Starting phenix.real_space_refine on Sat Aug 23 15:22:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kev_37168/08_2025/8kev_37168.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kev_37168/08_2025/8kev_37168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kev_37168/08_2025/8kev_37168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kev_37168/08_2025/8kev_37168.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kev_37168/08_2025/8kev_37168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kev_37168/08_2025/8kev_37168.map" } resolution = 3.5 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= 0.003 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 8138 2.51 5 N 2306 2.21 5 O 2507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s 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: 13001 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 3267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 438, 3266 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 6, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 7, 'GLU:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 139 Conformer: "B" Number of residues, atoms: 438, 3266 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 6, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 7, 'GLU:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 139 bond proxies already assigned to first conformer: 3330 Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "E" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1830 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 19, 'TRANS': 229} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 3, 'ASP:plan': 2, 'GLU:plan': 15, 'TYR:plan': 1, 'ASN:plan1': 4, 'ARG:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 121 Chain: "C" Number of atoms: 3276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 436, 3275 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 6, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 113 Conformer: "B" Number of residues, atoms: 436, 3275 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 6, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 113 bond proxies already assigned to first conformer: 3343 Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "F" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1492 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 19, 'TRANS': 228} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 563 Unresolved non-hydrogen angles: 715 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLU:plan': 25, 'PHE:plan': 4, 'ASP:plan': 2, 'TYR:plan': 10, 'ASN:plan1': 8, 'ARG:plan': 7, 'GLN:plan1': 5, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 314 Chain: "A" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 1427 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 204} Link IDs: {'PTRANS': 7, 'TRANS': 258} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 804 Unresolved non-hydrogen angles: 1033 Unresolved non-hydrogen dihedrals: 698 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'PHE:plan': 26, 'ARG:plan': 12, 'GLN:plan1': 4, 'GLU:plan': 9, 'HIS:plan': 7, 'TRP:plan': 4, 'TYR:plan': 8, 'ASP:plan': 8, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 428 Chain: "B" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 1423 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PTRANS': 7, 'TRANS': 258} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 808 Unresolved non-hydrogen angles: 1038 Unresolved non-hydrogen dihedrals: 701 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'PHE:plan': 26, 'ARG:plan': 12, 'GLN:plan1': 5, 'GLU:plan': 9, 'HIS:plan': 7, 'TRP:plan': 4, 'TYR:plan': 8, 'ASP:plan': 8, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 432 Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.81, per 1000 atoms: 0.37 Number of scatterers: 13001 At special positions: 0 Unit cell: (130.54, 119.84, 166.92, 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 50 16.00 O 2507 8.00 N 2306 7.00 C 8138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 311 " - pdb=" SG CYS D 539 " distance=2.04 Simple disulfide: pdb=" SG CYS E 79 " - pdb=" SG CYS E 261 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 199 " - pdb=" SG CYS E 232 " distance=2.04 Simple disulfide: pdb=" SG CYS E 215 " - pdb=" SG CYS E 244 " distance=2.04 Simple disulfide: pdb=" SG CYS C 311 " - pdb=" SG CYS C 539 " distance=2.01 Simple disulfide: pdb=" SG CYS F 79 " - pdb=" SG CYS F 261 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 215 " - pdb=" SG CYS F 244 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN I 4 " - " MAN I 5 " " MAN J 4 " - " MAN J 5 " ALPHA1-4 " NAG I 2 " - " MAN I 3 " " MAN I 3 " - " MAN I 7 " " NAG J 2 " - " MAN J 3 " " MAN J 3 " - " MAN J 7 " ALPHA1-6 " MAN I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 6 " " MAN J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 6 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG C 801 " - " ASN C 217 " " NAG C 802 " - " ASN C 272 " " NAG C 803 " - " ASN C 608 " " NAG D 801 " - " ASN D 217 " " NAG D 802 " - " ASN D 272 " " NAG D 803 " - " ASN D 608 " " NAG I 1 " - " ASN G 350 " " NAG J 1 " - " ASN H 350 " Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 11 sheets defined 65.5% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'D' and resid 175 through 197 removed outlier: 3.759A pdb=" N THR D 189 " --> pdb=" O MET D 185 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY D 190 " --> pdb=" O MET D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 216 removed outlier: 4.086A pdb=" N MET D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 230 removed outlier: 4.039A pdb=" N ALA D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 253 removed outlier: 3.502A pdb=" N ALA D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS D 248 " --> pdb=" O GLU D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 268 Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 291 through 303 Processing helix chain 'D' and resid 311 through 333 removed outlier: 4.265A pdb=" N VAL D 321 " --> pdb=" O HIS D 317 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N HIS D 324 " --> pdb=" O LEU D 320 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU D 331 " --> pdb=" O SER D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'D' and resid 460 through 481 removed outlier: 3.527A pdb=" N GLN D 464 " --> pdb=" O GLY D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 532 removed outlier: 3.712A pdb=" N GLY D 532 " --> pdb=" O MET D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 552 Processing helix chain 'D' and resid 556 through 565 removed outlier: 3.976A pdb=" N MET D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 570 removed outlier: 3.666A pdb=" N GLY D 569 " --> pdb=" O TYR D 566 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP D 570 " --> pdb=" O LYS D 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 566 through 570' Processing helix chain 'D' and resid 575 through 585 removed outlier: 4.005A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 599 Processing helix chain 'D' and resid 606 through 610 removed outlier: 3.978A pdb=" N THR D 610 " --> pdb=" O GLU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 623 removed outlier: 4.129A pdb=" N HIS D 617 " --> pdb=" O ARG D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 640 removed outlier: 3.597A pdb=" N ARG D 630 " --> pdb=" O TYR D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 662 removed outlier: 3.665A pdb=" N ILE D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 676 removed outlier: 3.578A pdb=" N LYS D 676 " --> pdb=" O TYR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 698 removed outlier: 3.782A pdb=" N SER D 698 " --> pdb=" O ALA D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 723 Processing helix chain 'E' and resid 104 through 110 Processing helix chain 'E' and resid 155 through 169 removed outlier: 3.550A pdb=" N LEU E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU E 160 " --> pdb=" O ALA E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 203 removed outlier: 3.742A pdb=" N GLN E 203 " --> pdb=" O SER E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 200 through 203' Processing helix chain 'E' and resid 242 through 246 Processing helix chain 'E' and resid 271 through 285 removed outlier: 3.903A pdb=" N GLN E 279 " --> pdb=" O ARG E 275 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 197 removed outlier: 3.547A pdb=" N GLU C 184 " --> pdb=" O MET C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 214 Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 218 through 230 removed outlier: 3.753A pdb=" N ALA C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 253 removed outlier: 4.190A pdb=" N LYS C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 267 removed outlier: 3.863A pdb=" N THR C 259 " --> pdb=" O PRO C 255 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 291 through 303 Processing helix chain 'C' and resid 311 through 333 removed outlier: 3.575A pdb=" N VAL C 321 " --> pdb=" O HIS C 317 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N HIS C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 331 " --> pdb=" O SER C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 483 removed outlier: 3.618A pdb=" N GLN C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 531 removed outlier: 3.642A pdb=" N SER C 531 " --> pdb=" O GLN C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 541 removed outlier: 3.658A pdb=" N THR C 541 " --> pdb=" O SER C 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 538 through 541' Processing helix chain 'C' and resid 542 through 551 Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.597A pdb=" N SER C 565 " --> pdb=" O THR C 561 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 568 " --> pdb=" O ASN C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 585 removed outlier: 3.734A pdb=" N ALA C 574 " --> pdb=" O ASP C 570 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL C 575 " --> pdb=" O TYR C 571 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 579 " --> pdb=" O VAL C 575 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 580 " --> pdb=" O ILE C 576 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 599 removed outlier: 3.568A pdb=" N GLN C 590 " --> pdb=" O TYR C 586 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN C 599 " --> pdb=" O PHE C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 624 removed outlier: 3.850A pdb=" N ARG C 613 " --> pdb=" O GLU C 609 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN C 624 " --> pdb=" O ARG C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 639 removed outlier: 3.997A pdb=" N ARG C 630 " --> pdb=" O TYR C 626 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 631 " --> pdb=" O THR C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 662 removed outlier: 3.717A pdb=" N ALA C 650 " --> pdb=" O ASP C 646 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN C 660 " --> pdb=" O LEU C 656 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 676 Processing helix chain 'C' and resid 684 through 698 removed outlier: 4.066A pdb=" N SER C 698 " --> pdb=" O ALA C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 723 removed outlier: 3.728A pdb=" N VAL C 705 " --> pdb=" O ALA C 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 111 removed outlier: 3.522A pdb=" N LYS F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 169 Processing helix chain 'F' and resid 242 through 250 removed outlier: 3.701A pdb=" N SER F 245 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS F 246 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Proline residue: F 247 - end of helix Processing helix chain 'F' and resid 272 through 284 removed outlier: 4.331A pdb=" N GLN F 276 " --> pdb=" O LEU F 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 26 removed outlier: 3.632A pdb=" N LEU A 25 " --> pdb=" O HIS A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 39 through 65 removed outlier: 3.598A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 96 removed outlier: 3.804A pdb=" N ARG A 80 " --> pdb=" O HIS A 76 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 86 " --> pdb=" O TRP A 82 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 128 removed outlier: 3.507A pdb=" N THR A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 165 removed outlier: 3.643A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY A 149 " --> pdb=" O MET A 145 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 162 " --> pdb=" O HIS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 201 removed outlier: 3.786A pdb=" N PHE A 174 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 197 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 232 removed outlier: 3.656A pdb=" N ALA A 209 " --> pdb=" O TRP A 205 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 245 through 266 removed outlier: 3.746A pdb=" N ALA A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 26 removed outlier: 3.538A pdb=" N ALA B 20 " --> pdb=" O GLY B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 removed outlier: 3.615A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 66 removed outlier: 4.000A pdb=" N VAL B 45 " --> pdb=" O PRO B 41 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR B 47 " --> pdb=" O MET B 43 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 95 removed outlier: 4.025A pdb=" N HIS B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B 86 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 93 " --> pdb=" O CYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 129 removed outlier: 3.571A pdb=" N PHE B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 166 removed outlier: 3.504A pdb=" N HIS B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 164 " --> pdb=" O TYR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 200 removed outlier: 4.383A pdb=" N VAL B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 188 " --> pdb=" O MET B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 237 removed outlier: 4.175A pdb=" N ALA B 209 " --> pdb=" O TRP B 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 266 removed outlier: 4.414A pdb=" N ASP B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 43 through 49 removed outlier: 6.152A pdb=" N ARG E 44 " --> pdb=" O ILE E 259 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N CYS E 261 " --> pdb=" O ARG E 44 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ASN E 46 " --> pdb=" O CYS E 261 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N SER E 263 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP E 258 " --> pdb=" O PRO E 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE E 260 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN E 65 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 122 through 126 removed outlier: 6.155A pdb=" N ILE E 131 " --> pdb=" O LEU E 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 136 through 138 Processing sheet with id=AA4, first strand: chain 'E' and resid 178 through 181 removed outlier: 3.640A pdb=" N THR E 186 " --> pdb=" O LYS E 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 189 through 193 removed outlier: 3.521A pdb=" N THR E 240 " --> pdb=" O ILE E 214 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N GLU E 233 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL E 229 " --> pdb=" O GLU E 233 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 198 through 199 removed outlier: 3.578A pdb=" N ARG E 205 " --> pdb=" O CYS E 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 43 through 46 removed outlier: 5.597A pdb=" N ARG F 44 " --> pdb=" O ILE F 259 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N CYS F 261 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASN F 46 " --> pdb=" O CYS F 261 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N SER F 263 " --> pdb=" O ASN F 46 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE F 260 " --> pdb=" O ILE F 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 122 through 125 removed outlier: 6.945A pdb=" N ILE F 131 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU F 151 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN F 133 " --> pdb=" O TYR F 149 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS F 135 " --> pdb=" O HIS F 147 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS F 147 " --> pdb=" O HIS F 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 178 through 181 Processing sheet with id=AB1, first strand: chain 'F' and resid 198 through 199 removed outlier: 3.683A pdb=" N ARG F 205 " --> pdb=" O CYS F 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 208 through 214 removed outlier: 3.655A pdb=" N TYR F 234 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR F 210 " --> pdb=" O TYR F 234 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 236 " --> pdb=" O THR F 210 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL F 237 " --> pdb=" O SER F 225 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER F 225 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU F 239 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE F 223 " --> pdb=" O LEU F 239 " (cutoff:3.500A) 898 hydrogen bonds defined for protein. 2656 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: 2.25 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4222 1.34 - 1.46: 3181 1.46 - 1.59: 5734 1.59 - 1.71: 4 1.71 - 1.83: 77 Bond restraints: 13218 Sorted by residual: bond pdb=" CG PRO E 198 " pdb=" CD PRO E 198 " ideal model delta sigma weight residual 1.503 1.295 0.208 3.40e-02 8.65e+02 3.73e+01 bond pdb=" C5 MAN J 3 " pdb=" O5 MAN J 3 " ideal model delta sigma weight residual 1.418 1.512 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" N PRO E 198 " pdb=" CD PRO E 198 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" CB PRO E 198 " pdb=" CG PRO E 198 " ideal model delta sigma weight residual 1.492 1.671 -0.179 5.00e-02 4.00e+02 1.29e+01 bond pdb=" C5 MAN I 3 " pdb=" O5 MAN I 3 " ideal model delta sigma weight residual 1.418 1.483 -0.065 2.00e-02 2.50e+03 1.07e+01 ... (remaining 13213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 17719 3.55 - 7.11: 284 7.11 - 10.66: 47 10.66 - 14.21: 13 14.21 - 17.77: 5 Bond angle restraints: 18068 Sorted by residual: angle pdb=" CA PRO E 198 " pdb=" N PRO E 198 " pdb=" CD PRO E 198 " ideal model delta sigma weight residual 112.00 94.23 17.77 1.40e+00 5.10e-01 1.61e+02 angle pdb=" CA PRO F 271 " pdb=" N PRO F 271 " pdb=" CD PRO F 271 " ideal model delta sigma weight residual 112.00 96.87 15.13 1.40e+00 5.10e-01 1.17e+02 angle pdb=" N PRO E 198 " pdb=" CD PRO E 198 " pdb=" CG PRO E 198 " ideal model delta sigma weight residual 103.20 90.00 13.20 1.50e+00 4.44e-01 7.74e+01 angle pdb=" CA PRO F 48 " pdb=" N PRO F 48 " pdb=" CD PRO F 48 " ideal model delta sigma weight residual 112.00 100.92 11.08 1.40e+00 5.10e-01 6.26e+01 angle pdb=" CA ARG F 275 " pdb=" CB ARG F 275 " pdb=" CG ARG F 275 " ideal model delta sigma weight residual 114.10 125.55 -11.45 2.00e+00 2.50e-01 3.28e+01 ... (remaining 18063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.15: 7370 25.15 - 50.29: 536 50.29 - 75.44: 82 75.44 - 100.58: 41 100.58 - 125.73: 13 Dihedral angle restraints: 8042 sinusoidal: 2474 harmonic: 5568 Sorted by residual: dihedral pdb=" CB CYS E 199 " pdb=" SG CYS E 199 " pdb=" SG CYS E 232 " pdb=" CB CYS E 232 " ideal model delta sinusoidal sigma weight residual -86.00 -1.74 -84.26 1 1.00e+01 1.00e-02 8.64e+01 dihedral pdb=" CA CYS E 244 " pdb=" C CYS E 244 " pdb=" N SER E 245 " pdb=" CA SER E 245 " ideal model delta harmonic sigma weight residual 180.00 142.84 37.16 0 5.00e+00 4.00e-02 5.52e+01 dihedral pdb=" CB CYS F 215 " pdb=" SG CYS F 215 " pdb=" SG CYS F 244 " pdb=" CB CYS F 244 " ideal model delta sinusoidal sigma weight residual 93.00 29.66 63.34 1 1.00e+01 1.00e-02 5.29e+01 ... (remaining 8039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1897 0.079 - 0.157: 240 0.157 - 0.236: 28 0.236 - 0.314: 7 0.314 - 0.393: 2 Chirality restraints: 2174 Sorted by residual: chirality pdb=" CB THR E 178 " pdb=" CA THR E 178 " pdb=" OG1 THR E 178 " pdb=" CG2 THR E 178 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CG LEU C 520 " pdb=" CB LEU C 520 " pdb=" CD1 LEU C 520 " pdb=" CD2 LEU C 520 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" C1 MAN I 5 " pdb=" O3 MAN I 4 " pdb=" C2 MAN I 5 " pdb=" O5 MAN I 5 " both_signs ideal model delta sigma weight residual False 2.40 2.43 -0.03 2.00e-02 2.50e+03 2.75e+00 ... (remaining 2171 not shown) Planarity restraints: 2380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 197 " -0.130 5.00e-02 4.00e+02 1.77e-01 5.04e+01 pdb=" N PRO E 198 " 0.306 5.00e-02 4.00e+02 pdb=" CA PRO E 198 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO E 198 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 270 " 0.119 5.00e-02 4.00e+02 1.67e-01 4.46e+01 pdb=" N PRO F 271 " -0.288 5.00e-02 4.00e+02 pdb=" CA PRO F 271 " 0.088 5.00e-02 4.00e+02 pdb=" CD PRO F 271 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 590 " -0.029 2.00e-02 2.50e+03 5.75e-02 3.31e+01 pdb=" C GLN D 590 " 0.099 2.00e-02 2.50e+03 pdb=" O GLN D 590 " -0.037 2.00e-02 2.50e+03 pdb=" N SER D 591 " -0.034 2.00e-02 2.50e+03 ... (remaining 2377 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 335 2.69 - 3.24: 12805 3.24 - 3.80: 20221 3.80 - 4.35: 24617 4.35 - 4.90: 39726 Nonbonded interactions: 97704 Sorted by model distance: nonbonded pdb=" OG SER A 39 " pdb=" OG SER A 42 " model vdw 2.138 3.040 nonbonded pdb=" OG SER B 39 " pdb=" OG SER B 42 " model vdw 2.157 3.040 nonbonded pdb=" OE2 GLU D 223 " pdb=" OG SER D 254 " model vdw 2.159 3.040 nonbonded pdb=" OD1 ASP D 635 " pdb=" OH TYR D 654 " model vdw 2.204 3.040 nonbonded pdb=" O ARG C 224 " pdb=" NH1 ARG C 224 " model vdw 2.220 3.120 ... (remaining 97699 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 1 through 48 or (resid 49 through 57 and (name N or name C \ A or name C or name O or name CB )) or resid 58 through 266)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 179 through 344 or (resid 458 through 459 and (name N or n \ ame CA or name C or name O or name CB )) or resid 460 through 481 or (resid 482 \ through 484 and (name N or name CA or name C or name O or name CB )) or (resid 4 \ 85 through 497 and (name N or name CA or name C or name O or name CB )) or resid \ 498 through 516 or resid 518 through 718 or (resid 719 through 723 and (name N \ or name CA or name C or name O or name CB )) or resid 801 through 803)) selection = (chain 'D' and ((resid 179 through 215 and (name N or name CA or name C or name \ O or name CB )) or resid 216 through 344 or resid 458 through 516 or resid 518 t \ hrough 803)) } ncs_group { reference = (chain 'E' and (resid 37 through 49 or (resid 50 through 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 111 or (resid 112 and ( \ name N or name CA or name C or name O or name CB )) or resid 113 or (resid 114 t \ hrough 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 124 or (resid 125 and (name N or name CA or name C or name O or name CB \ )) or resid 126 or (resid 127 and (name N or name CA or name C or name O or nam \ e CB )) or resid 128 or (resid 129 through 140 and (name N or name CA or name C \ or name O or name CB )) or (resid 141 through 151 and (name N or name CA or name \ C or name O or name CB )) or resid 152 or (resid 153 through 182 and (name N or \ name CA or name C or name O or name CB )) or resid 183 or (resid 184 through 19 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 192 or (resi \ d 193 and (name N or name CA or name C or name O or name CB )) or resid 194 or ( \ resid 195 and (name N or name CA or name C or name O or name CB )) or resid 196 \ or (resid 197 through 206 and (name N or name CA or name C or name O or name CB \ )) or resid 207 or (resid 208 through 214 and (name N or name CA or name C or na \ me O or name CB )) or resid 215 or (resid 216 through 231 and (name N or name CA \ or name C or name O or name CB )) or resid 232 or (resid 233 through 243 and (n \ ame N or name CA or name C or name O or name CB )) or resid 244 or (resid 245 th \ rough 253 and (name N or name CA or name C or name O or name CB )) or resid 254 \ through 284)) selection = (chain 'F' and (resid 37 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB )) or resid 87 through 284)) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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=0.50 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.990 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 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 : 0.006 0.208 13247 Z= 0.273 Angle : 1.193 17.766 18146 Z= 0.629 Chirality : 0.056 0.393 2174 Planarity : 0.009 0.177 2372 Dihedral : 19.655 125.728 4435 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.50 % Favored : 95.29 % Rotamer: Outliers : 0.66 % Allowed : 32.71 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.96 (0.16), residues: 1891 helix: -1.73 (0.12), residues: 1148 sheet: -1.10 (0.41), residues: 150 loop : -2.29 (0.23), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 689 TYR 0.068 0.002 TYR D 523 PHE 0.028 0.002 PHE C 546 TRP 0.030 0.002 TRP C 482 HIS 0.016 0.002 HIS E 246 Details of bonding type rmsd covalent geometry : bond 0.00618 (13218) covalent geometry : angle 1.15852 (18068) SS BOND : bond 0.00903 ( 9) SS BOND : angle 2.29583 ( 18) hydrogen bonds : bond 0.23437 ( 898) hydrogen bonds : angle 7.90285 ( 2656) link_ALPHA1-3 : bond 0.01422 ( 2) link_ALPHA1-3 : angle 2.97568 ( 6) link_ALPHA1-4 : bond 0.00828 ( 4) link_ALPHA1-4 : angle 4.14529 ( 12) link_ALPHA1-6 : bond 0.01141 ( 4) link_ALPHA1-6 : angle 1.45536 ( 12) link_BETA1-4 : bond 0.02636 ( 2) link_BETA1-4 : angle 10.89758 ( 6) link_NAG-ASN : bond 0.00795 ( 8) link_NAG-ASN : angle 4.47123 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 259 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 473 TYR cc_start: 0.8740 (m-80) cc_final: 0.8506 (m-80) REVERT: D 667 MET cc_start: 0.7940 (mtm) cc_final: 0.7664 (mtt) REVERT: C 501 ARG cc_start: 0.8682 (mtm110) cc_final: 0.8299 (mtm110) REVERT: C 505 GLN cc_start: 0.9106 (mt0) cc_final: 0.8832 (tt0) REVERT: C 667 MET cc_start: 0.8070 (mmm) cc_final: 0.7358 (mmt) REVERT: F 270 LYS cc_start: 0.7087 (pptt) cc_final: 0.6738 (pptt) REVERT: F 277 LEU cc_start: 0.8782 (tp) cc_final: 0.8448 (tp) REVERT: F 278 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7492 (tm-30) REVERT: F 279 GLN cc_start: 0.8419 (mm-40) cc_final: 0.7994 (mm-40) outliers start: 6 outliers final: 3 residues processed: 264 average time/residue: 0.1004 time to fit residues: 39.5498 Evaluate side-chains 242 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 239 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain F residue 272 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 475 GLN D 674 HIS ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.209691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.162255 restraints weight = 24339.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.158152 restraints weight = 13783.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.160193 restraints weight = 9662.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.160601 restraints weight = 8417.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.160796 restraints weight = 7661.958| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4179 r_free = 0.4179 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4179 r_free = 0.4179 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13247 Z= 0.173 Angle : 0.796 11.926 18146 Z= 0.388 Chirality : 0.046 0.256 2174 Planarity : 0.005 0.084 2372 Dihedral : 12.690 115.479 2442 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.23 % Favored : 96.61 % Rotamer: Outliers : 3.83 % Allowed : 29.54 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.18), residues: 1891 helix: 0.17 (0.14), residues: 1188 sheet: -1.07 (0.39), residues: 163 loop : -2.17 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 689 TYR 0.029 0.002 TYR D 523 PHE 0.019 0.002 PHE F 260 TRP 0.023 0.002 TRP C 482 HIS 0.005 0.001 HIS B 21 Details of bonding type rmsd covalent geometry : bond 0.00371 (13218) covalent geometry : angle 0.75862 (18068) SS BOND : bond 0.00477 ( 9) SS BOND : angle 1.63346 ( 18) hydrogen bonds : bond 0.04364 ( 898) hydrogen bonds : angle 4.51801 ( 2656) link_ALPHA1-3 : bond 0.02005 ( 2) link_ALPHA1-3 : angle 3.91435 ( 6) link_ALPHA1-4 : bond 0.01537 ( 4) link_ALPHA1-4 : angle 3.95700 ( 12) link_ALPHA1-6 : bond 0.01294 ( 4) link_ALPHA1-6 : angle 1.95986 ( 12) link_BETA1-4 : bond 0.01585 ( 2) link_BETA1-4 : angle 7.92286 ( 6) link_NAG-ASN : bond 0.00767 ( 8) link_NAG-ASN : angle 3.85256 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 248 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 570 ASP cc_start: 0.7215 (t70) cc_final: 0.7002 (t70) REVERT: E 127 HIS cc_start: 0.8067 (OUTLIER) cc_final: 0.7179 (m90) REVERT: C 667 MET cc_start: 0.8264 (mmm) cc_final: 0.7714 (mmt) REVERT: F 37 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7259 (mt) REVERT: F 47 TRP cc_start: 0.6732 (OUTLIER) cc_final: 0.5960 (m100) REVERT: F 270 LYS cc_start: 0.7492 (pptt) cc_final: 0.7165 (pptt) REVERT: F 277 LEU cc_start: 0.8777 (tp) cc_final: 0.8003 (tp) REVERT: F 281 GLU cc_start: 0.6569 (pm20) cc_final: 0.6212 (pm20) outliers start: 35 outliers final: 16 residues processed: 271 average time/residue: 0.0904 time to fit residues: 37.1202 Evaluate side-chains 249 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain E residue 127 HIS Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 47 TRP Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain B residue 46 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 0.0670 chunk 17 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 115 optimal weight: 40.0000 chunk 112 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 117 optimal weight: 40.0000 chunk 161 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 475 GLN ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.209721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.161157 restraints weight = 24395.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.157041 restraints weight = 13349.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.158894 restraints weight = 9522.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.159297 restraints weight = 8342.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.159535 restraints weight = 7675.954| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4184 r_free = 0.4184 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4184 r_free = 0.4184 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13247 Z= 0.160 Angle : 0.747 12.370 18146 Z= 0.356 Chirality : 0.044 0.271 2174 Planarity : 0.004 0.071 2372 Dihedral : 11.019 112.181 2440 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.65 % Favored : 96.24 % Rotamer: Outliers : 4.27 % Allowed : 30.63 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.19), residues: 1891 helix: 1.14 (0.14), residues: 1195 sheet: -1.02 (0.40), residues: 166 loop : -1.99 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 689 TYR 0.024 0.001 TYR D 523 PHE 0.017 0.001 PHE D 690 TRP 0.019 0.001 TRP C 482 HIS 0.005 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00350 (13218) covalent geometry : angle 0.71192 (18068) SS BOND : bond 0.00699 ( 9) SS BOND : angle 1.56177 ( 18) hydrogen bonds : bond 0.03603 ( 898) hydrogen bonds : angle 3.97505 ( 2656) link_ALPHA1-3 : bond 0.02871 ( 2) link_ALPHA1-3 : angle 3.89823 ( 6) link_ALPHA1-4 : bond 0.01352 ( 4) link_ALPHA1-4 : angle 3.42948 ( 12) link_ALPHA1-6 : bond 0.01506 ( 4) link_ALPHA1-6 : angle 2.02958 ( 12) link_BETA1-4 : bond 0.01466 ( 2) link_BETA1-4 : angle 7.66251 ( 6) link_NAG-ASN : bond 0.00741 ( 8) link_NAG-ASN : angle 3.48819 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 216 MET cc_start: 0.7682 (mmm) cc_final: 0.7433 (mmm) REVERT: D 473 TYR cc_start: 0.8427 (m-80) cc_final: 0.8058 (m-80) REVERT: D 667 MET cc_start: 0.8060 (mtm) cc_final: 0.7761 (mtt) REVERT: E 127 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.6839 (m90) REVERT: E 154 MET cc_start: 0.4594 (pmm) cc_final: 0.4034 (pmm) REVERT: C 466 ASN cc_start: 0.8136 (m-40) cc_final: 0.7329 (m-40) REVERT: C 549 VAL cc_start: 0.8415 (t) cc_final: 0.8198 (t) REVERT: F 37 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7341 (mt) REVERT: F 44 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7770 (ttp80) REVERT: F 47 TRP cc_start: 0.6847 (OUTLIER) cc_final: 0.6130 (m100) REVERT: A 39 SER cc_start: 0.7687 (t) cc_final: 0.7199 (p) outliers start: 39 outliers final: 22 residues processed: 262 average time/residue: 0.0838 time to fit residues: 33.3382 Evaluate side-chains 251 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 226 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 663 SER Chi-restraints excluded: chain E residue 127 HIS Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 555 TRP Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 47 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain B residue 46 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 156 optimal weight: 30.0000 chunk 94 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 171 optimal weight: 60.0000 chunk 135 optimal weight: 5.9990 chunk 185 optimal weight: 50.0000 chunk 31 optimal weight: 0.0170 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 HIS E 184 GLN ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 GLN ** C 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.207292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.155522 restraints weight = 24054.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.153149 restraints weight = 14668.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.154024 restraints weight = 9939.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.154806 restraints weight = 8979.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.155096 restraints weight = 7761.698| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4154 r_free = 0.4154 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4154 r_free = 0.4154 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13247 Z= 0.169 Angle : 0.733 12.806 18146 Z= 0.350 Chirality : 0.044 0.269 2174 Planarity : 0.004 0.064 2372 Dihedral : 10.522 114.798 2438 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.56 % Rotamer: Outliers : 4.92 % Allowed : 29.76 % Favored : 65.32 % 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: 0.62 (0.20), residues: 1891 helix: 1.61 (0.15), residues: 1201 sheet: -1.08 (0.40), residues: 166 loop : -1.96 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 275 TYR 0.025 0.001 TYR B 47 PHE 0.018 0.001 PHE D 595 TRP 0.011 0.001 TRP C 482 HIS 0.005 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00373 (13218) covalent geometry : angle 0.69946 (18068) SS BOND : bond 0.00418 ( 9) SS BOND : angle 1.53655 ( 18) hydrogen bonds : bond 0.03279 ( 898) hydrogen bonds : angle 3.81303 ( 2656) link_ALPHA1-3 : bond 0.01889 ( 2) link_ALPHA1-3 : angle 3.87525 ( 6) link_ALPHA1-4 : bond 0.01319 ( 4) link_ALPHA1-4 : angle 3.26293 ( 12) link_ALPHA1-6 : bond 0.01346 ( 4) link_ALPHA1-6 : angle 2.14455 ( 12) link_BETA1-4 : bond 0.01415 ( 2) link_BETA1-4 : angle 7.36611 ( 6) link_NAG-ASN : bond 0.00686 ( 8) link_NAG-ASN : angle 3.38652 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 667 MET cc_start: 0.8056 (mtm) cc_final: 0.7612 (mtt) REVERT: E 127 HIS cc_start: 0.7748 (OUTLIER) cc_final: 0.6890 (m90) REVERT: E 154 MET cc_start: 0.4528 (pmm) cc_final: 0.3922 (pmm) REVERT: C 549 VAL cc_start: 0.8432 (t) cc_final: 0.8211 (t) REVERT: F 37 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7264 (mt) REVERT: F 44 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7612 (ttp80) REVERT: F 47 TRP cc_start: 0.6874 (OUTLIER) cc_final: 0.6204 (m100) REVERT: A 39 SER cc_start: 0.7868 (t) cc_final: 0.7337 (p) outliers start: 45 outliers final: 28 residues processed: 261 average time/residue: 0.0817 time to fit residues: 32.7003 Evaluate side-chains 258 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 663 SER Chi-restraints excluded: chain E residue 127 HIS Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 555 TRP Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 47 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 48 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 126 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 182 optimal weight: 50.0000 chunk 177 optimal weight: 50.0000 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 158 optimal weight: 50.0000 chunk 144 optimal weight: 40.0000 chunk 48 optimal weight: 50.0000 chunk 132 optimal weight: 9.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.208247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.156272 restraints weight = 24633.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.156292 restraints weight = 14987.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.156842 restraints weight = 10613.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.158213 restraints weight = 9065.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.158296 restraints weight = 8208.284| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4100 r_free = 0.4100 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4100 r_free = 0.4100 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13247 Z= 0.130 Angle : 0.714 13.766 18146 Z= 0.338 Chirality : 0.043 0.259 2174 Planarity : 0.004 0.060 2372 Dihedral : 10.186 114.204 2438 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.23 % Favored : 96.66 % Rotamer: Outliers : 3.94 % Allowed : 31.18 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.20), residues: 1891 helix: 1.90 (0.15), residues: 1188 sheet: -1.07 (0.42), residues: 162 loop : -1.92 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 250 TYR 0.019 0.001 TYR B 47 PHE 0.020 0.001 PHE D 595 TRP 0.010 0.001 TRP C 482 HIS 0.007 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00279 (13218) covalent geometry : angle 0.67996 (18068) SS BOND : bond 0.00340 ( 9) SS BOND : angle 1.38073 ( 18) hydrogen bonds : bond 0.03057 ( 898) hydrogen bonds : angle 3.67562 ( 2656) link_ALPHA1-3 : bond 0.02128 ( 2) link_ALPHA1-3 : angle 4.04905 ( 6) link_ALPHA1-4 : bond 0.01345 ( 4) link_ALPHA1-4 : angle 3.26744 ( 12) link_ALPHA1-6 : bond 0.01473 ( 4) link_ALPHA1-6 : angle 2.10375 ( 12) link_BETA1-4 : bond 0.01404 ( 2) link_BETA1-4 : angle 7.30703 ( 6) link_NAG-ASN : bond 0.00665 ( 8) link_NAG-ASN : angle 3.25307 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 667 MET cc_start: 0.7881 (mtm) cc_final: 0.7459 (mtt) REVERT: E 127 HIS cc_start: 0.7617 (OUTLIER) cc_final: 0.6895 (m90) REVERT: E 154 MET cc_start: 0.4526 (pmm) cc_final: 0.3896 (pmm) REVERT: C 459 TYR cc_start: 0.3262 (OUTLIER) cc_final: 0.2055 (m-80) REVERT: F 37 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7095 (mt) REVERT: F 44 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7726 (ttp80) REVERT: F 47 TRP cc_start: 0.6822 (OUTLIER) cc_final: 0.6237 (m100) REVERT: F 278 GLU cc_start: 0.8628 (pt0) cc_final: 0.8014 (pp20) REVERT: F 279 GLN cc_start: 0.8467 (mm-40) cc_final: 0.7765 (mm-40) REVERT: A 39 SER cc_start: 0.7691 (t) cc_final: 0.7256 (p) outliers start: 36 outliers final: 22 residues processed: 259 average time/residue: 0.0857 time to fit residues: 33.7045 Evaluate side-chains 255 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 663 SER Chi-restraints excluded: chain E residue 127 HIS Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 459 TYR Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 555 TRP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 47 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 46 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 2 optimal weight: 20.0000 chunk 93 optimal weight: 0.5980 chunk 182 optimal weight: 50.0000 chunk 131 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 142 optimal weight: 40.0000 chunk 81 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 178 optimal weight: 20.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 ASN ** C 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.205406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.155391 restraints weight = 24045.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.156433 restraints weight = 15959.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.155251 restraints weight = 9985.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.156099 restraints weight = 9668.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.156138 restraints weight = 8715.718| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4115 r_free = 0.4115 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4115 r_free = 0.4115 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13247 Z= 0.153 Angle : 0.730 13.196 18146 Z= 0.347 Chirality : 0.043 0.280 2174 Planarity : 0.003 0.058 2372 Dihedral : 9.868 114.701 2438 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.39 % Favored : 96.51 % Rotamer: Outliers : 4.27 % Allowed : 30.53 % Favored : 65.21 % 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: 1.05 (0.20), residues: 1891 helix: 2.06 (0.15), residues: 1184 sheet: -1.07 (0.42), residues: 162 loop : -1.90 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 250 TYR 0.019 0.001 TYR B 47 PHE 0.019 0.001 PHE D 595 TRP 0.008 0.001 TRP D 555 HIS 0.008 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00334 (13218) covalent geometry : angle 0.69835 (18068) SS BOND : bond 0.00500 ( 9) SS BOND : angle 1.39883 ( 18) hydrogen bonds : bond 0.03084 ( 898) hydrogen bonds : angle 3.66249 ( 2656) link_ALPHA1-3 : bond 0.02068 ( 2) link_ALPHA1-3 : angle 4.09310 ( 6) link_ALPHA1-4 : bond 0.01218 ( 4) link_ALPHA1-4 : angle 3.21899 ( 12) link_ALPHA1-6 : bond 0.01403 ( 4) link_ALPHA1-6 : angle 2.17988 ( 12) link_BETA1-4 : bond 0.01356 ( 2) link_BETA1-4 : angle 7.20069 ( 6) link_NAG-ASN : bond 0.00738 ( 8) link_NAG-ASN : angle 3.14780 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 238 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 667 MET cc_start: 0.8003 (mtm) cc_final: 0.7543 (mtt) REVERT: E 127 HIS cc_start: 0.7849 (OUTLIER) cc_final: 0.7066 (m90) REVERT: E 153 ASN cc_start: 0.7794 (t0) cc_final: 0.7579 (m-40) REVERT: E 154 MET cc_start: 0.4587 (pmm) cc_final: 0.4034 (pmm) REVERT: C 459 TYR cc_start: 0.3452 (OUTLIER) cc_final: 0.2364 (m-80) REVERT: C 504 LYS cc_start: 0.8731 (mttp) cc_final: 0.8459 (mttp) REVERT: C 667 MET cc_start: 0.8283 (mmm) cc_final: 0.7682 (mmt) REVERT: F 37 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7277 (mt) REVERT: F 44 ARG cc_start: 0.8150 (ttp80) cc_final: 0.7710 (ttp80) REVERT: F 47 TRP cc_start: 0.6799 (OUTLIER) cc_final: 0.6257 (m100) REVERT: F 113 CYS cc_start: 0.5464 (OUTLIER) cc_final: 0.5261 (p) REVERT: F 275 ARG cc_start: 0.8534 (mmm-85) cc_final: 0.8172 (mpp80) REVERT: F 278 GLU cc_start: 0.8647 (pt0) cc_final: 0.8060 (pp20) REVERT: F 279 GLN cc_start: 0.8649 (mm-40) cc_final: 0.7929 (mm-40) REVERT: A 39 SER cc_start: 0.7818 (t) cc_final: 0.7324 (p) REVERT: B 28 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6052 (mm110) outliers start: 39 outliers final: 26 residues processed: 265 average time/residue: 0.0820 time to fit residues: 33.6686 Evaluate side-chains 258 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 663 SER Chi-restraints excluded: chain E residue 127 HIS Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 459 TYR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 555 TRP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 47 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 113 CYS Chi-restraints excluded: chain F residue 232 CYS Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 46 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 67 optimal weight: 30.0000 chunk 102 optimal weight: 5.9990 chunk 185 optimal weight: 60.0000 chunk 148 optimal weight: 20.0000 chunk 70 optimal weight: 30.0000 chunk 157 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 127 optimal weight: 40.0000 chunk 60 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 624 GLN E 221 HIS ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 GLN C 524 ASN ** C 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 276 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.203246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.158665 restraints weight = 23925.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.155826 restraints weight = 16200.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.157651 restraints weight = 14640.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.157222 restraints weight = 9747.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.160290 restraints weight = 9132.628| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4220 r_free = 0.4220 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4220 r_free = 0.4220 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 13247 Z= 0.303 Angle : 0.843 11.803 18146 Z= 0.412 Chirality : 0.048 0.313 2174 Planarity : 0.004 0.057 2372 Dihedral : 10.058 118.909 2438 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.61 % Favored : 95.29 % Rotamer: Outliers : 4.38 % Allowed : 31.29 % Favored : 64.33 % 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: 0.81 (0.20), residues: 1891 helix: 1.71 (0.15), residues: 1207 sheet: -0.96 (0.40), residues: 171 loop : -1.81 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 552 TYR 0.020 0.002 TYR B 47 PHE 0.019 0.002 PHE A 29 TRP 0.011 0.002 TRP D 302 HIS 0.007 0.002 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00679 (13218) covalent geometry : angle 0.81538 (18068) SS BOND : bond 0.00662 ( 9) SS BOND : angle 1.98426 ( 18) hydrogen bonds : bond 0.03845 ( 898) hydrogen bonds : angle 4.00954 ( 2656) link_ALPHA1-3 : bond 0.01611 ( 2) link_ALPHA1-3 : angle 3.83967 ( 6) link_ALPHA1-4 : bond 0.01006 ( 4) link_ALPHA1-4 : angle 3.13936 ( 12) link_ALPHA1-6 : bond 0.01313 ( 4) link_ALPHA1-6 : angle 2.32064 ( 12) link_BETA1-4 : bond 0.01292 ( 2) link_BETA1-4 : angle 7.02271 ( 6) link_NAG-ASN : bond 0.00663 ( 8) link_NAG-ASN : angle 3.23175 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 MET cc_start: 0.4572 (pmm) cc_final: 0.4117 (pmm) REVERT: C 459 TYR cc_start: 0.3720 (OUTLIER) cc_final: 0.2692 (m-80) REVERT: C 504 LYS cc_start: 0.8698 (mttp) cc_final: 0.8418 (mttp) REVERT: C 667 MET cc_start: 0.8010 (mmm) cc_final: 0.7653 (mmt) REVERT: C 696 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6306 (pm20) REVERT: F 44 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7720 (ttp80) REVERT: F 47 TRP cc_start: 0.7234 (OUTLIER) cc_final: 0.6955 (m100) REVERT: F 278 GLU cc_start: 0.8441 (pt0) cc_final: 0.8101 (pp20) REVERT: F 279 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7637 (mm-40) REVERT: A 39 SER cc_start: 0.7842 (t) cc_final: 0.7314 (p) REVERT: B 30 TYR cc_start: 0.7901 (t80) cc_final: 0.7644 (t80) outliers start: 40 outliers final: 31 residues processed: 252 average time/residue: 0.0820 time to fit residues: 31.8652 Evaluate side-chains 248 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 663 SER Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 459 TYR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 555 TRP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 696 GLU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 47 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 232 CYS Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 46 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 148 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 0.0370 chunk 113 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 156 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 139 optimal weight: 30.0000 chunk 61 optimal weight: 20.0000 overall best weight: 3.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 GLN C 524 ASN ** C 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.200262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.147576 restraints weight = 23795.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.147734 restraints weight = 14846.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.146849 restraints weight = 9460.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.147727 restraints weight = 9661.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.147674 restraints weight = 8857.556| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4030 r_free = 0.4030 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4030 r_free = 0.4030 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13247 Z= 0.269 Angle : 0.820 13.047 18146 Z= 0.399 Chirality : 0.047 0.326 2174 Planarity : 0.004 0.057 2372 Dihedral : 9.972 116.547 2438 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.02 % Favored : 95.87 % Rotamer: Outliers : 3.94 % Allowed : 32.06 % Favored : 64.00 % 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: 0.82 (0.20), residues: 1891 helix: 1.74 (0.15), residues: 1205 sheet: -0.99 (0.41), residues: 171 loop : -1.85 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 552 TYR 0.018 0.002 TYR B 47 PHE 0.019 0.002 PHE D 595 TRP 0.012 0.002 TRP E 121 HIS 0.008 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00600 (13218) covalent geometry : angle 0.79149 (18068) SS BOND : bond 0.00967 ( 9) SS BOND : angle 2.06419 ( 18) hydrogen bonds : bond 0.03637 ( 898) hydrogen bonds : angle 3.95194 ( 2656) link_ALPHA1-3 : bond 0.01747 ( 2) link_ALPHA1-3 : angle 3.98323 ( 6) link_ALPHA1-4 : bond 0.01093 ( 4) link_ALPHA1-4 : angle 3.13052 ( 12) link_ALPHA1-6 : bond 0.01457 ( 4) link_ALPHA1-6 : angle 2.31368 ( 12) link_BETA1-4 : bond 0.01356 ( 2) link_BETA1-4 : angle 6.99213 ( 6) link_NAG-ASN : bond 0.00558 ( 8) link_NAG-ASN : angle 3.07916 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 471 LEU cc_start: 0.8678 (mt) cc_final: 0.8452 (mt) REVERT: D 501 ARG cc_start: 0.8147 (ptp90) cc_final: 0.7885 (mpp-170) REVERT: E 154 MET cc_start: 0.4774 (pmm) cc_final: 0.4290 (pmm) REVERT: C 459 TYR cc_start: 0.3672 (OUTLIER) cc_final: 0.2711 (m-80) REVERT: C 504 LYS cc_start: 0.8679 (mttp) cc_final: 0.8384 (mttp) REVERT: C 667 MET cc_start: 0.8271 (mmm) cc_final: 0.7787 (mmt) REVERT: C 673 MET cc_start: 0.8650 (tpp) cc_final: 0.8183 (tmm) REVERT: F 44 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7743 (ttp80) REVERT: F 47 TRP cc_start: 0.7186 (OUTLIER) cc_final: 0.6824 (m100) REVERT: F 71 THR cc_start: 0.6717 (p) cc_final: 0.6442 (m) REVERT: F 278 GLU cc_start: 0.8665 (pt0) cc_final: 0.8117 (pp20) REVERT: F 279 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8101 (mm-40) REVERT: A 39 SER cc_start: 0.7929 (t) cc_final: 0.7301 (p) REVERT: B 28 GLN cc_start: 0.6819 (OUTLIER) cc_final: 0.6002 (mm-40) outliers start: 36 outliers final: 30 residues processed: 250 average time/residue: 0.0792 time to fit residues: 30.1145 Evaluate side-chains 248 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 663 SER Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 710 CYS Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 459 TYR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 555 TRP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 47 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 232 CYS Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 46 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 162 optimal weight: 8.9990 chunk 154 optimal weight: 50.0000 chunk 142 optimal weight: 40.0000 chunk 42 optimal weight: 0.9990 chunk 127 optimal weight: 30.0000 chunk 52 optimal weight: 0.6980 chunk 131 optimal weight: 30.0000 chunk 138 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 674 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 ASN ** C 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.204014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.149041 restraints weight = 24241.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.152960 restraints weight = 11678.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.153577 restraints weight = 8458.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.154036 restraints weight = 7099.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.154201 restraints weight = 7118.415| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4105 r_free = 0.4105 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4105 r_free = 0.4105 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13247 Z= 0.137 Angle : 0.755 14.634 18146 Z= 0.362 Chirality : 0.044 0.269 2174 Planarity : 0.003 0.056 2372 Dihedral : 9.499 113.802 2438 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.92 % Favored : 95.92 % Rotamer: Outliers : 3.39 % Allowed : 33.59 % Favored : 63.02 % 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: 1.16 (0.20), residues: 1891 helix: 2.09 (0.15), residues: 1195 sheet: -1.01 (0.42), residues: 167 loop : -1.79 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 250 TYR 0.017 0.001 TYR B 47 PHE 0.019 0.001 PHE D 595 TRP 0.015 0.001 TRP E 47 HIS 0.007 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00295 (13218) covalent geometry : angle 0.72658 (18068) SS BOND : bond 0.00369 ( 9) SS BOND : angle 1.43035 ( 18) hydrogen bonds : bond 0.03117 ( 898) hydrogen bonds : angle 3.70933 ( 2656) link_ALPHA1-3 : bond 0.02103 ( 2) link_ALPHA1-3 : angle 4.09330 ( 6) link_ALPHA1-4 : bond 0.01292 ( 4) link_ALPHA1-4 : angle 3.11758 ( 12) link_ALPHA1-6 : bond 0.01691 ( 4) link_ALPHA1-6 : angle 2.05621 ( 12) link_BETA1-4 : bond 0.01361 ( 2) link_BETA1-4 : angle 6.96443 ( 6) link_NAG-ASN : bond 0.00566 ( 8) link_NAG-ASN : angle 2.96210 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 471 LEU cc_start: 0.8596 (mt) cc_final: 0.8348 (mt) REVERT: E 127 HIS cc_start: 0.7427 (OUTLIER) cc_final: 0.6832 (m90) REVERT: E 154 MET cc_start: 0.4805 (pmm) cc_final: 0.4343 (pmm) REVERT: C 459 TYR cc_start: 0.3669 (OUTLIER) cc_final: 0.2787 (m-80) REVERT: C 467 TYR cc_start: 0.8682 (m-80) cc_final: 0.8340 (m-80) REVERT: C 504 LYS cc_start: 0.8669 (mttp) cc_final: 0.8434 (mttp) REVERT: C 557 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7810 (mm-30) REVERT: C 667 MET cc_start: 0.8258 (mmm) cc_final: 0.7802 (mmt) REVERT: F 44 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7697 (ttp80) REVERT: F 47 TRP cc_start: 0.7161 (OUTLIER) cc_final: 0.6811 (m100) REVERT: F 278 GLU cc_start: 0.8607 (pt0) cc_final: 0.8136 (pp20) REVERT: F 279 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8102 (mm-40) REVERT: A 39 SER cc_start: 0.7711 (t) cc_final: 0.7170 (p) outliers start: 31 outliers final: 22 residues processed: 252 average time/residue: 0.0769 time to fit residues: 29.8809 Evaluate side-chains 252 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 663 SER Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 710 CYS Chi-restraints excluded: chain E residue 127 HIS Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 459 TYR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 555 TRP Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain F residue 47 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 232 CYS Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 28 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 68 optimal weight: 20.0000 chunk 133 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 119 optimal weight: 0.0980 chunk 74 optimal weight: 0.0470 chunk 185 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 174 optimal weight: 50.0000 chunk 136 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 ASN B 27 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.206778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.153043 restraints weight = 24696.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.156751 restraints weight = 15327.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.156904 restraints weight = 9522.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.156907 restraints weight = 9295.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.157172 restraints weight = 8854.983| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4106 r_free = 0.4106 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4106 r_free = 0.4106 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13247 Z= 0.131 Angle : 0.747 14.485 18146 Z= 0.357 Chirality : 0.043 0.265 2174 Planarity : 0.003 0.055 2372 Dihedral : 9.117 113.639 2438 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.60 % Favored : 96.29 % Rotamer: Outliers : 2.95 % Allowed : 34.35 % Favored : 62.69 % 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: 1.40 (0.20), residues: 1891 helix: 2.29 (0.15), residues: 1197 sheet: -0.97 (0.42), residues: 167 loop : -1.73 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 689 TYR 0.018 0.001 TYR B 47 PHE 0.019 0.001 PHE D 595 TRP 0.024 0.001 TRP C 482 HIS 0.007 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00280 (13218) covalent geometry : angle 0.71933 (18068) SS BOND : bond 0.00266 ( 9) SS BOND : angle 1.55821 ( 18) hydrogen bonds : bond 0.03017 ( 898) hydrogen bonds : angle 3.62068 ( 2656) link_ALPHA1-3 : bond 0.02125 ( 2) link_ALPHA1-3 : angle 4.06989 ( 6) link_ALPHA1-4 : bond 0.01138 ( 4) link_ALPHA1-4 : angle 3.03810 ( 12) link_ALPHA1-6 : bond 0.01649 ( 4) link_ALPHA1-6 : angle 1.90683 ( 12) link_BETA1-4 : bond 0.01411 ( 2) link_BETA1-4 : angle 6.91512 ( 6) link_NAG-ASN : bond 0.00530 ( 8) link_NAG-ASN : angle 2.86564 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 471 LEU cc_start: 0.8515 (mt) cc_final: 0.8301 (mt) REVERT: D 473 TYR cc_start: 0.8185 (m-80) cc_final: 0.7974 (m-80) REVERT: D 663 SER cc_start: 0.7939 (OUTLIER) cc_final: 0.7641 (p) REVERT: D 667 MET cc_start: 0.7818 (mtm) cc_final: 0.7495 (mtt) REVERT: E 69 MET cc_start: 0.7504 (mmm) cc_final: 0.7169 (mmm) REVERT: E 127 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.6929 (m90) REVERT: E 154 MET cc_start: 0.4618 (pmm) cc_final: 0.4135 (pmm) REVERT: C 459 TYR cc_start: 0.3415 (OUTLIER) cc_final: 0.2591 (m-80) REVERT: C 467 TYR cc_start: 0.8493 (m-80) cc_final: 0.8127 (m-80) REVERT: C 504 LYS cc_start: 0.8834 (mttp) cc_final: 0.8514 (mttp) REVERT: C 557 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7583 (mm-30) REVERT: C 667 MET cc_start: 0.7991 (mmm) cc_final: 0.7639 (mmt) REVERT: F 44 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7683 (ttp80) REVERT: F 47 TRP cc_start: 0.7200 (OUTLIER) cc_final: 0.6899 (m100) REVERT: F 76 LYS cc_start: 0.7532 (tppt) cc_final: 0.6937 (ttmt) REVERT: F 278 GLU cc_start: 0.8573 (pt0) cc_final: 0.8199 (pp20) REVERT: F 279 GLN cc_start: 0.8353 (mm-40) cc_final: 0.7989 (mm-40) REVERT: A 39 SER cc_start: 0.7556 (t) cc_final: 0.7094 (p) outliers start: 27 outliers final: 19 residues processed: 252 average time/residue: 0.0885 time to fit residues: 34.0707 Evaluate side-chains 247 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 663 SER Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 710 CYS Chi-restraints excluded: chain E residue 127 HIS Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 459 TYR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 555 TRP Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain F residue 47 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 232 CYS Chi-restraints excluded: chain B residue 21 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 171 optimal weight: 50.0000 chunk 74 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 123 optimal weight: 0.0170 chunk 105 optimal weight: 0.8980 chunk 141 optimal weight: 20.0000 chunk 20 optimal weight: 40.0000 chunk 154 optimal weight: 50.0000 chunk 142 optimal weight: 30.0000 overall best weight: 3.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 GLN C 524 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.199645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.142273 restraints weight = 23813.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.146572 restraints weight = 13453.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.146461 restraints weight = 8551.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.146909 restraints weight = 8896.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.146908 restraints weight = 8097.686| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3989 r_free = 0.3989 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3989 r_free = 0.3989 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13247 Z= 0.276 Angle : 0.839 13.089 18146 Z= 0.409 Chirality : 0.047 0.274 2174 Planarity : 0.004 0.055 2372 Dihedral : 9.381 115.463 2438 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.45 % Favored : 95.45 % Rotamer: Outliers : 3.39 % Allowed : 34.03 % Favored : 62.58 % 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 (0.20), residues: 1891 helix: 2.03 (0.15), residues: 1202 sheet: -0.86 (0.42), residues: 170 loop : -1.72 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 224 TYR 0.022 0.002 TYR C 523 PHE 0.020 0.002 PHE D 595 TRP 0.016 0.002 TRP C 482 HIS 0.007 0.002 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00614 (13218) covalent geometry : angle 0.81211 (18068) SS BOND : bond 0.00495 ( 9) SS BOND : angle 2.45206 ( 18) hydrogen bonds : bond 0.03721 ( 898) hydrogen bonds : angle 3.91096 ( 2656) link_ALPHA1-3 : bond 0.01689 ( 2) link_ALPHA1-3 : angle 3.93364 ( 6) link_ALPHA1-4 : bond 0.00914 ( 4) link_ALPHA1-4 : angle 2.96626 ( 12) link_ALPHA1-6 : bond 0.01306 ( 4) link_ALPHA1-6 : angle 2.04487 ( 12) link_BETA1-4 : bond 0.01328 ( 2) link_BETA1-4 : angle 6.84423 ( 6) link_NAG-ASN : bond 0.00426 ( 8) link_NAG-ASN : angle 3.00740 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2577.99 seconds wall clock time: 44 minutes 57.05 seconds (2697.05 seconds total)