Starting phenix.real_space_refine on Sun Aug 24 08:11:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e99_27961/08_2025/8e99_27961.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e99_27961/08_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_27961/08_2025/8e99_27961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e99_27961/08_2025/8e99_27961.map" model { file = "/net/cci-nas-00/data/ceres_data/8e99_27961/08_2025/8e99_27961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e99_27961/08_2025/8e99_27961.cif" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.031 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASN:plan1': 25, 'ARG:plan': 32, 'HIS:plan': 13, 'GLU:plan': 42, 'GLN:plan1': 22, 'PHE:plan': 7, 'TRP:plan': 1, 'ASP:plan': 26, 'TYR:plan': 6} 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: {'ASN:plan1': 15, 'HIS:plan': 9, 'ASP:plan': 32, 'GLU:plan': 37, 'ARG:plan': 21, 'TRP:plan': 2, 'GLN:plan1': 14, 'PHE:plan': 5, 'TYR:plan': 3} 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: {'ASN:plan1': 25, 'ARG:plan': 29, 'HIS:plan': 5, 'GLU:plan': 40, 'GLN:plan1': 20, 'PHE:plan': 7, 'TRP:plan': 1, 'ASP:plan': 26, 'TYR:plan': 6} 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, 'PHE:plan': 5, 'ARG:plan': 33, 'ASP:plan': 27, 'GLU:plan': 30, 'ASN:plan1': 7, 'HIS:plan': 13, 'TRP:plan': 1, 'TYR:plan': 1} 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, 'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1} 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: 4.09, per 1000 atoms: 0.23 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: 1.45 Conformation dependent library (CDL) restraints added in 893.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.45 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: 2.48 Time building geometry restraints manager: 1.83 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: 5.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.510 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.930 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (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 ARG 0.008 0.001 ARG C 722 TYR 0.015 0.001 TYR B 281 PHE 0.019 0.001 PHE B 253 TRP 0.059 0.002 TRP A 151 HIS 0.005 0.001 HIS C 404 Details of bonding type rmsd covalent geometry : bond 0.00394 (17970) covalent geometry : angle 0.81874 (24897) SS BOND : bond 0.00522 ( 13) SS BOND : angle 1.28951 ( 26) hydrogen bonds : bond 0.22689 ( 704) hydrogen bonds : angle 7.59580 ( 2034) link_BETA1-4 : bond 0.01477 ( 4) link_BETA1-4 : angle 4.78921 ( 12) link_NAG-ASN : bond 0.01019 ( 6) link_NAG-ASN : angle 4.86598 ( 18) *********************** 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 : 0.606 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: 0.0834 time to fit residues: 45.1480 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 : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN D 483 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.100474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.080587 restraints weight = 71405.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.082698 restraints weight = 46394.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.084190 restraints weight = 34020.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.085256 restraints weight = 27115.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.086020 restraints weight = 22935.479| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 17993 Z= 0.131 Angle : 0.659 11.012 24953 Z= 0.336 Chirality : 0.046 0.280 3226 Planarity : 0.005 0.132 3169 Dihedral : 7.245 79.157 3004 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.47 % Favored : 92.23 % Rotamer: Outliers : 0.22 % Allowed : 6.22 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.16), residues: 2690 helix: 0.73 (0.18), residues: 858 sheet: -1.34 (0.24), residues: 425 loop : -2.28 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 722 TYR 0.013 0.001 TYR B 281 PHE 0.015 0.001 PHE A 784 TRP 0.036 0.002 TRP A 151 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00284 (17970) covalent geometry : angle 0.64537 (24897) SS BOND : bond 0.00627 ( 13) SS BOND : angle 1.24472 ( 26) hydrogen bonds : bond 0.04364 ( 704) hydrogen bonds : angle 5.62447 ( 2034) link_BETA1-4 : bond 0.01156 ( 4) link_BETA1-4 : angle 4.14373 ( 12) link_NAG-ASN : bond 0.00693 ( 6) link_NAG-ASN : angle 3.51066 ( 18) *********************** 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 307 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 304 time to evaluate : 0.529 Fit side-chains REVERT: B 124 ILE cc_start: 0.8132 (mm) cc_final: 0.7908 (mm) REVERT: B 462 ASP cc_start: 0.8860 (t70) cc_final: 0.8608 (t0) REVERT: B 728 PHE cc_start: 0.8856 (t80) cc_final: 0.8458 (t80) REVERT: C 195 LEU cc_start: 0.8740 (mm) cc_final: 0.8534 (mt) REVERT: C 226 ASP cc_start: 0.9057 (p0) cc_final: 0.8756 (t70) REVERT: C 314 ILE cc_start: 0.8106 (mm) cc_final: 0.7540 (tp) REVERT: C 454 CYS cc_start: 0.4388 (p) cc_final: 0.4083 (t) REVERT: D 780 PHE cc_start: 0.8749 (t80) cc_final: 0.8526 (t80) REVERT: E 93 TYR cc_start: 0.8286 (m-80) cc_final: 0.7954 (m-10) outliers start: 3 outliers final: 0 residues processed: 306 average time/residue: 0.0750 time to fit residues: 39.7209 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 : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 157 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 chunk 266 optimal weight: 20.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN D 213 GLN D 483 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.099006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.079047 restraints weight = 73027.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.081104 restraints weight = 47510.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082554 restraints weight = 35027.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.083587 restraints weight = 28032.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.084295 restraints weight = 23824.410| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 17993 Z= 0.150 Angle : 0.646 9.369 24953 Z= 0.330 Chirality : 0.045 0.276 3226 Planarity : 0.005 0.130 3169 Dihedral : 6.484 59.973 3004 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.84 % Favored : 91.86 % Rotamer: Outliers : 0.15 % Allowed : 6.00 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.16), residues: 2690 helix: 0.96 (0.18), residues: 854 sheet: -1.27 (0.24), residues: 416 loop : -2.24 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 179 TYR 0.014 0.001 TYR B 281 PHE 0.017 0.001 PHE A 529 TRP 0.026 0.002 TRP A 151 HIS 0.003 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00330 (17970) covalent geometry : angle 0.63367 (24897) SS BOND : bond 0.00769 ( 13) SS BOND : angle 1.89855 ( 26) hydrogen bonds : bond 0.04058 ( 704) hydrogen bonds : angle 5.22386 ( 2034) link_BETA1-4 : bond 0.01122 ( 4) link_BETA1-4 : angle 4.00787 ( 12) link_NAG-ASN : bond 0.00795 ( 6) link_NAG-ASN : angle 2.75903 ( 18) *********************** 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 : 0.517 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8608 (ppp) cc_final: 0.8382 (ppp) REVERT: B 124 ILE cc_start: 0.8108 (mm) cc_final: 0.7883 (mm) REVERT: B 462 ASP cc_start: 0.8929 (t70) cc_final: 0.8692 (t0) REVERT: B 728 PHE cc_start: 0.8925 (t80) cc_final: 0.8522 (t80) REVERT: C 226 ASP cc_start: 0.8923 (p0) cc_final: 0.8691 (t70) REVERT: C 317 THR cc_start: 0.9131 (t) cc_final: 0.8925 (t) REVERT: C 454 CYS cc_start: 0.4454 (p) cc_final: 0.4098 (t) REVERT: D 371 MET cc_start: 0.8769 (mpp) cc_final: 0.8261 (tmm) REVERT: D 495 ILE cc_start: 0.9486 (mm) cc_final: 0.9262 (tt) REVERT: E 93 TYR cc_start: 0.8299 (m-80) cc_final: 0.8004 (m-10) outliers start: 2 outliers final: 0 residues processed: 296 average time/residue: 0.0814 time to fit residues: 42.0011 Evaluate side-chains 239 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 66 optimal weight: 9.9990 chunk 152 optimal weight: 0.0970 chunk 84 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 254 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 214 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 57 optimal weight: 0.3980 overall best weight: 2.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 404 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 = 0.3611 r_free = 0.3611 target = 0.098501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078533 restraints weight = 72247.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.080594 restraints weight = 47059.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.082040 restraints weight = 34610.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.083071 restraints weight = 27729.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.083814 restraints weight = 23590.649| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 17993 Z= 0.142 Angle : 0.625 8.800 24953 Z= 0.320 Chirality : 0.045 0.268 3226 Planarity : 0.005 0.129 3169 Dihedral : 6.075 59.307 3004 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.47 % Favored : 92.30 % Rotamer: Outliers : 0.15 % Allowed : 4.52 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.16), residues: 2690 helix: 1.00 (0.18), residues: 848 sheet: -1.19 (0.25), residues: 392 loop : -2.25 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 179 TYR 0.012 0.001 TYR B 281 PHE 0.018 0.001 PHE D 780 TRP 0.049 0.002 TRP A 151 HIS 0.006 0.001 HIS C 705 Details of bonding type rmsd covalent geometry : bond 0.00308 (17970) covalent geometry : angle 0.61276 (24897) SS BOND : bond 0.00578 ( 13) SS BOND : angle 1.22269 ( 26) hydrogen bonds : bond 0.03657 ( 704) hydrogen bonds : angle 5.08309 ( 2034) link_BETA1-4 : bond 0.01171 ( 4) link_BETA1-4 : angle 4.19463 ( 12) link_NAG-ASN : bond 0.00424 ( 6) link_NAG-ASN : angle 2.91806 ( 18) *********************** 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 304 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 302 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8605 (ppp) cc_final: 0.8347 (ppp) REVERT: B 102 ASP cc_start: 0.7925 (t70) cc_final: 0.7673 (t70) REVERT: B 124 ILE cc_start: 0.8104 (mm) cc_final: 0.7869 (mm) REVERT: B 134 ILE cc_start: 0.8676 (tp) cc_final: 0.8468 (tp) REVERT: B 249 THR cc_start: 0.8395 (t) cc_final: 0.7949 (m) REVERT: B 462 ASP cc_start: 0.8922 (t70) cc_final: 0.8699 (t0) REVERT: B 728 PHE cc_start: 0.8940 (t80) cc_final: 0.8577 (t80) REVERT: C 226 ASP cc_start: 0.8923 (p0) cc_final: 0.8695 (t70) REVERT: C 317 THR cc_start: 0.9227 (t) cc_final: 0.8863 (t) REVERT: C 454 CYS cc_start: 0.4373 (p) cc_final: 0.4076 (t) REVERT: D 371 MET cc_start: 0.8841 (mpp) cc_final: 0.8285 (tmm) REVERT: D 495 ILE cc_start: 0.9488 (mm) cc_final: 0.9246 (tt) outliers start: 2 outliers final: 1 residues processed: 303 average time/residue: 0.0767 time to fit residues: 40.7684 Evaluate side-chains 240 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 174 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 173 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 B 702 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 = 0.3630 r_free = 0.3630 target = 0.099775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.080135 restraints weight = 71648.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.082146 restraints weight = 47355.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.083556 restraints weight = 35173.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.084586 restraints weight = 28307.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.085316 restraints weight = 24096.882| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 17993 Z= 0.111 Angle : 0.610 9.983 24953 Z= 0.307 Chirality : 0.044 0.254 3226 Planarity : 0.005 0.129 3169 Dihedral : 5.730 56.103 3004 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.10 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.16), residues: 2690 helix: 1.11 (0.18), residues: 851 sheet: -1.06 (0.25), residues: 394 loop : -2.20 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 695 TYR 0.036 0.001 TYR B 730 PHE 0.012 0.001 PHE A 784 TRP 0.036 0.002 TRP C 315 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00249 (17970) covalent geometry : angle 0.59923 (24897) SS BOND : bond 0.00565 ( 13) SS BOND : angle 1.24360 ( 26) hydrogen bonds : bond 0.03325 ( 704) hydrogen bonds : angle 4.89466 ( 2034) link_BETA1-4 : bond 0.01155 ( 4) link_BETA1-4 : angle 3.86580 ( 12) link_NAG-ASN : bond 0.00450 ( 6) link_NAG-ASN : angle 2.58466 ( 18) *********************** 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 298 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8550 (ppp) cc_final: 0.8307 (ppp) REVERT: B 102 ASP cc_start: 0.7935 (t70) cc_final: 0.7702 (t70) REVERT: B 124 ILE cc_start: 0.8057 (mm) cc_final: 0.7820 (mm) REVERT: B 134 ILE cc_start: 0.8645 (tp) cc_final: 0.8422 (tp) REVERT: B 249 THR cc_start: 0.8345 (t) cc_final: 0.7874 (m) REVERT: B 462 ASP cc_start: 0.8904 (t70) cc_final: 0.8683 (t0) REVERT: B 524 PHE cc_start: 0.8405 (m-80) cc_final: 0.8177 (m-80) REVERT: B 701 MET cc_start: 0.8691 (ttt) cc_final: 0.8069 (tmm) REVERT: B 728 PHE cc_start: 0.8864 (t80) cc_final: 0.8469 (t80) REVERT: C 226 ASP cc_start: 0.8907 (p0) cc_final: 0.8659 (t70) REVERT: C 315 TRP cc_start: 0.7771 (t60) cc_final: 0.7455 (t60) REVERT: C 454 CYS cc_start: 0.4526 (p) cc_final: 0.4266 (t) REVERT: D 371 MET cc_start: 0.8796 (mpp) cc_final: 0.8316 (tmm) REVERT: D 495 ILE cc_start: 0.9462 (mm) cc_final: 0.9210 (tt) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.0724 time to fit residues: 37.8777 Evaluate side-chains 246 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 237 optimal weight: 9.9990 chunk 204 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 264 optimal weight: 0.0010 chunk 166 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 100 optimal weight: 0.0170 chunk 128 optimal weight: 10.0000 overall best weight: 0.7428 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.100022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079836 restraints weight = 68538.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.082002 restraints weight = 44186.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.083511 restraints weight = 32221.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.084599 restraints weight = 25603.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.085384 restraints weight = 21615.469| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 17993 Z= 0.104 Angle : 0.597 8.806 24953 Z= 0.297 Chirality : 0.044 0.251 3226 Planarity : 0.005 0.131 3169 Dihedral : 5.373 55.938 3004 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.84 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.16), residues: 2690 helix: 1.17 (0.18), residues: 850 sheet: -1.06 (0.26), residues: 398 loop : -2.09 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 174 TYR 0.021 0.001 TYR B 730 PHE 0.021 0.001 PHE B 782 TRP 0.034 0.001 TRP A 151 HIS 0.003 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00229 (17970) covalent geometry : angle 0.58779 (24897) SS BOND : bond 0.00507 ( 13) SS BOND : angle 1.07955 ( 26) hydrogen bonds : bond 0.02924 ( 704) hydrogen bonds : angle 4.66681 ( 2034) link_BETA1-4 : bond 0.01311 ( 4) link_BETA1-4 : angle 3.84341 ( 12) link_NAG-ASN : bond 0.00487 ( 6) link_NAG-ASN : angle 2.30553 ( 18) *********************** 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 312 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8527 (ppp) cc_final: 0.8274 (ppp) REVERT: A 267 LEU cc_start: 0.9011 (tp) cc_final: 0.8801 (tp) REVERT: B 102 ASP cc_start: 0.7997 (t70) cc_final: 0.7757 (t70) REVERT: B 124 ILE cc_start: 0.8115 (mm) cc_final: 0.7864 (mm) REVERT: B 249 THR cc_start: 0.8228 (t) cc_final: 0.7720 (m) REVERT: B 503 GLN cc_start: 0.9253 (mm110) cc_final: 0.8682 (mp10) REVERT: B 524 PHE cc_start: 0.8438 (m-80) cc_final: 0.8223 (m-80) REVERT: B 728 PHE cc_start: 0.8887 (t80) cc_final: 0.8505 (t80) REVERT: C 165 LEU cc_start: 0.9272 (tt) cc_final: 0.8865 (pt) REVERT: C 226 ASP cc_start: 0.8882 (p0) cc_final: 0.8627 (t70) REVERT: C 315 TRP cc_start: 0.7557 (t60) cc_final: 0.7353 (t60) REVERT: C 454 CYS cc_start: 0.4553 (p) cc_final: 0.4315 (t) REVERT: D 371 MET cc_start: 0.8833 (mpp) cc_final: 0.8250 (tmm) REVERT: D 495 ILE cc_start: 0.9448 (mm) cc_final: 0.9178 (tt) REVERT: D 780 PHE cc_start: 0.8809 (t80) cc_final: 0.8579 (t80) REVERT: E 36 TRP cc_start: 0.8591 (m100) cc_final: 0.8317 (m100) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.0749 time to fit residues: 40.3172 Evaluate side-chains 247 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 106 optimal weight: 0.0570 chunk 131 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 124 optimal weight: 0.6980 chunk 205 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 241 optimal weight: 0.0070 chunk 171 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.100417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.080402 restraints weight = 68678.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.082513 restraints weight = 44720.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.084018 restraints weight = 32846.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.085099 restraints weight = 26180.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085868 restraints weight = 22149.977| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 17993 Z= 0.101 Angle : 0.593 9.129 24953 Z= 0.293 Chirality : 0.044 0.234 3226 Planarity : 0.005 0.130 3169 Dihedral : 5.242 56.266 3004 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.88 % Favored : 92.94 % Rotamer: Outliers : 0.07 % Allowed : 1.92 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.16), residues: 2690 helix: 1.23 (0.18), residues: 854 sheet: -1.04 (0.25), residues: 404 loop : -2.04 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 179 TYR 0.018 0.001 TYR B 730 PHE 0.010 0.001 PHE B 121 TRP 0.047 0.001 TRP C 247 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00225 (17970) covalent geometry : angle 0.58367 (24897) SS BOND : bond 0.00420 ( 13) SS BOND : angle 0.99597 ( 26) hydrogen bonds : bond 0.02928 ( 704) hydrogen bonds : angle 4.58280 ( 2034) link_BETA1-4 : bond 0.01109 ( 4) link_BETA1-4 : angle 3.75422 ( 12) link_NAG-ASN : bond 0.00468 ( 6) link_NAG-ASN : angle 2.22318 ( 18) *********************** 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 304 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8505 (ppp) cc_final: 0.8247 (ppp) REVERT: B 102 ASP cc_start: 0.8024 (t70) cc_final: 0.7756 (t70) REVERT: B 124 ILE cc_start: 0.8056 (mm) cc_final: 0.7825 (mm) REVERT: B 134 ILE cc_start: 0.8621 (tp) cc_final: 0.8401 (tp) REVERT: B 249 THR cc_start: 0.8246 (t) cc_final: 0.7749 (m) REVERT: B 503 GLN cc_start: 0.9236 (mm110) cc_final: 0.8664 (mp10) REVERT: B 728 PHE cc_start: 0.8842 (t80) cc_final: 0.8507 (t80) REVERT: C 226 ASP cc_start: 0.8875 (p0) cc_final: 0.8620 (t70) REVERT: D 371 MET cc_start: 0.8821 (mpp) cc_final: 0.8279 (tmm) REVERT: D 495 ILE cc_start: 0.9429 (mm) cc_final: 0.9163 (tt) REVERT: D 780 PHE cc_start: 0.8776 (t80) cc_final: 0.8457 (t80) REVERT: E 36 TRP cc_start: 0.8577 (m100) cc_final: 0.8317 (m100) outliers start: 1 outliers final: 1 residues processed: 303 average time/residue: 0.0772 time to fit residues: 40.7486 Evaluate side-chains 251 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 144 optimal weight: 6.9990 chunk 200 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 260 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 ** 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 = 0.3545 r_free = 0.3545 target = 0.094407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.074982 restraints weight = 73522.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.076857 restraints weight = 49085.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.078159 restraints weight = 36774.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.079073 restraints weight = 29879.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.079758 restraints weight = 25720.326| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 17993 Z= 0.240 Angle : 0.750 11.947 24953 Z= 0.389 Chirality : 0.047 0.262 3226 Planarity : 0.005 0.125 3169 Dihedral : 6.212 59.820 3004 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.37 % Favored : 90.45 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.16), residues: 2690 helix: 0.90 (0.18), residues: 843 sheet: -1.31 (0.27), residues: 363 loop : -2.30 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 434 TYR 0.027 0.002 TYR B 700 PHE 0.026 0.002 PHE A 784 TRP 0.068 0.003 TRP A 151 HIS 0.010 0.002 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00510 (17970) covalent geometry : angle 0.73499 (24897) SS BOND : bond 0.00766 ( 13) SS BOND : angle 1.82755 ( 26) hydrogen bonds : bond 0.04767 ( 704) hydrogen bonds : angle 5.22090 ( 2034) link_BETA1-4 : bond 0.01068 ( 4) link_BETA1-4 : angle 4.11517 ( 12) link_NAG-ASN : bond 0.00717 ( 6) link_NAG-ASN : angle 4.18052 ( 18) *********************** 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 283 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 124 ILE cc_start: 0.8257 (mm) cc_final: 0.8032 (mm) REVERT: B 134 ILE cc_start: 0.8701 (tp) cc_final: 0.8474 (tp) REVERT: B 249 THR cc_start: 0.8847 (t) cc_final: 0.8439 (m) REVERT: B 503 GLN cc_start: 0.9329 (mm110) cc_final: 0.8697 (mp10) REVERT: B 701 MET cc_start: 0.8743 (ttt) cc_final: 0.8064 (tmm) REVERT: B 728 PHE cc_start: 0.8956 (t80) cc_final: 0.8603 (t80) REVERT: C 410 TYR cc_start: 0.7539 (m-10) cc_final: 0.7309 (m-10) REVERT: D 371 MET cc_start: 0.8786 (mpp) cc_final: 0.8372 (tmm) REVERT: E 36 TRP cc_start: 0.8824 (m100) cc_final: 0.8505 (m100) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.0768 time to fit residues: 37.1163 Evaluate side-chains 227 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 103 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 168 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 257 optimal weight: 0.4980 overall best weight: 4.2988 ------------------------------------------------------------------------------- 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 702 HIS C 134 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 = 0.3540 r_free = 0.3540 target = 0.094008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.074806 restraints weight = 74386.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.076674 restraints weight = 49300.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.077975 restraints weight = 36814.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.078893 restraints weight = 29844.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.079555 restraints weight = 25697.556| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 17993 Z= 0.219 Angle : 0.710 12.396 24953 Z= 0.367 Chirality : 0.046 0.262 3226 Planarity : 0.005 0.123 3169 Dihedral : 6.213 57.514 3004 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.66 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.16), residues: 2690 helix: 0.96 (0.18), residues: 839 sheet: -1.46 (0.26), residues: 379 loop : -2.38 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 523 TYR 0.020 0.002 TYR C 456 PHE 0.020 0.002 PHE A 784 TRP 0.072 0.002 TRP A 151 HIS 0.006 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00470 (17970) covalent geometry : angle 0.69375 (24897) SS BOND : bond 0.00795 ( 13) SS BOND : angle 2.60545 ( 26) hydrogen bonds : bond 0.04154 ( 704) hydrogen bonds : angle 5.19009 ( 2034) link_BETA1-4 : bond 0.01049 ( 4) link_BETA1-4 : angle 3.77700 ( 12) link_NAG-ASN : bond 0.00524 ( 6) link_NAG-ASN : angle 3.82993 ( 18) *********************** 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 275 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.381 Fit side-chains REVERT: A 267 LEU cc_start: 0.9139 (tp) cc_final: 0.8851 (tt) REVERT: B 134 ILE cc_start: 0.8751 (tp) cc_final: 0.8522 (tp) REVERT: B 230 TYR cc_start: 0.8124 (t80) cc_final: 0.7791 (t80) REVERT: B 249 THR cc_start: 0.8869 (t) cc_final: 0.8420 (m) REVERT: B 252 ASP cc_start: 0.8878 (p0) cc_final: 0.8644 (p0) REVERT: B 496 MET cc_start: 0.8517 (mpp) cc_final: 0.8299 (mpp) REVERT: B 503 GLN cc_start: 0.9306 (mm110) cc_final: 0.8683 (mp10) REVERT: B 701 MET cc_start: 0.8763 (ttt) cc_final: 0.8085 (tmm) REVERT: B 728 PHE cc_start: 0.8976 (t80) cc_final: 0.8547 (t80) REVERT: D 371 MET cc_start: 0.8738 (mpp) cc_final: 0.8374 (tmm) REVERT: E 36 TRP cc_start: 0.8825 (m100) cc_final: 0.8539 (m100) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.0761 time to fit residues: 36.3558 Evaluate side-chains 231 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 150 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 177 optimal weight: 0.3980 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 356 GLN ** 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 = 0.3596 r_free = 0.3596 target = 0.097376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.077770 restraints weight = 71147.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.079763 restraints weight = 46489.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.081194 restraints weight = 34391.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082197 restraints weight = 27575.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082928 restraints weight = 23465.699| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 17993 Z= 0.117 Angle : 0.651 9.946 24953 Z= 0.327 Chirality : 0.045 0.235 3226 Planarity : 0.005 0.125 3169 Dihedral : 5.628 55.286 3004 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.92 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.16), residues: 2690 helix: 1.23 (0.18), residues: 849 sheet: -1.32 (0.26), residues: 384 loop : -2.25 (0.15), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 523 TYR 0.013 0.001 TYR B 730 PHE 0.012 0.001 PHE B 115 TRP 0.075 0.002 TRP A 151 HIS 0.005 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00263 (17970) covalent geometry : angle 0.63418 (24897) SS BOND : bond 0.00627 ( 13) SS BOND : angle 2.76688 ( 26) hydrogen bonds : bond 0.03338 ( 704) hydrogen bonds : angle 4.80166 ( 2034) link_BETA1-4 : bond 0.01166 ( 4) link_BETA1-4 : angle 3.77992 ( 12) link_NAG-ASN : bond 0.00495 ( 6) link_NAG-ASN : angle 3.20092 ( 18) ********************** 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 284 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.602 Fit side-chains REVERT: A 511 ASP cc_start: 0.9080 (t0) cc_final: 0.8521 (m-30) REVERT: B 124 ILE cc_start: 0.8092 (mm) cc_final: 0.7880 (mm) REVERT: B 230 TYR cc_start: 0.7948 (t80) cc_final: 0.7605 (t80) REVERT: B 249 THR cc_start: 0.8597 (t) cc_final: 0.8079 (m) REVERT: B 252 ASP cc_start: 0.8900 (p0) cc_final: 0.8635 (p0) REVERT: B 496 MET cc_start: 0.8425 (mpp) cc_final: 0.8191 (mpp) REVERT: B 503 GLN cc_start: 0.9252 (mm110) cc_final: 0.8616 (mp10) REVERT: B 701 MET cc_start: 0.8789 (ttt) cc_final: 0.8104 (tmm) REVERT: B 728 PHE cc_start: 0.8895 (t80) cc_final: 0.8439 (t80) REVERT: D 371 MET cc_start: 0.8688 (mpp) cc_final: 0.8329 (tmm) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.0788 time to fit residues: 38.4469 Evaluate side-chains 239 residues out of total 2313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 117 optimal weight: 0.5980 chunk 206 optimal weight: 0.5980 chunk 153 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 189 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 222 optimal weight: 7.9990 chunk 242 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- 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 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 = 0.3547 r_free = 0.3547 target = 0.094390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.075154 restraints weight = 74348.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.076996 restraints weight = 49566.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.078292 restraints weight = 37144.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.079217 restraints weight = 30154.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.079882 restraints weight = 25890.369| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17993 Z= 0.198 Angle : 0.691 9.434 24953 Z= 0.355 Chirality : 0.046 0.249 3226 Planarity : 0.005 0.122 3169 Dihedral : 5.950 59.806 3004 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.70 % Favored : 90.11 % Rotamer: Outliers : 0.07 % Allowed : 0.52 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.16), residues: 2690 helix: 1.14 (0.18), residues: 853 sheet: -1.42 (0.25), residues: 398 loop : -2.34 (0.15), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 124 TYR 0.016 0.002 TYR B 700 PHE 0.020 0.002 PHE A 784 TRP 0.067 0.002 TRP A 151 HIS 0.008 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00428 (17970) covalent geometry : angle 0.67745 (24897) SS BOND : bond 0.00765 ( 13) SS BOND : angle 2.33384 ( 26) hydrogen bonds : bond 0.04032 ( 704) hydrogen bonds : angle 5.01284 ( 2034) link_BETA1-4 : bond 0.01037 ( 4) link_BETA1-4 : angle 3.75686 ( 12) link_NAG-ASN : bond 0.00550 ( 6) link_NAG-ASN : angle 3.26643 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2465.96 seconds wall clock time: 43 minutes 16.62 seconds (2596.62 seconds total)