined 36.5% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.661A pdb=" N HIS A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 85 removed outlier: 3.830A pdb=" N SER A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 113 removed outlier: 4.043A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 removed outlier: 4.019A pdb=" N GLN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 188 removed outlier: 3.708A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 256 through 261 removed outlier: 4.221A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 296 Processing helix chain 'A' and resid 317 through 327 removed outlier: 3.713A pdb=" N PHE A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.029A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 694 removed outlier: 3.518A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.085A pdb=" N HIS A 709 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 723 removed outlier: 3.862A pdb=" N ILE A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 768 through 783 removed outlier: 3.607A pdb=" N VAL A 772 " --> pdb=" O TRP A 768 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 794 removed outlier: 3.694A pdb=" N ARG A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 61 removed outlier: 3.703A pdb=" N ARG B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B 51 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Proline residue: B 57 - end of helix Processing helix chain 'B' and resid 78 through 94 removed outlier: 3.913A pdb=" N CYS B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.788A pdb=" N ALA B 110 " --> pdb=" O GLN B 106 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 116 " --> pdb=" O MET B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 150 through 163 removed outlier: 3.815A pdb=" N VAL B 157 " --> pdb=" O GLN B 153 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET B 162 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 192 removed outlier: 3.507A pdb=" N PHE B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 232 through 247 removed outlier: 3.668A pdb=" N LEU B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 311 Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 458 through 468 removed outlier: 3.581A pdb=" N ASP B 462 " --> pdb=" O GLY B 458 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 502 Processing helix chain 'B' and resid 515 through 522 removed outlier: 4.033A pdb=" N VAL B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.763A pdb=" N ARG B 672 " --> pdb=" O LYS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 698 removed outlier: 3.969A pdb=" N ASN B 697 " --> pdb=" O ASN B 693 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR B 698 " --> pdb=" O ILE B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 708 removed outlier: 3.546A pdb=" N TYR B 704 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS B 707 " --> pdb=" O GLN B 703 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE B 708 " --> pdb=" O TYR B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 732 through 741 removed outlier: 4.460A pdb=" N TYR B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 785 removed outlier: 4.621A pdb=" N GLN B 774 " --> pdb=" O PRO B 770 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 783 " --> pdb=" O LEU B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 796 removed outlier: 3.500A pdb=" N LEU B 794 " --> pdb=" O GLU B 790 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRP B 795 " --> pdb=" O LEU B 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 53 removed outlier: 3.717A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 84 Processing helix chain 'C' and resid 99 through 102 Processing helix chain 'C' and resid 103 through 113 removed outlier: 4.750A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.675A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 204 through 214 removed outlier: 3.724A pdb=" N LEU C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 removed outlier: 4.096A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 234 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 261 removed outlier: 3.764A pdb=" N ASN C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA C 258 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 297 removed outlier: 3.514A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 500 through 508 removed outlier: 3.509A pdb=" N GLY C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.776A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 695 removed outlier: 3.670A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 707 Processing helix chain 'C' and resid 713 through 724 removed outlier: 3.779A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG C 722 " --> pdb=" O ILE C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 767 through 783 removed outlier: 4.596A pdb=" N ASN C 771 " --> pdb=" O PRO C 767 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 778 " --> pdb=" O LEU C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 removed outlier: 3.888A pdb=" N LYS C 790 " --> pdb=" O GLU C 786 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 791 " --> pdb=" O ASP C 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 51 removed outlier: 3.952A pdb=" N GLN D 45 " --> pdb=" O PRO D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 89 removed outlier: 3.889A pdb=" N LEU D 84 " --> pdb=" O GLN D 80 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 116 removed outlier: 3.889A pdb=" N LEU D 108 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 160 removed outlier: 3.949A pdb=" N VAL D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU D 153 " --> pdb=" O GLN D 149 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU D 159 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 188 removed outlier: 3.518A pdb=" N PHE D 178 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 217 Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 284 through 308 removed outlier: 4.158A pdb=" N ARG D 305 " --> pdb=" O HIS D 301 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN D 306 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.513A pdb=" N LEU D 336 " --> pdb=" O TYR D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 470 removed outlier: 3.982A pdb=" N ARG D 467 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL D 468 " --> pdb=" O LYS D 464 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 469 " --> pdb=" O LEU D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.681A pdb=" N GLU D 518 " --> pdb=" O GLU D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 686 through 696 removed outlier: 3.613A pdb=" N ARG D 690 " --> pdb=" O GLY D 686 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN D 691 " --> pdb=" O SER D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 703 Processing helix chain 'D' and resid 712 through 721 Processing helix chain 'D' and resid 730 through 737 removed outlier: 3.909A pdb=" N TYR D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 784 removed outlier: 3.979A pdb=" N ARG D 771 " --> pdb=" O SER D 767 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 794 removed outlier: 4.168A pdb=" N LYS D 788 " --> pdb=" O GLY D 784 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 3.574A pdb=" N THR A 63 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.381A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 138 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 196 removed outlier: 4.084A pdb=" N LEU A 195 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 167 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 219 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 248 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 221 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 270 removed outlier: 3.549A pdb=" N GLY A 268 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 352 " --> pdb=" O GLN A 270 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 366 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 475 through 478 removed outlier: 5.959A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 761 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 412 removed outlier: 3.675A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 728 through 732 removed outlier: 3.674A pdb=" N PHE A 729 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 728 through 732 removed outlier: 3.674A pdb=" N PHE A 729 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 758 " --> pdb=" O LYS A 534 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.562A pdb=" N VAL B 38 " --> pdb=" O VAL B 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 100 removed outlier: 6.615A pdb=" N LEU B 98 " --> pdb=" O LEU B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 202 through 205 removed outlier: 5.817A pdb=" N LEU B 172 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N SER B 171 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N TYR B 230 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL B 173 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 229 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 279 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B 363 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 475 through 479 removed outlier: 3.663A pdb=" N ASP B 476 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B 410 " --> pdb=" O TYR B 478 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N SER B 407 " --> pdb=" O MET B 507 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B 523 " --> pdb=" O LEU B 765 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 418 through 419 Processing sheet with id=AB5, first strand: chain 'B' and resid 437 through 438 removed outlier: 3.573A pdb=" N LYS B 438 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 452 " --> pdb=" O LYS B 438 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 728 through 731 removed outlier: 3.649A pdb=" N VAL B 537 " --> pdb=" O VAL B 748 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 748 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 728 through 731 removed outlier: 4.026A pdb=" N VAL B 529 " --> pdb=" O TYR B 761 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE B 533 " --> pdb=" O ALA B 757 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ALA B 757 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 59 through 62 removed outlier: 6.207A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 59 through 62 removed outlier: 6.207A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 194 through 197 removed outlier: 7.133A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 164 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE C 220 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C 222 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER C 168 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 248 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 221 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 268 through 270 removed outlier: 3.542A pdb=" N MET C 354 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 473 through 478 removed outlier: 7.546A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C 512 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 401 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 761 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET C 762 " --> pdb=" O GLU C 528 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 409 through 412 removed outlier: 3.594A pdb=" N CYS C 454 " --> pdb=" O LYS C 412 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 486 through 488 Processing sheet with id=AC6, first strand: chain 'C' and resid 534 through 536 removed outlier: 4.160A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN C 536 " --> pdb=" O SER C 756 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 681 through 682 removed outlier: 7.546A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE C 729 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR C 539 " --> pdb=" O TRP C 731 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 66 through 69 removed outlier: 3.668A pdb=" N VAL D 69 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 35 " --> pdb=" O VAL D 94 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 197 through 201 removed outlier: 3.632A pdb=" N SER D 170 " --> pdb=" O TYR D 227 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 274 through 278 removed outlier: 4.069A pdb=" N MET D 358 " --> pdb=" O TRP D 375 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP D 375 " --> pdb=" O MET D 358 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 373 " --> pdb=" O VAL D 360 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA D 362 " --> pdb=" O MET D 371 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N MET D 371 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 346 through 347 removed outlier: 4.409A pdb=" N SER D 346 " --> pdb=" O VAL D 354 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 473 through 477 removed outlier: 3.545A pdb=" N TYR D 476 " --> pdb=" O VAL D 405 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR D 407 " --> pdb=" O TYR D 476 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 506 " --> pdb=" O ALA D 762 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA D 762 " --> pdb=" O ALA D 506 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP D 521 " --> pdb=" O MET D 763 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 415 through 417 removed outlier: 3.560A pdb=" N CYS D 453 " --> pdb=" O GLU D 417 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 725 through 729 removed outlier: 3.573A pdb=" N TYR D 728 " --> pdb=" O SER D 532 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE D 531 " --> pdb=" O ALA D 755 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA D 755 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 4 through 7 removed outlier: 4.734A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP E 72 " --> pdb=" O THR E 77 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR E 79 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER E 70 " --> pdb=" O TYR E 79 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.421A pdb=" N GLY E 10 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N SER E 117 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL E 12 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR E 112 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL E 92 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN E 39 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA E 34 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA E 50 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP E 36 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA E 58 " --> pdb=" O ALA E 50 " (cutoff:3.500A) 711 hydrogen bonds defined for protein. 2034 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.75 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2825 1.29 - 1.43: 4606 1.43 - 1.56: 10478 1.56 - 1.70: 1 1.70 - 1.84: 60 Bond restraints: 17970 Sorted by residual: bond pdb=" C ALA E 98 " pdb=" O ALA E 98 " ideal model delta sigma weight residual 1.234 1.158 0.076 1.20e-02 6.94e+03 4.01e+01 bond pdb=" C ALA E 99 " pdb=" O ALA E 99 " ideal model delta sigma weight residual 1.235 1.179 0.056 1.26e-02 6.30e+03 1.99e+01 bond pdb=" C PRO A 304 " pdb=" O PRO A 304 " ideal model delta sigma weight residual 1.240 1.192 0.048 1.12e-02 7.97e+03 1.87e+01 bond pdb=" CA SER B 224 " pdb=" CB SER B 224 " ideal model delta sigma weight residual 1.530 1.468 0.063 1.53e-02 4.27e+03 1.67e+01 bond pdb=" N LYS A 298 " pdb=" CA LYS A 298 " ideal model delta sigma weight residual 1.457 1.505 -0.047 1.29e-02 6.01e+03 1.34e+01 ... (remaining 17965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 24006 1.98 - 3.97: 768 3.97 - 5.95: 94 5.95 - 7.94: 23 7.94 - 9.92: 6 Bond angle restraints: 24897 Sorted by residual: angle pdb=" C ALA E 99 " pdb=" N ALA E 100 " pdb=" CA ALA E 100 " ideal model delta sigma weight residual 122.36 130.84 -8.48 1.42e+00 4.96e-01 3.56e+01 angle pdb=" C LYS A 298 " pdb=" N GLU A 299 " pdb=" CA GLU A 299 " ideal model delta sigma weight residual 120.28 127.67 -7.39 1.34e+00 5.57e-01 3.04e+01 angle pdb=" C GLU A 299 " pdb=" N ASN A 300 " pdb=" CA ASN A 300 " ideal model delta sigma weight residual 123.03 115.97 7.06 1.34e+00 5.57e-01 2.78e+01 angle pdb=" C SER B 224 " pdb=" N SER B 225 " pdb=" CA SER B 225 " ideal model delta sigma weight residual 122.42 114.39 8.03 1.55e+00 4.16e-01 2.69e+01 angle pdb=" C GLU A 297 " pdb=" N LYS A 298 " pdb=" CA LYS A 298 " ideal model delta sigma weight residual 121.54 131.31 -9.77 1.91e+00 2.74e-01 2.62e+01 ... (remaining 24892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.07: 9999 21.07 - 42.13: 363 42.13 - 63.20: 41 63.20 - 84.26: 4 84.26 - 105.33: 9 Dihedral angle restraints: 10416 sinusoidal: 2607 harmonic: 7809 Sorted by residual: dihedral pdb=" CB CYS D 426 " pdb=" SG CYS D 426 " pdb=" SG CYS D 453 " pdb=" CB CYS D 453 " ideal model delta sinusoidal sigma weight residual 93.00 178.13 -85.13 1 1.00e+01 1.00e-02 8.79e+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 93.00 168.16 -75.16 1 1.00e+01 1.00e-02 7.14e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 95 " pdb=" CB CYS E 95 " ideal model delta sinusoidal sigma weight residual 93.00 32.62 60.38 1 1.00e+01 1.00e-02 4.86e+01 ... (remaining 10413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3121 0.108 - 0.216: 98 0.216 - 0.324: 4 0.324 - 0.432: 0 0.432 - 0.540: 3 Chirality restraints: 3226 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.14e+02 chirality pdb=" CA LYS A 298 " pdb=" N LYS A 298 " pdb=" C LYS A 298 " pdb=" CB LYS A 298 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.29e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 337 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.02e+00 ... (remaining 3223 not shown) Planarity restraints: 3175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " 0.363 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG I 2 " -0.092 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " -0.540 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.305 2.00e-02 2.50e+03 2.56e-01 8.21e+02 pdb=" C7 NAG I 1 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.438 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 60 " 0.030 2.00e-02 2.50e+03 6.25e-02 3.91e+01 pdb=" C ALA B 60 " -0.108 2.00e-02 2.50e+03 pdb=" O ALA B 60 " 0.042 2.00e-02 2.50e+03 pdb=" N ALA B 61 " 0.036 2.00e-02 2.50e+03 ... (remaining 3172 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 8 2.24 - 2.91: 7443 2.91 - 3.57: 24516 3.57 - 4.24: 32776 4.24 - 4.90: 54057 Nonbonded interactions: 118800 Sorted by model distance: nonbonded pdb=" CE1 PHE E 67 " pdb=" CB MET E 82 " model vdw 1.579 3.740 nonbonded pdb=" CD1 PHE E 67 " pdb=" CB MET E 82 " model vdw 1.606 3.740 nonbonded pdb=" O LEU A 295 " pdb=" N GLU A 297 " model vdw 2.033 3.120 nonbonded pdb=" CD1 PHE E 67 " pdb=" CA MET E 82 " model vdw 2.081 3.770 nonbonded pdb=" O3 NAG I 1 " pdb=" O7 NAG I 1 " model vdw 2.142 3.040 ... (remaining 118795 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 34 or (resid 35 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 82 or (resid 83 and (na \ me N or name CA or name C or name O or name CB )) or resid 84 through 98 or (res \ id 99 through 102 and (name N or name CA or name C or name O or name CB )) or re \ sid 103 through 115 or (resid 116 and (name N or name CA or name C or name O or \ name CB )) or resid 117 through 153 or (resid 154 through 156 and (name N or nam \ e CA or name C or name O or name CB )) or resid 157 through 158 or (resid 159 an \ d (name N or name CA or name C or name O or name CB )) or resid 160 through 188 \ or (resid 189 through 193 and (name N or name CA or name C or name O or name CB \ )) or resid 194 through 195 or (resid 196 and (name N or name CA or name C or na \ me O or name CB )) or resid 197 or (resid 198 and (name N or name CA or name C o \ r name O or name CB )) or resid 199 through 200 or (resid 201 through 202 and (n \ ame N or name CA or name C or name O or name CB )) or resid 203 through 244 or ( \ resid 245 and (name N or name CA or name C or name O or name CB )) or resid 246 \ through 253 or (resid 254 and (name N or name CA or name C or name O or name CB \ )) or resid 255 through 258 or (resid 259 through 262 and (name N or name CA or \ name C or name O or name CB )) or resid 263 through 265 or (resid 266 and (name \ N or name CA or name C or name O or name CB )) or resid 267 through 327 or (resi \ d 328 through 332 and (name N or name CA or name C or name O or name CB )) or re \ sid 333 through 355 or (resid 356 through 361 and (name N or name CA or name C o \ r name O or name CB )) or resid 362 through 392 or (resid 393 through 394 and (n \ ame N or name CA or name C or name O or name CB )) or resid 395 through 396 or ( \ resid 397 and (name N or name CA or name C or name O or name CB )) or resid 398 \ through 414 or (resid 415 and (name N or name CA or name C or name O or name CB \ )) or resid 416 through 418 or (resid 419 and (name N or name CA or name C or na \ me O or name CB )) or resid 420 through 441 or (resid 442 through 443 and (name \ N or name CA or name C or name O or name CB )) or resid 444 through 445 or (resi \ d 446 and (name N or name CA or name C or name O or name CB )) or resid 447 thro \ ugh 460 or (resid 461 and (name N or name CA or name C or name O or name CB )) o \ r resid 462 through 480 or (resid 481 and (name N or name CA or name C or name O \ or name CB )) or resid 482 through 510 or (resid 511 and (name N or name CA or \ name C or name O or name CB )) or resid 512 through 526 or (resid 527 through 52 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 530 through \ 666 or (resid 667 through 669 and (name N or name CA or name C or name O or name \ CB )) or resid 670 through 679 or (resid 680 through 682 and (name N or name CA \ or name C or name O or name CB )) or resid 683 through 690 or (resid 691 and (n \ ame N or name CA or name C or name O or name CB )) or resid 692 through 720 or ( \ resid 721 through 728 and (name N or name CA or name C or name O or name CB )) o \ r resid 729 through 754 or (resid 755 and (name N or name CA or name C or name O \ or name CB )) or resid 756 through 772 or (resid 773 through 774 and (name N or \ name CA or name C or name O or name CB )) or resid 775 through 783 or (resid 78 \ 4 through 790 and (name N or name CA or name C or name O or name CB )) or resid \ 791 through 795)) selection = (chain 'C' and ((resid 25 through 28 and (name N or name CA or name C or name O \ or name CB )) or resid 29 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 57 or (resid 58 through 60 and (n \ ame N or name CA or name C or name O or name CB )) or resid 61 through 66 or (re \ sid 67 through 68 and (name N or name CA or name C or name O or name CB )) or re \ sid 69 through 71 or (resid 72 through 73 and (name N or name CA or name C or na \ me O or name CB )) or resid 74 through 75 or (resid 76 and (name N or name CA or \ name C or name O or name CB )) or resid 77 through 79 or (resid 80 through 81 a \ nd (name N or name CA or name C or name O or name CB )) or resid 82 through 87 o \ r (resid 88 through 89 and (name N or name CA or name C or name O or name CB )) \ or resid 90 through 93 or (resid 94 and (name N or name CA or name C or name O o \ r name CB )) or resid 95 through 100 or (resid 101 through 102 and (name N or na \ me CA or name C or name O or name CB )) or resid 103 through 112 or (resid 113 a \ nd (name N or name CA or name C or name O or name CB )) or resid 114 through 120 \ or (resid 121 and (name N or name CA or name C or name O or name CB )) or resid \ 122 through 123 or (resid 124 through 125 and (name N or name CA or name C or n \ ame O or name CB )) or resid 126 or (resid 127 and (name N or name CA or name C \ or name O or name CB )) or resid 128 through 132 or (resid 133 through 135 and ( \ name N or name CA or name C or name O or name CB )) or resid 136 through 161 or \ (resid 162 and (name N or name CA or name C or name O or name CB )) or resid 163 \ through 178 or (resid 179 and (name N or name CA or name C or name O or name CB \ )) or resid 180 or (resid 181 and (name N or name CA or name C or name O or nam \ e CB )) or resid 182 or (resid 183 and (name N or name CA or name C or name O or \ name CB )) or resid 184 through 201 or (resid 202 and (name N or name CA or nam \ e C or name O or name CB )) or resid 203 through 213 or (resid 214 through 217 a \ nd (name N or name CA or name C or name O or name CB )) or resid 218 through 225 \ or (resid 226 through 229 and (name N or name CA or name C or name O or name CB \ )) or resid 230 through 232 or (resid 233 through 237 and (name N or name CA or \ name C or name O or name CB )) or resid 238 through 269 or (resid 270 through 2 \ 73 and (name N or name CA or name C or name O or name CB )) or (resid 274 throug \ h 277 and (name N or name CA or name C or name O or name CB )) or resid 278 thro \ ugh 282 or (resid 283 through 284 and (name N or name CA or name C or name O or \ name CB )) or resid 285 through 289 or (resid 290 through 291 and (name N or nam \ e CA or name C or name O or name CB )) or resid 292 through 301 or (resid 302 th \ rough 303 and (name N or name CA or name C or name O or name CB )) or resid 304 \ through 311 or (resid 312 through 313 and (name N or name CA or name C or name O \ or name CB )) or resid 314 through 333 or (resid 334 through 335 and (name N or \ name CA or name C or name O or name CB )) or resid 336 through 366 or (resid 36 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 368 through \ 378 or (resid 379 and (name N or name CA or name C or name O or name CB )) or re \ sid 380 through 391 or (resid 392 through 394 and (name N or name CA or name C o \ r name O or name CB )) or resid 395 through 425 or (resid 426 through 427 and (n \ ame N or name CA or name C or name O or name CB )) or resid 428 through 469 or ( \ resid 470 and (name N or name CA or name C or name O or name CB )) or resid 471 \ through 476 or (resid 477 and (name N or name CA or name C or name O or name CB \ )) or resid 478 through 498 or (resid 499 and (name N or name CA or name C or na \ me O or name CB )) or resid 500 through 540 or (resid 541 and (name N or name CA \ or name C or name O or name CB )) or resid 542 through 696 or (resid 697 throug \ h 699 and (name N or name CA or name C or name O or name CB )) or resid 700 thro \ ugh 704 or (resid 705 through 708 and (name N or name CA or name C or name O or \ name CB )) or resid 709 through 721 or (resid 722 through 728 and (name N or nam \ e CA or name C or name O or name CB )) or resid 729 through 745 or (resid 746 an \ d (name N or name CA or name C or name O or name CB )) or resid 747 through 752 \ or (resid 753 and (name N or name CA or name C or name O or name CB )) or resid \ 754 through 761 or (resid 762 through 765 and (name N or name CA or name C or na \ me O or name CB )) or resid 766 through 781 or (resid 782 and (name N or name CA \ or name C or name O or name CB )) or resid 783 through 795)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 40.730 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.080 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 0.097 17993 Z= 0.231 Angle : 0.836 9.919 24953 Z= 0.492 Chirality : 0.048 0.540 3226 Planarity : 0.009 0.307 3169 Dihedral : 11.614 105.327 5341 Min Nonbonded Distance : 1.579 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.43 % Favored : 92.23 % Rotamer: Outliers : 0.30 % Allowed : 0.44 % Favored : 99.26 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.16), residues: 2690 helix: 0.56 (0.18), residues: 838 sheet: -1.17 (0.24), residues: 417 loop : -2.36 (0.15), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 151 HIS 0.005 0.001 HIS C 404 PHE 0.019 0.001 PHE B 253 TYR 0.015 0.001 TYR B 281 ARG 0.008 0.001 ARG C 722 Details of bonding type rmsd link_NAG-ASN : bond 0.01019 ( 6) link_NAG-ASN : angle 4.86598 ( 18) link_BETA1-4 : bond 0.01477 ( 4) link_BETA1-4 : angle 4.78921 ( 12) hydrogen bonds : bond 0.22689 ( 704) hydrogen bonds : angle 7.59580 ( 2034) SS BOND : bond 0.00522 ( 13) SS BOND : angle 1.28951 ( 26) covalent geometry : bond 0.00394 (17970) covalent geometry : angle 0.81874 (24897) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 312 time to evaluate : 2.004 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8614 (ppp) cc_final: 0.8410 (ppp) REVERT: A 280 HIS cc_start: 0.8263 (m-70) cc_final: 0.7991 (m-70) REVERT: B 248 LEU cc_start: 0.7069 (mt) cc_final: 0.6814 (mp) REVERT: B 462 ASP cc_start: 0.9159 (t70) cc_final: 0.8749 (t0) REVERT: B 701 MET cc_start: 0.8734 (ttt) cc_final: 0.8221 (tmm) REVERT: B 728 PHE cc_start: 0.8947 (t80) cc_final: 0.8502 (t80) REVERT: C 195 LEU cc_start: 0.8757 (mm) cc_final: 0.8442 (mt) REVERT: C 226 ASP cc_start: 0.8929 (p0) cc_final: 0.8705 (t70) REVERT: C 317 THR cc_start: 0.9361 (t) cc_final: 0.9103 (t) REVERT: C 470 MET cc_start: 0.8043 (mpp) cc_final: 0.7620 (mpp) REVERT: D 224 PHE cc_start: 0.8257 (m-10) cc_final: 0.8002 (m-10) REVERT: D 780 PHE cc_start: 0.8782 (t80) cc_final: 0.8549 (t80) outliers start: 4 outliers final: 2 residues processed: 315 average time/residue: 0.2132 time to fit residues: 113.6387 Evaluate side-chains 262 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 260 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.0270 chunk 203 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 chunk 243 optimal weight: 9.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.099679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.079810 restraints weight = 71420.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081903 restraints weight = 46495.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.083359 restraints weight = 34164.417| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 17993 Z= 0.145 Angle : 0.664 9.941 24953 Z= 0.340 Chirality : 0.045 0.284 3226 Planarity : 0.005 0.131 3169 Dihedral : 7.347 80.264 3004 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.58 % Favored : 92.12 % Rotamer: Outliers : 0.22 % Allowed : 6.37 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.16), residues: 2690 helix: 0.74 (0.18), residues: 857 sheet: -1.18 (0.24), residues: 420 loop : -2.33 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 151 HIS 0.004 0.001 HIS B 119 PHE 0.016 0.001 PHE A 784 TYR 0.014 0.001 TYR B 281 ARG 0.003 0.000 ARG C 722 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 6) link_NAG-ASN : angle 3.53049 ( 18) link_BETA1-4 : bond 0.01019 ( 4) link_BETA1-4 : angle 4.16660 ( 12) hydrogen bonds : bond 0.04543 ( 704) hydrogen bonds : angle 5.68857 ( 2034) SS BOND : bond 0.00534 ( 13) SS BOND : angle 1.25990 ( 26) covalent geometry : bond 0.00312 (17970) covalent geometry : angle 0.65037 (24897) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 302 time to evaluate : 1.965 Fit side-chains REVERT: B 124 ILE cc_start: 0.8167 (mm) cc_final: 0.7934 (mm) REVERT: B 462 ASP cc_start: 0.8915 (t70) cc_final: 0.8668 (t0) REVERT: B 728 PHE cc_start: 0.8902 (t80) cc_final: 0.8515 (t80) REVERT: B 761 TYR cc_start: 0.7669 (m-10) cc_final: 0.7461 (m-10) REVERT: C 195 LEU cc_start: 0.8759 (mm) cc_final: 0.8538 (mm) REVERT: C 226 ASP cc_start: 0.9040 (p0) cc_final: 0.8777 (t70) REVERT: C 314 ILE cc_start: 0.8169 (mm) cc_final: 0.7620 (tp) REVERT: C 315 TRP cc_start: 0.7696 (t60) cc_final: 0.7441 (t60) REVERT: C 454 CYS cc_start: 0.4687 (p) cc_final: 0.4268 (t) REVERT: E 93 TYR cc_start: 0.8316 (m-80) cc_final: 0.7956 (m-10) outliers start: 3 outliers final: 0 residues processed: 304 average time/residue: 0.2020 time to fit residues: 105.6613 Evaluate side-chains 250 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 57 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 chunk 10 optimal weight: 0.0770 chunk 220 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 251 optimal weight: 7.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS D 213 GLN D 483 HIS D 695 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.096455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.076892 restraints weight = 73037.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.078766 restraints weight = 48879.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.080083 restraints weight = 36731.988| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 17993 Z= 0.216 Angle : 0.702 8.825 24953 Z= 0.366 Chirality : 0.046 0.282 3226 Planarity : 0.005 0.128 3169 Dihedral : 6.850 60.208 3004 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.66 % Favored : 91.04 % Rotamer: Outliers : 0.15 % Allowed : 6.59 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.16), residues: 2690 helix: 0.75 (0.18), residues: 855 sheet: -1.20 (0.26), residues: 370 loop : -2.36 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 151 HIS 0.005 0.001 HIS B 168 PHE 0.022 0.002 PHE A 529 TYR 0.018 0.002 TYR B 700 ARG 0.005 0.001 ARG C 179 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 6) link_NAG-ASN : angle 3.09031 ( 18) link_BETA1-4 : bond 0.01224 ( 4) link_BETA1-4 : angle 3.98399 ( 12) hydrogen bonds : bond 0.04627 ( 704) hydrogen bonds : angle 5.50105 ( 2034) SS BOND : bond 0.00737 ( 13) SS BOND : angle 2.00786 ( 26) covalent geometry : bond 0.00463 (17970) covalent geometry : angle 0.68916 (24897) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 295 time to evaluate : 1.959 Fit side-chains REVERT: A 74 MET cc_start: 0.8676 (ppp) cc_final: 0.8385 (ppp) REVERT: B 124 ILE cc_start: 0.8167 (mm) cc_final: 0.7927 (mm) REVERT: B 249 THR cc_start: 0.8539 (t) cc_final: 0.8109 (m) REVERT: B 462 ASP cc_start: 0.8952 (t70) cc_final: 0.8716 (t0) REVERT: C 195 LEU cc_start: 0.8696 (mm) cc_final: 0.8479 (mm) REVERT: C 454 CYS cc_start: 0.4550 (p) cc_final: 0.4209 (t) REVERT: D 495 ILE cc_start: 0.9510 (mm) cc_final: 0.9277 (tt) outliers start: 2 outliers final: 0 residues processed: 296 average time/residue: 0.1955 time to fit residues: 100.2191 Evaluate side-chains 237 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.094119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.074728 restraints weight = 73560.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.076549 restraints weight = 49443.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.077807 restraints weight = 37221.266| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 17993 Z= 0.231 Angle : 0.724 9.726 24953 Z= 0.378 Chirality : 0.047 0.273 3226 Planarity : 0.005 0.126 3169 Dihedral : 6.759 59.681 3004 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.41 % Favored : 90.33 % Rotamer: Outliers : 0.22 % Allowed : 6.74 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.15), residues: 2690 helix: 0.60 (0.18), residues: 830 sheet: -1.41 (0.25), residues: 389 loop : -2.51 (0.15), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 151 HIS 0.009 0.002 HIS C 705 PHE 0.025 0.002 PHE A 458 TYR 0.018 0.002 TYR B 700 ARG 0.005 0.001 ARG B 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 6) link_NAG-ASN : angle 3.25208 ( 18) link_BETA1-4 : bond 0.01457 ( 4) link_BETA1-4 : angle 4.37779 ( 12) hydrogen bonds : bond 0.04592 ( 704) hydrogen bonds : angle 5.56954 ( 2034) SS BOND : bond 0.00856 ( 13) SS BOND : angle 1.72062 ( 26) covalent geometry : bond 0.00491 (17970) covalent geometry : angle 0.71088 (24897) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 295 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8684 (ppp) cc_final: 0.8363 (ppp) REVERT: B 102 ASP cc_start: 0.8129 (t70) cc_final: 0.7883 (t70) REVERT: B 124 ILE cc_start: 0.8202 (mm) cc_final: 0.7955 (mm) REVERT: B 230 TYR cc_start: 0.8160 (t80) cc_final: 0.7908 (t80) REVERT: B 249 THR cc_start: 0.8757 (t) cc_final: 0.8345 (m) REVERT: B 701 MET cc_start: 0.8717 (ttt) cc_final: 0.8176 (tmm) REVERT: B 728 PHE cc_start: 0.9044 (t80) cc_final: 0.8684 (t80) REVERT: B 774 GLN cc_start: 0.9459 (mm-40) cc_final: 0.9240 (mm-40) REVERT: C 454 CYS cc_start: 0.4458 (p) cc_final: 0.4195 (t) REVERT: D 371 MET cc_start: 0.8808 (mpp) cc_final: 0.8410 (tmm) REVERT: D 507 ILE cc_start: 0.9264 (tt) cc_final: 0.9037 (tt) REVERT: E 36 TRP cc_start: 0.8798 (m100) cc_final: 0.8575 (m100) REVERT: E 80 LEU cc_start: 0.8760 (tp) cc_final: 0.8554 (tp) outliers start: 3 outliers final: 0 residues processed: 297 average time/residue: 0.1884 time to fit residues: 97.0795 Evaluate side-chains 234 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 51 optimal weight: 10.0000 chunk 255 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 141 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.097086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.077533 restraints weight = 72816.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.079475 restraints weight = 48266.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.080831 restraints weight = 35967.670| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 17993 Z= 0.121 Angle : 0.638 9.238 24953 Z= 0.325 Chirality : 0.045 0.253 3226 Planarity : 0.005 0.128 3169 Dihedral : 6.129 56.266 3004 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.43 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.16), residues: 2690 helix: 0.95 (0.18), residues: 839 sheet: -1.26 (0.25), residues: 396 loop : -2.37 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 151 HIS 0.003 0.001 HIS B 128 PHE 0.014 0.001 PHE A 784 TYR 0.034 0.001 TYR B 730 ARG 0.004 0.000 ARG B 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 6) link_NAG-ASN : angle 2.74903 ( 18) link_BETA1-4 : bond 0.01120 ( 4) link_BETA1-4 : angle 3.93435 ( 12) hydrogen bonds : bond 0.03696 ( 704) hydrogen bonds : angle 5.11888 ( 2034) SS BOND : bond 0.00605 ( 13) SS BOND : angle 1.27570 ( 26) covalent geometry : bond 0.00264 (17970) covalent geometry : angle 0.62762 (24897) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 1.980 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8567 (ppp) cc_final: 0.8297 (ppp) REVERT: B 124 ILE cc_start: 0.8100 (mm) cc_final: 0.7857 (mm) REVERT: B 230 TYR cc_start: 0.8079 (t80) cc_final: 0.7835 (t80) REVERT: B 249 THR cc_start: 0.8563 (t) cc_final: 0.8080 (m) REVERT: B 496 MET cc_start: 0.8413 (mpp) cc_final: 0.8196 (mpp) REVERT: B 503 GLN cc_start: 0.9267 (mm110) cc_final: 0.8702 (mp10) REVERT: B 701 MET cc_start: 0.8654 (ttt) cc_final: 0.8123 (tmm) REVERT: B 728 PHE cc_start: 0.8946 (t80) cc_final: 0.8600 (t80) REVERT: B 774 GLN cc_start: 0.9443 (mm-40) cc_final: 0.9224 (mm-40) REVERT: C 195 LEU cc_start: 0.8638 (mm) cc_final: 0.8361 (mt) REVERT: C 454 CYS cc_start: 0.4364 (p) cc_final: 0.4130 (t) REVERT: D 371 MET cc_start: 0.8779 (mpp) cc_final: 0.8423 (tmm) REVERT: D 780 PHE cc_start: 0.8772 (t80) cc_final: 0.8386 (t80) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.2155 time to fit residues: 112.7929 Evaluate side-chains 244 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 220 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 222 optimal weight: 6.9990 chunk 60 optimal weight: 0.4980 chunk 151 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 164 optimal weight: 0.0170 chunk 203 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.5024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS B 702 HIS ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.097273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.077875 restraints weight = 72953.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079795 restraints weight = 48313.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.081150 restraints weight = 36092.500| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17993 Z= 0.120 Angle : 0.624 8.855 24953 Z= 0.316 Chirality : 0.045 0.253 3226 Planarity : 0.005 0.129 3169 Dihedral : 5.806 57.078 3004 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.96 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.16), residues: 2690 helix: 1.04 (0.18), residues: 843 sheet: -1.16 (0.26), residues: 380 loop : -2.34 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 151 HIS 0.003 0.001 HIS B 128 PHE 0.015 0.001 PHE B 782 TYR 0.023 0.001 TYR B 730 ARG 0.004 0.001 ARG B 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 6) link_NAG-ASN : angle 2.43761 ( 18) link_BETA1-4 : bond 0.01094 ( 4) link_BETA1-4 : angle 3.90278 ( 12) hydrogen bonds : bond 0.03444 ( 704) hydrogen bonds : angle 4.91350 ( 2034) SS BOND : bond 0.00614 ( 13) SS BOND : angle 1.27328 ( 26) covalent geometry : bond 0.00269 (17970) covalent geometry : angle 0.61354 (24897) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 ASP cc_start: 0.8223 (t0) cc_final: 0.7981 (t70) REVERT: B 124 ILE cc_start: 0.8098 (mm) cc_final: 0.7846 (mm) REVERT: B 230 TYR cc_start: 0.8030 (t80) cc_final: 0.7752 (t80) REVERT: B 249 THR cc_start: 0.8593 (t) cc_final: 0.8083 (m) REVERT: B 252 ASP cc_start: 0.8871 (p0) cc_final: 0.8662 (p0) REVERT: B 496 MET cc_start: 0.8429 (mpp) cc_final: 0.8228 (mpp) REVERT: B 503 GLN cc_start: 0.9240 (mm110) cc_final: 0.8660 (mp10) REVERT: B 701 MET cc_start: 0.8689 (ttt) cc_final: 0.8075 (tmm) REVERT: B 728 PHE cc_start: 0.8950 (t80) cc_final: 0.8596 (t80) REVERT: B 774 GLN cc_start: 0.9439 (mm-40) cc_final: 0.9226 (mm-40) REVERT: C 454 CYS cc_start: 0.4220 (p) cc_final: 0.4020 (t) REVERT: D 371 MET cc_start: 0.8763 (mpp) cc_final: 0.8430 (tmm) REVERT: E 93 TYR cc_start: 0.8135 (m-10) cc_final: 0.7834 (m-10) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.1972 time to fit residues: 97.4497 Evaluate side-chains 235 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 230 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 260 optimal weight: 7.9990 chunk 180 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 HIS ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 HIS D 695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.092551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.073411 restraints weight = 75034.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.075195 restraints weight = 50282.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.076419 restraints weight = 37817.772| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 17993 Z= 0.270 Angle : 0.756 10.826 24953 Z= 0.395 Chirality : 0.047 0.277 3226 Planarity : 0.005 0.122 3169 Dihedral : 6.545 58.724 3004 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.22 % Favored : 89.59 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.16), residues: 2690 helix: 0.65 (0.18), residues: 843 sheet: -1.53 (0.26), residues: 373 loop : -2.52 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 731 HIS 0.011 0.002 HIS C 134 PHE 0.025 0.002 PHE A 784 TYR 0.020 0.002 TYR B 730 ARG 0.008 0.001 ARG C 523 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 6) link_NAG-ASN : angle 2.82263 ( 18) link_BETA1-4 : bond 0.01058 ( 4) link_BETA1-4 : angle 3.89899 ( 12) hydrogen bonds : bond 0.04814 ( 704) hydrogen bonds : angle 5.46712 ( 2034) SS BOND : bond 0.00940 ( 13) SS BOND : angle 1.53556 ( 26) covalent geometry : bond 0.00574 (17970) covalent geometry : angle 0.74664 (24897) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 2.024 Fit side-chains revert: symmetry clash REVERT: B 230 TYR cc_start: 0.8355 (t80) cc_final: 0.8117 (t80) REVERT: B 249 THR cc_start: 0.8940 (t) cc_final: 0.8514 (m) REVERT: B 252 ASP cc_start: 0.8865 (p0) cc_final: 0.8656 (p0) REVERT: B 496 MET cc_start: 0.8608 (mpp) cc_final: 0.8383 (mpp) REVERT: B 503 GLN cc_start: 0.9323 (mm110) cc_final: 0.8721 (mp10) REVERT: B 701 MET cc_start: 0.8684 (ttt) cc_final: 0.8099 (tmm) REVERT: B 728 PHE cc_start: 0.9065 (t80) cc_final: 0.8725 (t80) REVERT: D 363 LEU cc_start: 0.9157 (tp) cc_final: 0.8920 (tp) REVERT: D 371 MET cc_start: 0.8793 (mpp) cc_final: 0.8439 (tmm) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.2021 time to fit residues: 92.6178 Evaluate side-chains 219 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 90 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 206 optimal weight: 2.9990 chunk 159 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 184 optimal weight: 0.0980 chunk 167 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 142 optimal weight: 0.8980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 HIS ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 ASN E 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.095886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.076729 restraints weight = 72552.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.078608 restraints weight = 48284.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.079942 restraints weight = 36009.510| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 17993 Z= 0.132 Angle : 0.648 9.615 24953 Z= 0.329 Chirality : 0.045 0.244 3226 Planarity : 0.005 0.125 3169 Dihedral : 5.975 57.518 3004 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.73 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.16), residues: 2690 helix: 1.00 (0.18), residues: 855 sheet: -1.42 (0.26), residues: 357 loop : -2.42 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 731 HIS 0.003 0.001 HIS B 405 PHE 0.020 0.001 PHE D 780 TYR 0.016 0.001 TYR B 730 ARG 0.010 0.001 ARG C 523 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 6) link_NAG-ASN : angle 3.94695 ( 18) link_BETA1-4 : bond 0.00996 ( 4) link_BETA1-4 : angle 3.95172 ( 12) hydrogen bonds : bond 0.03627 ( 704) hydrogen bonds : angle 5.00290 ( 2034) SS BOND : bond 0.00595 ( 13) SS BOND : angle 1.29143 ( 26) covalent geometry : bond 0.00287 (17970) covalent geometry : angle 0.63226 (24897) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8222 (ppp) cc_final: 0.7887 (ppp) REVERT: A 511 ASP cc_start: 0.8941 (t70) cc_final: 0.8647 (t0) REVERT: B 124 ILE cc_start: 0.8099 (mm) cc_final: 0.7861 (mm) REVERT: B 230 TYR cc_start: 0.8121 (t80) cc_final: 0.7921 (t80) REVERT: B 249 THR cc_start: 0.8745 (t) cc_final: 0.8272 (m) REVERT: B 252 ASP cc_start: 0.8867 (p0) cc_final: 0.8631 (p0) REVERT: B 496 MET cc_start: 0.8475 (mpp) cc_final: 0.8239 (mpp) REVERT: B 503 GLN cc_start: 0.9253 (mm110) cc_final: 0.8661 (mp10) REVERT: B 701 MET cc_start: 0.8760 (ttt) cc_final: 0.8147 (tmm) REVERT: B 728 PHE cc_start: 0.8933 (t80) cc_final: 0.8584 (t80) REVERT: D 371 MET cc_start: 0.8745 (mpp) cc_final: 0.8426 (tmm) REVERT: E 18 LEU cc_start: 0.8557 (tp) cc_final: 0.8331 (tt) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2051 time to fit residues: 101.0389 Evaluate side-chains 230 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 101 optimal weight: 0.1980 chunk 226 optimal weight: 4.9990 chunk 259 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 55 optimal weight: 0.0970 chunk 192 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.096868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.077532 restraints weight = 72683.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.079488 restraints weight = 47932.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.080850 restraints weight = 35550.021| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 17993 Z= 0.114 Angle : 0.646 12.617 24953 Z= 0.324 Chirality : 0.045 0.236 3226 Planarity : 0.005 0.127 3169 Dihedral : 5.667 57.819 3004 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.03 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.52 (0.16), residues: 2690 helix: 1.09 (0.18), residues: 863 sheet: -1.39 (0.25), residues: 393 loop : -2.34 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 731 HIS 0.002 0.001 HIS B 702 PHE 0.017 0.001 PHE B 782 TYR 0.014 0.001 TYR B 737 ARG 0.010 0.001 ARG C 523 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 6) link_NAG-ASN : angle 3.38143 ( 18) link_BETA1-4 : bond 0.01110 ( 4) link_BETA1-4 : angle 3.84977 ( 12) hydrogen bonds : bond 0.03360 ( 704) hydrogen bonds : angle 4.79222 ( 2034) SS BOND : bond 0.00499 ( 13) SS BOND : angle 2.48195 ( 26) covalent geometry : bond 0.00259 (17970) covalent geometry : angle 0.62974 (24897) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 1.917 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8138 (ppp) cc_final: 0.7821 (ppp) REVERT: B 124 ILE cc_start: 0.8136 (mm) cc_final: 0.7898 (mm) REVERT: B 230 TYR cc_start: 0.8064 (t80) cc_final: 0.7850 (t80) REVERT: B 249 THR cc_start: 0.8702 (t) cc_final: 0.8199 (m) REVERT: B 252 ASP cc_start: 0.8913 (p0) cc_final: 0.8669 (p0) REVERT: B 496 MET cc_start: 0.8407 (mpp) cc_final: 0.8193 (mpp) REVERT: B 503 GLN cc_start: 0.9206 (mm110) cc_final: 0.8572 (mp10) REVERT: B 701 MET cc_start: 0.8795 (ttt) cc_final: 0.8148 (tmm) REVERT: B 728 PHE cc_start: 0.8941 (t80) cc_final: 0.8409 (t80) REVERT: C 137 PHE cc_start: 0.8601 (t80) cc_final: 0.8374 (t80) REVERT: C 269 LEU cc_start: 0.6911 (pt) cc_final: 0.6635 (pt) REVERT: D 371 MET cc_start: 0.8763 (mpp) cc_final: 0.8382 (tmm) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.2295 time to fit residues: 110.9390 Evaluate side-chains 235 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 56 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 235 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 88 optimal weight: 0.2980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.096862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.077370 restraints weight = 72268.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.079342 restraints weight = 47399.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.080727 restraints weight = 35103.373| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 17993 Z= 0.121 Angle : 0.633 11.147 24953 Z= 0.318 Chirality : 0.045 0.238 3226 Planarity : 0.005 0.126 3169 Dihedral : 5.568 58.972 3004 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.99 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.45 (0.16), residues: 2690 helix: 1.19 (0.18), residues: 857 sheet: -1.34 (0.25), residues: 393 loop : -2.32 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 731 HIS 0.003 0.001 HIS C 134 PHE 0.013 0.001 PHE A 784 TYR 0.013 0.001 TYR B 737 ARG 0.010 0.001 ARG C 523 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 6) link_NAG-ASN : angle 3.08148 ( 18) link_BETA1-4 : bond 0.01077 ( 4) link_BETA1-4 : angle 3.79827 ( 12) hydrogen bonds : bond 0.03321 ( 704) hydrogen bonds : angle 4.74518 ( 2034) SS BOND : bond 0.00547 ( 13) SS BOND : angle 2.41773 ( 26) covalent geometry : bond 0.00275 (17970) covalent geometry : angle 0.61756 (24897) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5380 Ramachandran restraints generated. 2690 Oldfield, 0 Emsley, 2690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 1.907 Fit side-chains revert: symmetry clash REVERT: A 511 ASP cc_start: 0.8909 (t70) cc_final: 0.8694 (t0) REVERT: B 124 ILE cc_start: 0.8178 (mm) cc_final: 0.7942 (mm) REVERT: B 230 TYR cc_start: 0.8054 (t80) cc_final: 0.7830 (t80) REVERT: B 249 THR cc_start: 0.8752 (t) cc_final: 0.8264 (m) REVERT: B 252 ASP cc_start: 0.8947 (p0) cc_final: 0.8703 (p0) REVERT: B 496 MET cc_start: 0.8439 (mpp) cc_final: 0.8211 (mpp) REVERT: B 503 GLN cc_start: 0.9210 (mm110) cc_final: 0.8562 (mp10) REVERT: B 701 MET cc_start: 0.8809 (ttt) cc_final: 0.8133 (tmm) REVERT: B 728 PHE cc_start: 0.8979 (t80) cc_final: 0.8469 (t80) REVERT: D 154 PHE cc_start: 0.8374 (m-10) cc_final: 0.8145 (m-10) REVERT: D 371 MET cc_start: 0.8795 (mpp) cc_final: 0.8365 (tmm) REVERT: D 375 TRP cc_start: 0.8728 (t-100) cc_final: 0.8171 (t-100) REVERT: D 780 PHE cc_start: 0.8852 (t80) cc_final: 0.8619 (t80) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.2060 time to fit residues: 99.6498 Evaluate side-chains 230 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 102 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 191 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 196 optimal weight: 0.0970 chunk 85 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 11 optimal weight: 0.0050 chunk 232 optimal weight: 9.9990 chunk 216 optimal weight: 3.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS E 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.098744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.079385 restraints weight = 72178.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.081383 restraints weight = 47592.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.082799 restraints weight = 35233.260| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 17993 Z= 0.103 Angle : 0.615 10.257 24953 Z= 0.306 Chirality : 0.044 0.224 3226 Planarity : 0.005 0.127 3169 Dihedral : 5.267 57.213 3004 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.25 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.33 (0.16), residues: 2690 helix: 1.25 (0.18), residues: 859 sheet: -1.20 (0.25), residues: 391 loop : -2.24 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 731 HIS 0.002 0.000 HIS B 168 PHE 0.015 0.001 PHE B 782 TYR 0.012 0.001 TYR B 761 ARG 0.010 0.001 ARG C 523 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 6) link_NAG-ASN : angle 2.82329 ( 18) link_BETA1-4 : bond 0.01113 ( 4) link_BETA1-4 : angle 3.73368 ( 12) hydrogen bonds : bond 0.02891 ( 704) hydrogen bonds : angle 4.55233 ( 2034) SS BOND : bond 0.00413 ( 13) SS BOND : angle 1.93852 ( 26) covalent geometry : bond 0.00232 (17970) covalent geometry : angle 0.60235 (24897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5324.21 seconds wall clock time: 93 minutes 41.31 seconds (5621.31 seconds total)