Starting phenix.real_space_refine on Thu May 15 09:08:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kev_37168/05_2025/8kev_37168.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kev_37168/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8kev_37168/05_2025/8kev_37168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kev_37168/05_2025/8kev_37168.map" model { file = "/net/cci-nas-00/data/ceres_data/8kev_37168/05_2025/8kev_37168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kev_37168/05_2025/8kev_37168.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 7, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} 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: {'GLN:plan1': 7, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 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, 'TYR:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} 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, 'TYR:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} 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: {'GLN:plan1': 5, 'HIS:plan': 7, 'TYR:plan': 10, 'ASN:plan1': 8, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 25, 'ARG: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: {'GLN:plan1': 4, 'ASP:plan': 8, 'TYR:plan': 8, 'ASN:plan1': 3, 'TRP:plan': 4, 'HIS:plan': 7, 'PHE:plan': 26, 'GLU:plan': 9, 'ARG:plan': 12} 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: {'GLN:plan1': 5, 'ASP:plan': 8, 'TYR:plan': 8, 'ASN:plan1': 3, 'TRP:plan': 4, 'HIS:plan': 7, 'PHE:plan': 26, 'GLU:plan': 9, 'ARG:plan': 12} 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: 10.95, per 1000 atoms: 0.84 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: 3.40 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 1.26 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: 3.64 Time building geometry restraints manager: 3.93 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 723 or resid 801 through 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: 1.000 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.680 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.720 ------------------------------------------------------------------------------- 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 : 7.73 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.030 0.002 TRP C 482 HIS 0.016 0.002 HIS E 246 PHE 0.028 0.002 PHE C 546 TYR 0.068 0.002 TYR D 523 ARG 0.025 0.001 ARG C 689 Details of bonding type rmsd link_NAG-ASN : bond 0.00795 ( 8) link_NAG-ASN : angle 4.47123 ( 24) 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_ALPHA1-3 : bond 0.01422 ( 2) link_ALPHA1-3 : angle 2.97568 ( 6) hydrogen bonds : bond 0.23437 ( 898) hydrogen bonds : angle 7.90285 ( 2656) SS BOND : bond 0.00903 ( 9) SS BOND : angle 2.29583 ( 18) covalent geometry : bond 0.00618 (13218) covalent geometry : angle 1.15852 (18068) *********************** 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 : 1.381 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: 0.2230 time to fit residues: 87.3617 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 : 1.314 ------------------------------------------------------------------------------- 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 157 optimal weight: 30.0000 chunk 140 optimal weight: 50.0000 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 40.0000 chunk 95 optimal weight: 0.2980 chunk 75 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 chunk 56 optimal weight: 40.0000 chunk 88 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.4726 r_free = 0.4726 target = 0.205166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.154442 restraints weight = 24133.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.156802 restraints weight = 15176.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.156144 restraints weight = 8849.371| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4135 r_free = 0.4135 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4135 r_free = 0.4135 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13247 Z= 0.191 Angle : 0.812 11.861 18146 Z= 0.397 Chirality : 0.046 0.262 2174 Planarity : 0.005 0.084 2372 Dihedral : 12.715 115.884 2442 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.34 % Favored : 96.51 % Rotamer: Outliers : 4.05 % Allowed : 29.54 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.18), residues: 1891 helix: 0.14 (0.14), residues: 1188 sheet: -1.08 (0.39), residues: 163 loop : -2.17 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 482 HIS 0.005 0.001 HIS B 21 PHE 0.019 0.002 PHE F 260 TYR 0.028 0.002 TYR D 654 ARG 0.011 0.001 ARG C 689 Details of bonding type rmsd link_NAG-ASN : bond 0.00771 ( 8) link_NAG-ASN : angle 3.87063 ( 24) link_ALPHA1-4 : bond 0.01488 ( 4) link_ALPHA1-4 : angle 3.94933 ( 12) link_ALPHA1-6 : bond 0.01294 ( 4) link_ALPHA1-6 : angle 1.96974 ( 12) link_BETA1-4 : bond 0.01515 ( 2) link_BETA1-4 : angle 8.02302 ( 6) link_ALPHA1-3 : bond 0.01706 ( 2) link_ALPHA1-3 : angle 3.87345 ( 6) hydrogen bonds : bond 0.04473 ( 898) hydrogen bonds : angle 4.54791 ( 2656) SS BOND : bond 0.00458 ( 9) SS BOND : angle 1.72652 ( 18) covalent geometry : bond 0.00414 (13218) covalent geometry : angle 0.77421 (18068) *********************** 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: 37 poor density : 246 time to evaluate : 1.323 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: E 127 HIS cc_start: 0.8160 (OUTLIER) cc_final: 0.7269 (m90) REVERT: C 224 ARG cc_start: 0.7080 (tpt90) cc_final: 0.6872 (tpt90) REVERT: C 667 MET cc_start: 0.8418 (mmm) cc_final: 0.7836 (mmt) REVERT: F 37 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7276 (mt) REVERT: F 47 TRP cc_start: 0.6686 (OUTLIER) cc_final: 0.5904 (m100) REVERT: F 270 LYS cc_start: 0.7510 (pptt) cc_final: 0.7196 (pptt) REVERT: F 277 LEU cc_start: 0.8749 (tp) cc_final: 0.8017 (tp) REVERT: F 281 GLU cc_start: 0.6653 (pm20) cc_final: 0.6275 (pm20) outliers start: 37 outliers final: 15 residues processed: 270 average time/residue: 0.2198 time to fit residues: 90.1843 Evaluate side-chains 245 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 217 ASN 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 16 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 chunk 121 optimal weight: 50.0000 chunk 51 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 170 optimal weight: 50.0000 chunk 103 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.210791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.160254 restraints weight = 24295.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.157316 restraints weight = 13898.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.157711 restraints weight = 11052.533| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4183 r_free = 0.4183 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 = 0.4183 r_free = 0.4183 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13247 Z= 0.143 Angle : 0.736 12.987 18146 Z= 0.351 Chirality : 0.044 0.262 2174 Planarity : 0.004 0.071 2372 Dihedral : 11.233 115.027 2440 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.39 % Favored : 96.51 % Rotamer: Outliers : 4.16 % Allowed : 29.76 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.19), residues: 1891 helix: 1.12 (0.15), residues: 1193 sheet: -1.03 (0.40), residues: 166 loop : -2.01 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 482 HIS 0.005 0.001 HIS E 130 PHE 0.019 0.001 PHE D 595 TYR 0.027 0.001 TYR D 654 ARG 0.011 0.001 ARG C 689 Details of bonding type rmsd link_NAG-ASN : bond 0.00741 ( 8) link_NAG-ASN : angle 3.53911 ( 24) link_ALPHA1-4 : bond 0.01558 ( 4) link_ALPHA1-4 : angle 3.57449 ( 12) link_ALPHA1-6 : bond 0.01544 ( 4) link_ALPHA1-6 : angle 1.98108 ( 12) link_BETA1-4 : bond 0.01359 ( 2) link_BETA1-4 : angle 7.75113 ( 6) link_ALPHA1-3 : bond 0.02385 ( 2) link_ALPHA1-3 : angle 3.68545 ( 6) hydrogen bonds : bond 0.03601 ( 898) hydrogen bonds : angle 3.98575 ( 2656) SS BOND : bond 0.00431 ( 9) SS BOND : angle 1.38964 ( 18) covalent geometry : bond 0.00305 (13218) covalent geometry : angle 0.70038 (18068) *********************** 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 280 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 242 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 216 MET cc_start: 0.7726 (mmm) cc_final: 0.7487 (mmm) REVERT: D 473 TYR cc_start: 0.8437 (m-80) cc_final: 0.8084 (m-80) REVERT: D 667 MET cc_start: 0.8056 (mtm) cc_final: 0.7765 (mtt) REVERT: E 127 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.6848 (m90) REVERT: E 279 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8506 (mm-40) REVERT: C 297 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8130 (mm) REVERT: C 466 ASN cc_start: 0.8101 (m-40) cc_final: 0.7325 (m-40) REVERT: C 505 GLN cc_start: 0.8898 (tt0) cc_final: 0.8663 (tt0) REVERT: C 549 VAL cc_start: 0.8450 (t) cc_final: 0.8166 (t) REVERT: F 37 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7316 (mt) REVERT: F 44 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7775 (ttp80) REVERT: F 47 TRP cc_start: 0.6820 (OUTLIER) cc_final: 0.6066 (m100) REVERT: F 270 LYS cc_start: 0.7340 (pptt) cc_final: 0.7004 (pptt) REVERT: A 39 SER cc_start: 0.7739 (t) cc_final: 0.7215 (p) outliers start: 38 outliers final: 23 residues processed: 266 average time/residue: 0.2196 time to fit residues: 87.6332 Evaluate side-chains 253 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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 E residue 279 GLN Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 297 LEU 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 533 THR 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 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 115 optimal weight: 50.0000 chunk 74 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 58 optimal weight: 0.0000 chunk 112 optimal weight: 6.9990 chunk 93 optimal weight: 0.0270 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 160 optimal weight: 60.0000 overall best weight: 0.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 637 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.209665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.163244 restraints weight = 24131.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.160090 restraints weight = 12811.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.161330 restraints weight = 9743.184| |-----------------------------------------------------------------------------| r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4224 r_free = 0.4224 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 = 0.4224 r_free = 0.4224 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13247 Z= 0.125 Angle : 0.711 13.345 18146 Z= 0.336 Chirality : 0.043 0.262 2174 Planarity : 0.004 0.064 2372 Dihedral : 10.493 114.533 2440 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 3.94 % Allowed : 30.20 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1891 helix: 1.69 (0.15), residues: 1184 sheet: -1.04 (0.41), residues: 159 loop : -2.00 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 482 HIS 0.004 0.001 HIS C 518 PHE 0.020 0.001 PHE D 595 TYR 0.016 0.001 TYR D 523 ARG 0.006 0.000 ARG C 689 Details of bonding type rmsd link_NAG-ASN : bond 0.00712 ( 8) link_NAG-ASN : angle 3.34200 ( 24) link_ALPHA1-4 : bond 0.01404 ( 4) link_ALPHA1-4 : angle 3.29110 ( 12) link_ALPHA1-6 : bond 0.01469 ( 4) link_ALPHA1-6 : angle 2.06373 ( 12) link_BETA1-4 : bond 0.01433 ( 2) link_BETA1-4 : angle 7.45737 ( 6) link_ALPHA1-3 : bond 0.02135 ( 2) link_ALPHA1-3 : angle 3.94001 ( 6) hydrogen bonds : bond 0.03111 ( 898) hydrogen bonds : angle 3.74540 ( 2656) SS BOND : bond 0.00429 ( 9) SS BOND : angle 1.22745 ( 18) covalent geometry : bond 0.00262 (13218) covalent geometry : angle 0.67691 (18068) *********************** 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 278 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 216 MET cc_start: 0.7678 (mmm) cc_final: 0.7474 (mmm) REVERT: D 667 MET cc_start: 0.8027 (mtm) cc_final: 0.7613 (mtt) REVERT: E 127 HIS cc_start: 0.7841 (OUTLIER) cc_final: 0.7210 (m90) REVERT: E 279 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8611 (mp10) REVERT: C 224 ARG cc_start: 0.7136 (tpt90) cc_final: 0.6815 (tpt90) REVERT: C 505 GLN cc_start: 0.8835 (tt0) cc_final: 0.8624 (tt0) REVERT: C 667 MET cc_start: 0.8171 (mmm) cc_final: 0.7707 (mmt) REVERT: F 37 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7288 (mt) REVERT: F 44 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7514 (ttp80) REVERT: F 47 TRP cc_start: 0.6755 (OUTLIER) cc_final: 0.5923 (m100) REVERT: A 39 SER cc_start: 0.7722 (t) cc_final: 0.7243 (p) outliers start: 36 outliers final: 22 residues processed: 263 average time/residue: 0.2109 time to fit residues: 84.1003 Evaluate side-chains 253 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 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 E residue 279 GLN 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 535 VAL 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 84 VAL Chi-restraints excluded: chain B residue 42 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 94 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 143 optimal weight: 20.0000 chunk 79 optimal weight: 0.7980 chunk 181 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.208461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.158411 restraints weight = 24563.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.158607 restraints weight = 16806.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.158110 restraints weight = 10371.735| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4097 r_free = 0.4097 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4097 r_free = 0.4097 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2541 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= 0.140 Angle : 0.707 13.156 18146 Z= 0.335 Chirality : 0.043 0.263 2174 Planarity : 0.003 0.060 2372 Dihedral : 10.035 113.961 2438 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.49 % Favored : 96.40 % Rotamer: Outliers : 3.94 % Allowed : 30.85 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1891 helix: 1.94 (0.15), residues: 1184 sheet: -1.13 (0.41), residues: 162 loop : -1.96 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 482 HIS 0.008 0.001 HIS C 518 PHE 0.019 0.001 PHE D 595 TYR 0.014 0.001 TYR E 150 ARG 0.007 0.001 ARG E 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00672 ( 8) link_NAG-ASN : angle 3.22004 ( 24) link_ALPHA1-4 : bond 0.01278 ( 4) link_ALPHA1-4 : angle 3.28549 ( 12) link_ALPHA1-6 : bond 0.01446 ( 4) link_ALPHA1-6 : angle 2.11455 ( 12) link_BETA1-4 : bond 0.01437 ( 2) link_BETA1-4 : angle 7.32126 ( 6) link_ALPHA1-3 : bond 0.02041 ( 2) link_ALPHA1-3 : angle 4.02779 ( 6) hydrogen bonds : bond 0.03054 ( 898) hydrogen bonds : angle 3.66528 ( 2656) SS BOND : bond 0.00472 ( 9) SS BOND : angle 1.18118 ( 18) covalent geometry : bond 0.00304 (13218) covalent geometry : angle 0.67314 (18068) *********************** 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 279 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 501 ARG cc_start: 0.7813 (ptp90) cc_final: 0.7580 (mpp-170) REVERT: D 667 MET cc_start: 0.7907 (mtm) cc_final: 0.7489 (mtt) REVERT: E 127 HIS cc_start: 0.7819 (OUTLIER) cc_final: 0.7059 (m90) REVERT: F 37 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7254 (mt) REVERT: F 44 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7579 (ttp80) REVERT: F 47 TRP cc_start: 0.6678 (OUTLIER) cc_final: 0.6052 (m100) REVERT: F 278 GLU cc_start: 0.8723 (pt0) cc_final: 0.8147 (pp20) REVERT: F 279 GLN cc_start: 0.8475 (mm-40) cc_final: 0.7792 (mm-40) REVERT: A 39 SER cc_start: 0.7745 (t) cc_final: 0.7303 (p) outliers start: 36 outliers final: 20 residues processed: 265 average time/residue: 0.2144 time to fit residues: 85.0424 Evaluate side-chains 246 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 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 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 604 ILE 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 84 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 137 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 136 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 221 HIS ** 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 = 0.4748 r_free = 0.4748 target = 0.209022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.154888 restraints weight = 24342.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.156746 restraints weight = 15616.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.155798 restraints weight = 11133.033| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4138 r_free = 0.4138 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4138 r_free = 0.4138 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2738 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 : 0.726 13.989 18146 Z= 0.343 Chirality : 0.043 0.278 2174 Planarity : 0.003 0.058 2372 Dihedral : 9.760 113.932 2438 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.12 % Favored : 96.77 % Rotamer: Outliers : 3.72 % Allowed : 32.06 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1891 helix: 2.05 (0.15), residues: 1191 sheet: -1.09 (0.41), residues: 162 loop : -1.96 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 482 HIS 0.007 0.001 HIS C 518 PHE 0.019 0.001 PHE D 595 TYR 0.013 0.001 TYR C 509 ARG 0.006 0.001 ARG E 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00722 ( 8) link_NAG-ASN : angle 3.21362 ( 24) link_ALPHA1-4 : bond 0.01264 ( 4) link_ALPHA1-4 : angle 3.22084 ( 12) link_ALPHA1-6 : bond 0.01479 ( 4) link_ALPHA1-6 : angle 2.17597 ( 12) link_BETA1-4 : bond 0.01370 ( 2) link_BETA1-4 : angle 7.22771 ( 6) link_ALPHA1-3 : bond 0.02210 ( 2) link_ALPHA1-3 : angle 4.12269 ( 6) hydrogen bonds : bond 0.02971 ( 898) hydrogen bonds : angle 3.61657 ( 2656) SS BOND : bond 0.00393 ( 9) SS BOND : angle 1.21632 ( 18) covalent geometry : bond 0.00296 (13218) covalent geometry : angle 0.69411 (18068) *********************** 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 268 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 473 TYR cc_start: 0.8247 (m-80) cc_final: 0.8001 (m-80) REVERT: E 127 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.7007 (m90) REVERT: C 224 ARG cc_start: 0.7044 (tpt90) cc_final: 0.6647 (tpt90) REVERT: C 459 TYR cc_start: 0.3206 (OUTLIER) cc_final: 0.2053 (m-80) REVERT: F 37 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7405 (mt) REVERT: F 44 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7573 (ttp80) REVERT: F 47 TRP cc_start: 0.6728 (OUTLIER) cc_final: 0.5999 (m100) REVERT: F 275 ARG cc_start: 0.8176 (mpp80) cc_final: 0.7847 (mpp80) REVERT: F 278 GLU cc_start: 0.8755 (pt0) cc_final: 0.8147 (pp20) REVERT: F 279 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8004 (mm-40) REVERT: A 39 SER cc_start: 0.7811 (t) cc_final: 0.7357 (p) outliers start: 34 outliers final: 22 residues processed: 256 average time/residue: 0.2160 time to fit residues: 83.7012 Evaluate side-chains 254 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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 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 604 ILE Chi-restraints excluded: chain C residue 659 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 B residue 21 HIS Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 130 optimal weight: 50.0000 chunk 94 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 113 optimal weight: 0.9980 chunk 147 optimal weight: 0.0070 chunk 131 optimal weight: 0.0670 chunk 115 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 674 HIS E 195 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.209371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.160035 restraints weight = 24166.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.158463 restraints weight = 13129.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.158727 restraints weight = 11795.541| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4167 r_free = 0.4167 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 = 0.4167 r_free = 0.4167 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2927 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= 0.131 Angle : 0.714 13.913 18146 Z= 0.338 Chirality : 0.042 0.282 2174 Planarity : 0.003 0.057 2372 Dihedral : 9.376 113.778 2438 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.45 % Rotamer: Outliers : 3.94 % Allowed : 31.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.20), residues: 1891 helix: 2.14 (0.15), residues: 1190 sheet: -0.96 (0.42), residues: 162 loop : -1.92 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 555 HIS 0.007 0.001 HIS E 130 PHE 0.019 0.001 PHE D 595 TYR 0.027 0.001 TYR B 47 ARG 0.005 0.001 ARG C 689 Details of bonding type rmsd link_NAG-ASN : bond 0.00640 ( 8) link_NAG-ASN : angle 3.03166 ( 24) link_ALPHA1-4 : bond 0.01233 ( 4) link_ALPHA1-4 : angle 3.13976 ( 12) link_ALPHA1-6 : bond 0.01561 ( 4) link_ALPHA1-6 : angle 2.13797 ( 12) link_BETA1-4 : bond 0.01344 ( 2) link_BETA1-4 : angle 7.13858 ( 6) link_ALPHA1-3 : bond 0.02168 ( 2) link_ALPHA1-3 : angle 4.20278 ( 6) hydrogen bonds : bond 0.02936 ( 898) hydrogen bonds : angle 3.56123 ( 2656) SS BOND : bond 0.00560 ( 9) SS BOND : angle 1.13797 ( 18) covalent geometry : bond 0.00280 (13218) covalent geometry : angle 0.68233 (18068) *********************** 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 272 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 473 TYR cc_start: 0.8021 (m-80) cc_final: 0.7757 (m-80) REVERT: D 663 SER cc_start: 0.8113 (t) cc_final: 0.7849 (p) REVERT: E 127 HIS cc_start: 0.7497 (OUTLIER) cc_final: 0.6583 (m90) REVERT: E 129 LYS cc_start: 0.7354 (pptt) cc_final: 0.7122 (pptt) REVERT: E 153 ASN cc_start: 0.7545 (t0) cc_final: 0.7333 (m-40) REVERT: E 250 ARG cc_start: 0.8344 (mpt-90) cc_final: 0.8087 (mtt90) REVERT: C 297 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8164 (mm) REVERT: C 459 TYR cc_start: 0.3371 (OUTLIER) cc_final: 0.2243 (m-80) REVERT: C 696 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6685 (pm20) REVERT: F 37 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7391 (mt) REVERT: F 44 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7614 (ttp80) REVERT: F 47 TRP cc_start: 0.6727 (OUTLIER) cc_final: 0.6092 (m100) REVERT: F 278 GLU cc_start: 0.8741 (pt0) cc_final: 0.8167 (pp20) REVERT: F 279 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8066 (mm-40) REVERT: A 39 SER cc_start: 0.7695 (t) cc_final: 0.7211 (p) outliers start: 36 outliers final: 22 residues processed: 260 average time/residue: 0.2133 time to fit residues: 84.0241 Evaluate side-chains 257 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 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 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 604 ILE 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 B residue 21 HIS 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 146 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 179 optimal weight: 40.0000 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 41 optimal weight: 0.0060 chunk 53 optimal weight: 5.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 540 HIS ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 GLN C 524 ASN C 674 HIS B 27 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.205761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.154788 restraints weight = 24159.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.158060 restraints weight = 15111.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.156398 restraints weight = 10329.619| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4130 r_free = 0.4130 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4130 r_free = 0.4130 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13247 Z= 0.149 Angle : 0.726 13.387 18146 Z= 0.347 Chirality : 0.043 0.283 2174 Planarity : 0.003 0.056 2372 Dihedral : 9.154 114.543 2438 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.56 % Rotamer: Outliers : 2.95 % Allowed : 33.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.20), residues: 1891 helix: 2.20 (0.15), residues: 1191 sheet: -1.02 (0.42), residues: 163 loop : -1.89 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 47 HIS 0.008 0.001 HIS E 130 PHE 0.018 0.001 PHE D 595 TYR 0.019 0.001 TYR B 47 ARG 0.006 0.001 ARG C 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 8) link_NAG-ASN : angle 3.04421 ( 24) link_ALPHA1-4 : bond 0.01170 ( 4) link_ALPHA1-4 : angle 3.11627 ( 12) link_ALPHA1-6 : bond 0.01591 ( 4) link_ALPHA1-6 : angle 2.09404 ( 12) link_BETA1-4 : bond 0.01337 ( 2) link_BETA1-4 : angle 7.05282 ( 6) link_ALPHA1-3 : bond 0.02122 ( 2) link_ALPHA1-3 : angle 4.16825 ( 6) hydrogen bonds : bond 0.02989 ( 898) hydrogen bonds : angle 3.57126 ( 2656) SS BOND : bond 0.00345 ( 9) SS BOND : angle 1.31048 ( 18) covalent geometry : bond 0.00329 (13218) covalent geometry : angle 0.69571 (18068) *********************** 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: 27 poor density : 234 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 250 ARG cc_start: 0.8404 (mpt-90) cc_final: 0.8167 (mtt90) REVERT: C 459 TYR cc_start: 0.3509 (OUTLIER) cc_final: 0.2465 (m-80) REVERT: C 673 MET cc_start: 0.8446 (tpp) cc_final: 0.8180 (tmm) REVERT: C 688 LYS cc_start: 0.8158 (pttp) cc_final: 0.7895 (pttp) REVERT: F 37 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7312 (mt) REVERT: F 44 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7601 (ttp80) REVERT: F 47 TRP cc_start: 0.6788 (OUTLIER) cc_final: 0.6185 (m100) REVERT: F 270 LYS cc_start: 0.6863 (pttm) cc_final: 0.6607 (pptt) REVERT: F 278 GLU cc_start: 0.8755 (pt0) cc_final: 0.8173 (pp20) REVERT: F 279 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8104 (mm-40) REVERT: A 39 SER cc_start: 0.7814 (t) cc_final: 0.7214 (p) outliers start: 27 outliers final: 20 residues processed: 250 average time/residue: 0.2112 time to fit residues: 79.8746 Evaluate side-chains 241 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 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 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 604 ILE 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 B residue 21 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 158 optimal weight: 50.0000 chunk 167 optimal weight: 40.0000 chunk 37 optimal weight: 1.9990 chunk 116 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 637 HIS ** D 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 ASN ** C 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.203847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.146772 restraints weight = 24164.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.150826 restraints weight = 12346.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.151548 restraints weight = 8762.490| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13247 Z= 0.185 Angle : 0.773 13.312 18146 Z= 0.374 Chirality : 0.044 0.272 2174 Planarity : 0.004 0.055 2372 Dihedral : 9.035 115.923 2438 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 3.39 % Allowed : 32.71 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.20), residues: 1891 helix: 2.21 (0.15), residues: 1196 sheet: -0.88 (0.42), residues: 167 loop : -1.80 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 302 HIS 0.006 0.001 HIS D 674 PHE 0.018 0.002 PHE D 474 TYR 0.022 0.001 TYR B 47 ARG 0.007 0.001 ARG C 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 8) link_NAG-ASN : angle 3.05961 ( 24) link_ALPHA1-4 : bond 0.01090 ( 4) link_ALPHA1-4 : angle 3.05128 ( 12) link_ALPHA1-6 : bond 0.01536 ( 4) link_ALPHA1-6 : angle 2.03986 ( 12) link_BETA1-4 : bond 0.01358 ( 2) link_BETA1-4 : angle 6.90965 ( 6) link_ALPHA1-3 : bond 0.01909 ( 2) link_ALPHA1-3 : angle 4.01358 ( 6) hydrogen bonds : bond 0.03295 ( 898) hydrogen bonds : angle 3.64395 ( 2656) SS BOND : bond 0.00415 ( 9) SS BOND : angle 1.67481 ( 18) covalent geometry : bond 0.00414 (13218) covalent geometry : angle 0.74485 (18068) *********************** 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 256 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 476 LYS cc_start: 0.8975 (pttt) cc_final: 0.8766 (pttp) REVERT: E 127 HIS cc_start: 0.7442 (OUTLIER) cc_final: 0.6887 (m90) REVERT: E 250 ARG cc_start: 0.8369 (mpt-90) cc_final: 0.8042 (mpt90) REVERT: C 459 TYR cc_start: 0.3426 (OUTLIER) cc_final: 0.2515 (m-80) REVERT: C 696 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6713 (pm20) REVERT: F 44 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7693 (ttp80) REVERT: F 47 TRP cc_start: 0.7000 (OUTLIER) cc_final: 0.6504 (m100) REVERT: F 270 LYS cc_start: 0.7312 (pttm) cc_final: 0.7042 (pptt) REVERT: F 278 GLU cc_start: 0.8721 (pt0) cc_final: 0.8170 (pp20) REVERT: F 279 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8057 (mm-40) REVERT: A 39 SER cc_start: 0.7744 (t) cc_final: 0.7158 (p) outliers start: 31 outliers final: 22 residues processed: 246 average time/residue: 0.2012 time to fit residues: 76.4844 Evaluate side-chains 244 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 604 ILE 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 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 604 ILE Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 696 GLU 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 B residue 21 HIS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 11 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 122 optimal weight: 90.0000 chunk 37 optimal weight: 0.9980 chunk 125 optimal weight: 0.0980 chunk 88 optimal weight: 8.9990 chunk 124 optimal weight: 0.5980 chunk 48 optimal weight: 50.0000 chunk 149 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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** B 27 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.205467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.147671 restraints weight = 24038.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.151950 restraints weight = 11478.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.154587 restraints weight = 7488.410| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3489 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= 0.133 Angle : 0.747 14.398 18146 Z= 0.358 Chirality : 0.043 0.267 2174 Planarity : 0.003 0.055 2372 Dihedral : 8.829 113.860 2438 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.44 % Favored : 96.45 % Rotamer: Outliers : 2.63 % Allowed : 33.92 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.20), residues: 1891 helix: 2.33 (0.15), residues: 1194 sheet: -0.87 (0.42), residues: 163 loop : -1.78 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 121 HIS 0.007 0.001 HIS E 130 PHE 0.017 0.001 PHE C 522 TYR 0.022 0.001 TYR B 47 ARG 0.004 0.000 ARG C 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 8) link_NAG-ASN : angle 3.01572 ( 24) link_ALPHA1-4 : bond 0.01147 ( 4) link_ALPHA1-4 : angle 3.04898 ( 12) link_ALPHA1-6 : bond 0.01534 ( 4) link_ALPHA1-6 : angle 1.95563 ( 12) link_BETA1-4 : bond 0.01385 ( 2) link_BETA1-4 : angle 6.88292 ( 6) link_ALPHA1-3 : bond 0.02127 ( 2) link_ALPHA1-3 : angle 4.13012 ( 6) hydrogen bonds : bond 0.02966 ( 898) hydrogen bonds : angle 3.55146 ( 2656) SS BOND : bond 0.00419 ( 9) SS BOND : angle 1.28132 ( 18) covalent geometry : bond 0.00288 (13218) covalent geometry : angle 0.71823 (18068) ********************** 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 251 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 663 SER cc_start: 0.8310 (t) cc_final: 0.7965 (p) REVERT: D 693 MET cc_start: 0.6754 (ptt) cc_final: 0.6526 (ptt) REVERT: E 127 HIS cc_start: 0.7009 (OUTLIER) cc_final: 0.6441 (m90) REVERT: C 459 TYR cc_start: 0.3318 (OUTLIER) cc_final: 0.2318 (m-80) REVERT: C 557 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7933 (mm-30) REVERT: C 667 MET cc_start: 0.8131 (mmm) cc_final: 0.7674 (mmt) REVERT: C 696 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6794 (pm20) REVERT: F 44 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7641 (ttp80) REVERT: F 47 TRP cc_start: 0.7050 (OUTLIER) cc_final: 0.6592 (m100) REVERT: F 76 LYS cc_start: 0.7576 (tppt) cc_final: 0.7126 (ttmt) REVERT: F 270 LYS cc_start: 0.7197 (pttm) cc_final: 0.6921 (pptt) REVERT: F 275 ARG cc_start: 0.7089 (ptp-110) cc_final: 0.6675 (ptp-110) REVERT: F 278 GLU cc_start: 0.8518 (pt0) cc_final: 0.8129 (pp20) REVERT: A 39 SER cc_start: 0.7681 (t) cc_final: 0.7124 (p) outliers start: 24 outliers final: 17 residues processed: 244 average time/residue: 0.2060 time to fit residues: 76.4079 Evaluate side-chains 244 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 604 ILE 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 535 VAL Chi-restraints excluded: chain C residue 555 TRP Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 696 GLU 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 B residue 21 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 32 optimal weight: 0.6980 chunk 158 optimal weight: 0.0870 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 160 optimal weight: 70.0000 chunk 120 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- 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** 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 = 0.206571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.154675 restraints weight = 24628.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.157130 restraints weight = 14206.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.156109 restraints weight = 9207.810| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4038 r_free = 0.4038 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4038 r_free = 0.4038 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13247 Z= 0.158 Angle : 0.754 13.838 18146 Z= 0.364 Chirality : 0.044 0.274 2174 Planarity : 0.003 0.055 2372 Dihedral : 8.765 113.981 2438 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.55 % Favored : 96.29 % Rotamer: Outliers : 2.74 % Allowed : 33.81 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.20), residues: 1891 helix: 2.33 (0.15), residues: 1200 sheet: -0.78 (0.42), residues: 167 loop : -1.71 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 47 HIS 0.006 0.001 HIS E 130 PHE 0.018 0.001 PHE D 595 TYR 0.025 0.001 TYR D 523 ARG 0.006 0.001 ARG C 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 8) link_NAG-ASN : angle 2.98881 ( 24) link_ALPHA1-4 : bond 0.01077 ( 4) link_ALPHA1-4 : angle 2.99946 ( 12) link_ALPHA1-6 : bond 0.01511 ( 4) link_ALPHA1-6 : angle 1.94080 ( 12) link_BETA1-4 : bond 0.01360 ( 2) link_BETA1-4 : angle 6.82238 ( 6) link_ALPHA1-3 : bond 0.02080 ( 2) link_ALPHA1-3 : angle 4.07256 ( 6) hydrogen bonds : bond 0.03087 ( 898) hydrogen bonds : angle 3.57272 ( 2656) SS BOND : bond 0.00364 ( 9) SS BOND : angle 1.33926 ( 18) covalent geometry : bond 0.00350 (13218) covalent geometry : angle 0.72635 (18068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5396.51 seconds wall clock time: 94 minutes 23.60 seconds (5663.60 seconds total)