Starting phenix.real_space_refine on Thu Jul 31 01:18:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kev_37168/07_2025/8kev_37168.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kev_37168/07_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_37168/07_2025/8kev_37168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kev_37168/07_2025/8kev_37168.map" model { file = "/net/cci-nas-00/data/ceres_data/8kev_37168/07_2025/8kev_37168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kev_37168/07_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 11.35, per 1000 atoms: 0.87 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: 3.50 Conformation dependent library (CDL) restraints added in 2.6 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: 1.40 Creating SS restraints... Processing helix chain 'D' and resid 175 through 197 removed outlier: 3.759A pdb=" N THR D 189 " --> pdb=" O MET D 185 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY D 190 " --> pdb=" O MET D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 216 removed outlier: 4.086A pdb=" N MET D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 230 removed outlier: 4.039A pdb=" N ALA D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 253 removed outlier: 3.502A pdb=" N ALA D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS D 248 " --> pdb=" O GLU D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 268 Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 291 through 303 Processing helix chain 'D' and resid 311 through 333 removed outlier: 4.265A pdb=" N VAL D 321 " --> pdb=" O HIS D 317 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N HIS D 324 " --> pdb=" O LEU D 320 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU D 331 " --> pdb=" O SER D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'D' and resid 460 through 481 removed outlier: 3.527A pdb=" N GLN D 464 " --> pdb=" O GLY D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 532 removed outlier: 3.712A pdb=" N GLY D 532 " --> pdb=" O MET D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 552 Processing helix chain 'D' and resid 556 through 565 removed outlier: 3.976A pdb=" N MET D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 570 removed outlier: 3.666A pdb=" N GLY D 569 " --> pdb=" O TYR D 566 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP D 570 " --> pdb=" O LYS D 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 566 through 570' Processing helix chain 'D' and resid 575 through 585 removed outlier: 4.005A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 599 Processing helix chain 'D' and resid 606 through 610 removed outlier: 3.978A pdb=" N THR D 610 " --> pdb=" O GLU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 623 removed outlier: 4.129A pdb=" N HIS D 617 " --> pdb=" O ARG D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 640 removed outlier: 3.597A pdb=" N ARG D 630 " --> pdb=" O TYR D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 662 removed outlier: 3.665A pdb=" N ILE D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 676 removed outlier: 3.578A pdb=" N LYS D 676 " --> pdb=" O TYR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 698 removed outlier: 3.782A pdb=" N SER D 698 " --> pdb=" O ALA D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 723 Processing helix chain 'E' and resid 104 through 110 Processing helix chain 'E' and resid 155 through 169 removed outlier: 3.550A pdb=" N LEU E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU E 160 " --> pdb=" O ALA E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 203 removed outlier: 3.742A pdb=" N GLN E 203 " --> pdb=" O SER E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 200 through 203' Processing helix chain 'E' and resid 242 through 246 Processing helix chain 'E' and resid 271 through 285 removed outlier: 3.903A pdb=" N GLN E 279 " --> pdb=" O ARG E 275 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 197 removed outlier: 3.547A pdb=" N GLU C 184 " --> pdb=" O MET C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 214 Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 218 through 230 removed outlier: 3.753A pdb=" N ALA C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 253 removed outlier: 4.190A pdb=" N LYS C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 267 removed outlier: 3.863A pdb=" N THR C 259 " --> pdb=" O PRO C 255 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 291 through 303 Processing helix chain 'C' and resid 311 through 333 removed outlier: 3.575A pdb=" N VAL C 321 " --> pdb=" O HIS C 317 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N HIS C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 331 " --> pdb=" O SER C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 483 removed outlier: 3.618A pdb=" N GLN C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 531 removed outlier: 3.642A pdb=" N SER C 531 " --> pdb=" O GLN C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 541 removed outlier: 3.658A pdb=" N THR C 541 " --> pdb=" O SER C 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 538 through 541' Processing helix chain 'C' and resid 542 through 551 Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.597A pdb=" N SER C 565 " --> pdb=" O THR C 561 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 568 " --> pdb=" O ASN C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 585 removed outlier: 3.734A pdb=" N ALA C 574 " --> pdb=" O ASP C 570 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL C 575 " --> pdb=" O TYR C 571 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 579 " --> pdb=" O VAL C 575 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 580 " --> pdb=" O ILE C 576 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 599 removed outlier: 3.568A pdb=" N GLN C 590 " --> pdb=" O TYR C 586 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN C 599 " --> pdb=" O PHE C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 624 removed outlier: 3.850A pdb=" N ARG C 613 " --> pdb=" O GLU C 609 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN C 624 " --> pdb=" O ARG C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 639 removed outlier: 3.997A pdb=" N ARG C 630 " --> pdb=" O TYR C 626 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 631 " --> pdb=" O THR C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 662 removed outlier: 3.717A pdb=" N ALA C 650 " --> pdb=" O ASP C 646 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN C 660 " --> pdb=" O LEU C 656 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 676 Processing helix chain 'C' and resid 684 through 698 removed outlier: 4.066A pdb=" N SER C 698 " --> pdb=" O ALA C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 723 removed outlier: 3.728A pdb=" N VAL C 705 " --> pdb=" O ALA C 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 111 removed outlier: 3.522A pdb=" N LYS F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 169 Processing helix chain 'F' and resid 242 through 250 removed outlier: 3.701A pdb=" N SER F 245 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS F 246 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Proline residue: F 247 - end of helix Processing helix chain 'F' and resid 272 through 284 removed outlier: 4.331A pdb=" N GLN F 276 " --> pdb=" O LEU F 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 26 removed outlier: 3.632A pdb=" N LEU A 25 " --> pdb=" O HIS A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 39 through 65 removed outlier: 3.598A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 96 removed outlier: 3.804A pdb=" N ARG A 80 " --> pdb=" O HIS A 76 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 86 " --> pdb=" O TRP A 82 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 128 removed outlier: 3.507A pdb=" N THR A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 165 removed outlier: 3.643A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY A 149 " --> pdb=" O MET A 145 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 162 " --> pdb=" O HIS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 201 removed outlier: 3.786A pdb=" N PHE A 174 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 197 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 232 removed outlier: 3.656A pdb=" N ALA A 209 " --> pdb=" O TRP A 205 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 245 through 266 removed outlier: 3.746A pdb=" N ALA A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 26 removed outlier: 3.538A pdb=" N ALA B 20 " --> pdb=" O GLY B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 removed outlier: 3.615A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 66 removed outlier: 4.000A pdb=" N VAL B 45 " --> pdb=" O PRO B 41 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR B 47 " --> pdb=" O MET B 43 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 95 removed outlier: 4.025A pdb=" N HIS B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B 86 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 93 " --> pdb=" O CYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 129 removed outlier: 3.571A pdb=" N PHE B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 166 removed outlier: 3.504A pdb=" N HIS B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 164 " --> pdb=" O TYR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 200 removed outlier: 4.383A pdb=" N VAL B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 188 " --> pdb=" O MET B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 237 removed outlier: 4.175A pdb=" N ALA B 209 " --> pdb=" O TRP B 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 266 removed outlier: 4.414A pdb=" N ASP B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 43 through 49 removed outlier: 6.152A pdb=" N ARG E 44 " --> pdb=" O ILE E 259 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N CYS E 261 " --> pdb=" O ARG E 44 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ASN E 46 " --> pdb=" O CYS E 261 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N SER E 263 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP E 258 " --> pdb=" O PRO E 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE E 260 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN E 65 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 122 through 126 removed outlier: 6.155A pdb=" N ILE E 131 " --> pdb=" O LEU E 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 136 through 138 Processing sheet with id=AA4, first strand: chain 'E' and resid 178 through 181 removed outlier: 3.640A pdb=" N THR E 186 " --> pdb=" O LYS E 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 189 through 193 removed outlier: 3.521A pdb=" N THR E 240 " --> pdb=" O ILE E 214 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N GLU E 233 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL E 229 " --> pdb=" O GLU E 233 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 198 through 199 removed outlier: 3.578A pdb=" N ARG E 205 " --> pdb=" O CYS E 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 43 through 46 removed outlier: 5.597A pdb=" N ARG F 44 " --> pdb=" O ILE F 259 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N CYS F 261 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASN F 46 " --> pdb=" O CYS F 261 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N SER F 263 " --> pdb=" O ASN F 46 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE F 260 " --> pdb=" O ILE F 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 122 through 125 removed outlier: 6.945A pdb=" N ILE F 131 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU F 151 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN F 133 " --> pdb=" O TYR F 149 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS F 135 " --> pdb=" O HIS F 147 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS F 147 " --> pdb=" O HIS F 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 178 through 181 Processing sheet with id=AB1, first strand: chain 'F' and resid 198 through 199 removed outlier: 3.683A pdb=" N ARG F 205 " --> pdb=" O CYS F 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 208 through 214 removed outlier: 3.655A pdb=" N TYR F 234 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR F 210 " --> pdb=" O TYR F 234 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 236 " --> pdb=" O THR F 210 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL F 237 " --> pdb=" O SER F 225 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER F 225 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU F 239 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE F 223 " --> pdb=" O LEU F 239 " (cutoff:3.500A) 898 hydrogen bonds defined for protein. 2656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 4.09 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: 1.610 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 36.410 Find NCS groups from input model: 0.650 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.600 ------------------------------------------------------------------------------- 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 : 1.521 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: 0.2325 time to fit residues: 90.7871 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 : 1.403 ------------------------------------------------------------------------------- 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 = 0.156797 restraints weight = 15187.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.156148 restraints weight = 8855.746| |-----------------------------------------------------------------------------| 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 : 1.488 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: 0.8162 (OUTLIER) cc_final: 0.7271 (m90) REVERT: C 224 ARG cc_start: 0.7079 (tpt90) cc_final: 0.6871 (tpt90) REVERT: C 667 MET cc_start: 0.8421 (mmm) cc_final: 0.7837 (mmt) REVERT: F 37 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7275 (mt) REVERT: F 47 TRP cc_start: 0.6684 (OUTLIER) cc_final: 0.5903 (m100) REVERT: F 270 LYS cc_start: 0.7508 (pptt) cc_final: 0.7195 (pptt) REVERT: F 277 LEU cc_start: 0.8749 (tp) cc_final: 0.8017 (tp) REVERT: F 281 GLU cc_start: 0.6654 (pm20) cc_final: 0.6277 (pm20) outliers start: 37 outliers final: 15 residues processed: 270 average time/residue: 0.2386 time to fit residues: 97.7061 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 : 1.381 ------------------------------------------------------------------------------- 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: 0.8980 chunk 149 optimal weight: 7.9990 chunk 121 optimal weight: 50.0000 chunk 51 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 165 optimal weight: 9.9990 chunk 170 optimal weight: 50.0000 chunk 103 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4747 r_free = 0.4747 target = 0.207968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.157897 restraints weight = 24327.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.154643 restraints weight = 14774.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.155658 restraints weight = 9942.528| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4133 r_free = 0.4133 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13247 Z= 0.154 Angle : 0.741 12.656 18146 Z= 0.354 Chirality : 0.044 0.263 2174 Planarity : 0.004 0.072 2372 Dihedral : 11.388 116.999 2440 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.44 % Favored : 96.45 % Rotamer: Outliers : 4.05 % Allowed : 30.09 % Favored : 65.86 % 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: 0.03 (0.19), residues: 1891 helix: 1.06 (0.15), residues: 1195 sheet: -1.03 (0.40), residues: 167 loop : -2.02 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 482 HIS 0.005 0.001 HIS E 130 PHE 0.018 0.001 PHE D 595 TYR 0.025 0.001 TYR D 654 ARG 0.011 0.001 ARG C 689 Details of bonding type rmsd link_NAG-ASN : bond 0.00742 ( 8) link_NAG-ASN : angle 3.58299 ( 24) link_ALPHA1-4 : bond 0.01331 ( 4) link_ALPHA1-4 : angle 3.60312 ( 12) link_ALPHA1-6 : bond 0.01398 ( 4) link_ALPHA1-6 : angle 1.99262 ( 12) link_BETA1-4 : bond 0.01442 ( 2) link_BETA1-4 : angle 7.76484 ( 6) link_ALPHA1-3 : bond 0.02385 ( 2) link_ALPHA1-3 : angle 3.61448 ( 6) hydrogen bonds : bond 0.03683 ( 898) hydrogen bonds : angle 4.03896 ( 2656) SS BOND : bond 0.00376 ( 9) SS BOND : angle 1.44700 ( 18) covalent geometry : bond 0.00335 (13218) covalent geometry : angle 0.70480 (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 276 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 1.572 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: 0.7685 (mmm) cc_final: 0.7466 (mmm) REVERT: D 667 MET cc_start: 0.8052 (mtm) cc_final: 0.7742 (mtt) REVERT: E 127 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.6990 (m90) REVERT: E 279 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8524 (mm-40) REVERT: C 505 GLN cc_start: 0.8927 (tt0) cc_final: 0.8695 (tt0) REVERT: C 549 VAL cc_start: 0.8488 (t) cc_final: 0.8204 (t) REVERT: F 37 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7325 (mt) REVERT: F 44 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7768 (ttp80) REVERT: F 47 TRP cc_start: 0.6791 (OUTLIER) cc_final: 0.6107 (m100) REVERT: F 270 LYS cc_start: 0.7324 (pptt) cc_final: 0.7075 (pptt) REVERT: A 39 SER cc_start: 0.7812 (t) cc_final: 0.7270 (p) outliers start: 37 outliers final: 23 residues processed: 262 average time/residue: 0.2223 time to fit residues: 87.4717 Evaluate side-chains 253 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 46 optimal weight: 0.0000 chunk 88 optimal weight: 10.0000 chunk 58 optimal weight: 0.0010 chunk 112 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 chunk 160 optimal weight: 60.0000 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 ASN ** C 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.208360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.160897 restraints weight = 24066.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.158195 restraints weight = 13642.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.158319 restraints weight = 9769.241| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4157 r_free = 0.4157 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 = 0.4157 r_free = 0.4157 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13247 Z= 0.139 Angle : 0.719 12.862 18146 Z= 0.341 Chirality : 0.043 0.264 2174 Planarity : 0.004 0.065 2372 Dihedral : 10.649 116.228 2440 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.56 % Rotamer: Outliers : 4.16 % Allowed : 30.63 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.20), residues: 1891 helix: 1.59 (0.15), residues: 1193 sheet: -1.10 (0.40), residues: 166 loop : -1.96 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 482 HIS 0.005 0.001 HIS E 130 PHE 0.019 0.001 PHE D 595 TYR 0.021 0.001 TYR D 672 ARG 0.007 0.001 ARG C 689 Details of bonding type rmsd link_NAG-ASN : bond 0.00707 ( 8) link_NAG-ASN : angle 3.38016 ( 24) link_ALPHA1-4 : bond 0.01411 ( 4) link_ALPHA1-4 : angle 3.27174 ( 12) link_ALPHA1-6 : bond 0.01396 ( 4) link_ALPHA1-6 : angle 2.06211 ( 12) link_BETA1-4 : bond 0.01431 ( 2) link_BETA1-4 : angle 7.47457 ( 6) link_ALPHA1-3 : bond 0.02050 ( 2) link_ALPHA1-3 : angle 3.88412 ( 6) hydrogen bonds : bond 0.03199 ( 898) hydrogen bonds : angle 3.79677 ( 2656) SS BOND : bond 0.00456 ( 9) SS BOND : angle 1.30443 ( 18) covalent geometry : bond 0.00301 (13218) covalent geometry : angle 0.68477 (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 277 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 1.505 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: 0.7717 (mmm) cc_final: 0.7501 (mmm) REVERT: D 667 MET cc_start: 0.8073 (mtm) cc_final: 0.7643 (mtt) REVERT: E 69 MET cc_start: 0.8201 (tpp) cc_final: 0.7943 (mmm) REVERT: E 127 HIS cc_start: 0.7919 (OUTLIER) cc_final: 0.7059 (m90) REVERT: C 297 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8217 (mm) REVERT: C 549 VAL cc_start: 0.8444 (t) cc_final: 0.8225 (t) REVERT: C 667 MET cc_start: 0.8209 (mmm) cc_final: 0.7732 (mmt) REVERT: F 37 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7325 (mt) REVERT: F 44 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7565 (ttp80) REVERT: F 47 TRP cc_start: 0.6831 (OUTLIER) cc_final: 0.6088 (m100) REVERT: A 39 SER cc_start: 0.7781 (t) cc_final: 0.7281 (p) outliers start: 38 outliers final: 21 residues processed: 264 average time/residue: 0.2196 time to fit residues: 87.5873 Evaluate side-chains 254 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 94 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 143 optimal weight: 40.0000 chunk 79 optimal weight: 0.5980 chunk 181 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4757 r_free = 0.4757 target = 0.210057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.161066 restraints weight = 24185.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.158713 restraints weight = 13444.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.159760 restraints weight = 9986.600| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4185 r_free = 0.4185 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 = 0.4185 r_free = 0.4185 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2531 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= 0.127 Angle : 0.714 13.585 18146 Z= 0.337 Chirality : 0.043 0.259 2174 Planarity : 0.003 0.061 2372 Dihedral : 10.099 113.553 2438 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 3.28 % Allowed : 30.74 % Favored : 65.97 % 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: 0.86 (0.20), residues: 1891 helix: 1.90 (0.15), residues: 1184 sheet: -1.11 (0.41), residues: 166 loop : -1.96 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 482 HIS 0.007 0.001 HIS C 518 PHE 0.020 0.001 PHE D 595 TYR 0.023 0.001 TYR B 47 ARG 0.012 0.001 ARG E 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00673 ( 8) link_NAG-ASN : angle 3.26876 ( 24) link_ALPHA1-4 : bond 0.01293 ( 4) link_ALPHA1-4 : angle 3.32617 ( 12) link_ALPHA1-6 : bond 0.01551 ( 4) link_ALPHA1-6 : angle 2.13889 ( 12) link_BETA1-4 : bond 0.01388 ( 2) link_BETA1-4 : angle 7.34096 ( 6) link_ALPHA1-3 : bond 0.02125 ( 2) link_ALPHA1-3 : angle 4.10602 ( 6) hydrogen bonds : bond 0.02986 ( 898) hydrogen bonds : angle 3.65700 ( 2656) SS BOND : bond 0.00315 ( 9) SS BOND : angle 1.10434 ( 18) covalent geometry : bond 0.00268 (13218) covalent geometry : angle 0.67995 (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 272 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 242 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 473 TYR cc_start: 0.8190 (m-80) cc_final: 0.7936 (m-80) REVERT: D 501 ARG cc_start: 0.7856 (ptp90) cc_final: 0.7635 (mpp-170) REVERT: E 127 HIS cc_start: 0.7708 (OUTLIER) cc_final: 0.6967 (m90) REVERT: C 297 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8177 (mm) REVERT: C 688 LYS cc_start: 0.7779 (pttp) cc_final: 0.7484 (pttp) REVERT: F 37 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7440 (mt) REVERT: F 44 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7568 (ttp80) REVERT: F 47 TRP cc_start: 0.6726 (OUTLIER) cc_final: 0.6072 (m100) REVERT: F 270 LYS cc_start: 0.7842 (pttm) cc_final: 0.7541 (pttm) REVERT: F 278 GLU cc_start: 0.8604 (pt0) cc_final: 0.8074 (pp20) REVERT: F 279 GLN cc_start: 0.8547 (mm-40) cc_final: 0.7869 (mm-40) REVERT: A 39 SER cc_start: 0.7774 (t) cc_final: 0.7312 (p) outliers start: 30 outliers final: 20 residues processed: 261 average time/residue: 0.2544 time to fit residues: 99.8741 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 : 1.360 ------------------------------------------------------------------------------- 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 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 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 F residue 37 LEU Chi-restraints excluded: chain F residue 47 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 137 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 GLN 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 = 0.4735 r_free = 0.4735 target = 0.206013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.150811 restraints weight = 24251.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.156773 restraints weight = 12368.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.156201 restraints weight = 7132.169| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4114 r_free = 0.4114 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4114 r_free = 0.4114 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13247 Z= 0.154 Angle : 0.724 13.025 18146 Z= 0.345 Chirality : 0.043 0.283 2174 Planarity : 0.004 0.059 2372 Dihedral : 9.759 114.763 2438 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.76 % Favored : 96.14 % Rotamer: Outliers : 4.05 % Allowed : 31.18 % Favored : 64.77 % 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: 1.00 (0.20), residues: 1891 helix: 2.02 (0.15), residues: 1188 sheet: -1.06 (0.41), residues: 162 loop : -1.97 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 555 HIS 0.007 0.001 HIS C 518 PHE 0.018 0.001 PHE D 595 TYR 0.018 0.001 TYR B 47 ARG 0.006 0.001 ARG F 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00706 ( 8) link_NAG-ASN : angle 3.15825 ( 24) link_ALPHA1-4 : bond 0.01245 ( 4) link_ALPHA1-4 : angle 3.18756 ( 12) link_ALPHA1-6 : bond 0.01449 ( 4) link_ALPHA1-6 : angle 2.24632 ( 12) link_BETA1-4 : bond 0.01339 ( 2) link_BETA1-4 : angle 7.20191 ( 6) link_ALPHA1-3 : bond 0.02040 ( 2) link_ALPHA1-3 : angle 4.07481 ( 6) hydrogen bonds : bond 0.03093 ( 898) hydrogen bonds : angle 3.66217 ( 2656) SS BOND : bond 0.00401 ( 9) SS BOND : angle 1.36841 ( 18) covalent geometry : bond 0.00339 (13218) covalent geometry : angle 0.69218 (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 272 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 663 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.7830 (p) REVERT: D 667 MET cc_start: 0.8036 (mtm) cc_final: 0.7585 (mtt) REVERT: E 127 HIS cc_start: 0.7750 (OUTLIER) cc_final: 0.6984 (m90) REVERT: C 459 TYR cc_start: 0.3302 (OUTLIER) cc_final: 0.2234 (m-80) REVERT: C 667 MET cc_start: 0.8364 (mmm) cc_final: 0.7744 (mmt) REVERT: F 37 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7441 (mt) REVERT: F 44 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7588 (ttp80) REVERT: F 47 TRP cc_start: 0.6810 (OUTLIER) cc_final: 0.6150 (m100) REVERT: F 113 CYS cc_start: 0.5442 (OUTLIER) cc_final: 0.5241 (p) REVERT: F 278 GLU cc_start: 0.8688 (pt0) cc_final: 0.8212 (pp20) REVERT: F 279 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8131 (mm-40) REVERT: A 39 SER cc_start: 0.7824 (t) cc_final: 0.7326 (p) outliers start: 37 outliers final: 20 residues processed: 260 average time/residue: 0.2145 time to fit residues: 85.0590 Evaluate side-chains 250 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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 459 TYR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 555 TRP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 47 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 113 CYS Chi-restraints excluded: chain B residue 21 HIS 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: 1.9990 chunk 54 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 115 optimal weight: 0.0570 chunk 151 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- 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** B 27 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.207335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.153695 restraints weight = 24024.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.150800 restraints weight = 13323.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.153026 restraints weight = 10215.924| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4121 r_free = 0.4121 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4121 r_free = 0.4121 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13247 Z= 0.169 Angle : 0.733 13.071 18146 Z= 0.351 Chirality : 0.043 0.284 2174 Planarity : 0.003 0.058 2372 Dihedral : 9.580 115.274 2438 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.60 % Favored : 96.29 % Rotamer: Outliers : 3.50 % Allowed : 32.17 % 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: 1.12 (0.20), residues: 1891 helix: 2.10 (0.15), residues: 1190 sheet: -1.00 (0.41), residues: 167 loop : -1.91 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 555 HIS 0.007 0.001 HIS E 130 PHE 0.018 0.001 PHE D 595 TYR 0.020 0.001 TYR B 47 ARG 0.006 0.001 ARG F 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 8) link_NAG-ASN : angle 3.16258 ( 24) link_ALPHA1-4 : bond 0.01211 ( 4) link_ALPHA1-4 : angle 3.14870 ( 12) link_ALPHA1-6 : bond 0.01487 ( 4) link_ALPHA1-6 : angle 2.18774 ( 12) link_BETA1-4 : bond 0.01330 ( 2) link_BETA1-4 : angle 7.11375 ( 6) link_ALPHA1-3 : bond 0.01956 ( 2) link_ALPHA1-3 : angle 4.07686 ( 6) hydrogen bonds : bond 0.03123 ( 898) hydrogen bonds : angle 3.62909 ( 2656) SS BOND : bond 0.00430 ( 9) SS BOND : angle 1.30989 ( 18) covalent geometry : bond 0.00377 (13218) covalent geometry : angle 0.70230 (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 260 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 HIS cc_start: 0.7543 (OUTLIER) cc_final: 0.6618 (m90) REVERT: C 459 TYR cc_start: 0.3580 (OUTLIER) cc_final: 0.2462 (m-80) REVERT: C 667 MET cc_start: 0.8275 (mmm) cc_final: 0.7747 (mmt) REVERT: C 673 MET cc_start: 0.8486 (tpp) cc_final: 0.8024 (tmm) REVERT: F 37 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7319 (mt) REVERT: F 44 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7701 (ttp80) REVERT: F 47 TRP cc_start: 0.6929 (OUTLIER) cc_final: 0.6354 (m100) REVERT: F 270 LYS cc_start: 0.7074 (pttm) cc_final: 0.6869 (pttm) REVERT: F 278 GLU cc_start: 0.8644 (pt0) cc_final: 0.8091 (pp20) REVERT: F 279 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8006 (mm-40) REVERT: A 39 SER cc_start: 0.7801 (t) cc_final: 0.7263 (p) outliers start: 32 outliers final: 22 residues processed: 248 average time/residue: 0.2002 time to fit residues: 76.4181 Evaluate side-chains 247 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 643 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 47 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 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: 0.9980 chunk 80 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 179 optimal weight: 50.0000 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 170 optimal weight: 20.0000 chunk 41 optimal weight: 0.4980 chunk 53 optimal weight: 10.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 505 GLN 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 = 0.4721 r_free = 0.4721 target = 0.204622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.153066 restraints weight = 24092.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.153293 restraints weight = 15669.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.154366 restraints weight = 10152.623| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4111 r_free = 0.4111 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4111 r_free = 0.4111 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13247 Z= 0.150 Angle : 0.730 13.999 18146 Z= 0.349 Chirality : 0.043 0.280 2174 Planarity : 0.003 0.057 2372 Dihedral : 9.358 115.068 2438 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.23 % Favored : 96.66 % Rotamer: Outliers : 3.50 % Allowed : 32.17 % 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: 1.21 (0.20), residues: 1891 helix: 2.19 (0.15), residues: 1188 sheet: -0.98 (0.41), residues: 168 loop : -1.88 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 555 HIS 0.007 0.001 HIS E 130 PHE 0.018 0.001 PHE D 595 TYR 0.020 0.001 TYR B 47 ARG 0.004 0.001 ARG C 689 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 8) link_NAG-ASN : angle 3.04570 ( 24) link_ALPHA1-4 : bond 0.01198 ( 4) link_ALPHA1-4 : angle 3.13748 ( 12) link_ALPHA1-6 : bond 0.01537 ( 4) link_ALPHA1-6 : angle 2.10803 ( 12) link_BETA1-4 : bond 0.01343 ( 2) link_BETA1-4 : angle 7.05091 ( 6) link_ALPHA1-3 : bond 0.02023 ( 2) link_ALPHA1-3 : angle 4.08167 ( 6) hydrogen bonds : bond 0.03038 ( 898) hydrogen bonds : angle 3.60858 ( 2656) SS BOND : bond 0.00396 ( 9) SS BOND : angle 1.39925 ( 18) covalent geometry : bond 0.00330 (13218) covalent geometry : angle 0.69931 (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 260 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 476 LYS cc_start: 0.8935 (pttt) cc_final: 0.8705 (pttp) REVERT: E 127 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.6613 (m90) REVERT: E 153 ASN cc_start: 0.7420 (t0) cc_final: 0.7170 (m-40) REVERT: C 459 TYR cc_start: 0.3416 (OUTLIER) cc_final: 0.2450 (m-80) REVERT: C 502 ASP cc_start: 0.8018 (p0) cc_final: 0.7602 (p0) REVERT: C 504 LYS cc_start: 0.8726 (mttp) cc_final: 0.8479 (mttp) REVERT: F 37 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7254 (mt) REVERT: F 44 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7574 (ttp80) REVERT: F 47 TRP cc_start: 0.7004 (OUTLIER) cc_final: 0.6491 (m100) REVERT: F 278 GLU cc_start: 0.8584 (pt0) cc_final: 0.7995 (pp20) REVERT: F 279 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7871 (mm-40) REVERT: A 39 SER cc_start: 0.7660 (t) cc_final: 0.7221 (p) REVERT: B 28 GLN cc_start: 0.6692 (OUTLIER) cc_final: 0.5703 (mm110) outliers start: 32 outliers final: 23 residues processed: 249 average time/residue: 0.2195 time to fit residues: 83.4256 Evaluate side-chains 244 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 1.628 ------------------------------------------------------------------------------- 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 643 THR Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 47 TRP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 46 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 158 optimal weight: 5.9990 chunk 167 optimal weight: 40.0000 chunk 37 optimal weight: 0.7980 chunk 116 optimal weight: 0.0060 chunk 75 optimal weight: 0.9980 chunk 120 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.206142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.154584 restraints weight = 24214.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.153505 restraints weight = 19150.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.154324 restraints weight = 12341.570| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4051 r_free = 0.4051 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4051 r_free = 0.4051 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13247 Z= 0.134 Angle : 0.744 14.421 18146 Z= 0.358 Chirality : 0.043 0.272 2174 Planarity : 0.003 0.056 2372 Dihedral : 9.171 118.042 2438 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.18 % Favored : 96.66 % Rotamer: Outliers : 2.84 % Allowed : 32.71 % Favored : 64.44 % 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: 2.27 (0.15), residues: 1187 sheet: -0.98 (0.42), residues: 162 loop : -1.85 (0.25), residues: 542 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 0.019 0.001 TYR B 47 ARG 0.005 0.001 ARG F 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 8) link_NAG-ASN : angle 2.99458 ( 24) link_ALPHA1-4 : bond 0.01190 ( 4) link_ALPHA1-4 : angle 3.11380 ( 12) link_ALPHA1-6 : bond 0.01640 ( 4) link_ALPHA1-6 : angle 2.04441 ( 12) link_BETA1-4 : bond 0.01366 ( 2) link_BETA1-4 : angle 7.00336 ( 6) link_ALPHA1-3 : bond 0.02073 ( 2) link_ALPHA1-3 : angle 3.88759 ( 6) hydrogen bonds : bond 0.02970 ( 898) hydrogen bonds : angle 3.55548 ( 2656) SS BOND : bond 0.00416 ( 9) SS BOND : angle 1.34071 ( 18) covalent geometry : bond 0.00287 (13218) covalent geometry : angle 0.71544 (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 255 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 663 SER cc_start: 0.8101 (OUTLIER) cc_final: 0.7881 (p) REVERT: E 127 HIS cc_start: 0.7479 (OUTLIER) cc_final: 0.6747 (m90) REVERT: E 153 ASN cc_start: 0.7842 (t0) cc_final: 0.7530 (m-40) REVERT: C 224 ARG cc_start: 0.7134 (tpt90) cc_final: 0.6764 (tpt90) REVERT: C 459 TYR cc_start: 0.3454 (OUTLIER) cc_final: 0.2502 (m-80) REVERT: C 504 LYS cc_start: 0.8728 (mttp) cc_final: 0.8466 (mttp) REVERT: C 557 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7704 (mm-30) REVERT: C 688 LYS cc_start: 0.7819 (pttp) cc_final: 0.7608 (pptt) REVERT: F 44 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7618 (ttp80) REVERT: F 47 TRP cc_start: 0.6882 (OUTLIER) cc_final: 0.6300 (m100) REVERT: F 275 ARG cc_start: 0.7805 (ptp-110) cc_final: 0.7209 (ptp-110) REVERT: F 278 GLU cc_start: 0.8615 (pt0) cc_final: 0.7997 (pp20) REVERT: F 279 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8138 (mm-40) REVERT: A 39 SER cc_start: 0.7798 (t) cc_final: 0.7224 (p) REVERT: B 28 GLN cc_start: 0.6579 (OUTLIER) cc_final: 0.5932 (mm110) outliers start: 26 outliers final: 19 residues processed: 246 average time/residue: 0.2125 time to fit residues: 80.6729 Evaluate side-chains 247 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 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 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 28 GLN Chi-restraints excluded: chain B residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 122 optimal weight: 80.0000 chunk 37 optimal weight: 0.7980 chunk 125 optimal weight: 50.0000 chunk 88 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.202467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.147159 restraints weight = 23855.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.149482 restraints weight = 17698.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.150545 restraints weight = 10146.154| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4022 r_free = 0.4022 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4022 r_free = 0.4022 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13247 Z= 0.201 Angle : 0.791 13.417 18146 Z= 0.383 Chirality : 0.045 0.281 2174 Planarity : 0.004 0.056 2372 Dihedral : 9.115 115.335 2438 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.71 % Favored : 96.19 % Rotamer: Outliers : 2.74 % Allowed : 32.49 % Favored : 64.77 % 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: 1.27 (0.20), residues: 1891 helix: 2.14 (0.15), residues: 1204 sheet: -0.89 (0.40), residues: 171 loop : -1.76 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 121 HIS 0.006 0.002 HIS E 130 PHE 0.020 0.002 PHE D 595 TYR 0.019 0.001 TYR B 47 ARG 0.007 0.001 ARG C 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 8) link_NAG-ASN : angle 3.04359 ( 24) link_ALPHA1-4 : bond 0.01046 ( 4) link_ALPHA1-4 : angle 3.03213 ( 12) link_ALPHA1-6 : bond 0.01507 ( 4) link_ALPHA1-6 : angle 2.03975 ( 12) link_BETA1-4 : bond 0.01329 ( 2) link_BETA1-4 : angle 6.87776 ( 6) link_ALPHA1-3 : bond 0.01950 ( 2) link_ALPHA1-3 : angle 3.91237 ( 6) hydrogen bonds : bond 0.03370 ( 898) hydrogen bonds : angle 3.68563 ( 2656) SS BOND : bond 0.00450 ( 9) SS BOND : angle 1.55152 ( 18) covalent geometry : bond 0.00449 (13218) covalent geometry : angle 0.76375 (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 253 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 667 MET cc_start: 0.8090 (mtm) cc_final: 0.7790 (mtt) REVERT: E 127 HIS cc_start: 0.7327 (OUTLIER) cc_final: 0.6778 (m90) REVERT: C 459 TYR cc_start: 0.3563 (OUTLIER) cc_final: 0.2669 (m-80) REVERT: C 504 LYS cc_start: 0.8776 (mttp) cc_final: 0.8522 (mttp) REVERT: C 667 MET cc_start: 0.8148 (mmm) cc_final: 0.7623 (mmt) REVERT: F 44 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7690 (ttp80) REVERT: F 47 TRP cc_start: 0.7132 (OUTLIER) cc_final: 0.6679 (m100) REVERT: F 62 LYS cc_start: 0.8002 (tptm) cc_final: 0.7769 (tptm) REVERT: F 275 ARG cc_start: 0.7796 (ptp-110) cc_final: 0.7092 (ptp-110) REVERT: F 278 GLU cc_start: 0.8634 (pt0) cc_final: 0.8070 (pp20) REVERT: F 279 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8258 (mm-40) REVERT: A 39 SER cc_start: 0.7867 (t) cc_final: 0.7228 (p) REVERT: B 28 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.6035 (mm110) outliers start: 25 outliers final: 20 residues processed: 246 average time/residue: 0.2368 time to fit residues: 92.5206 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 : 1.437 ------------------------------------------------------------------------------- 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 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 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 A residue 19 VAL Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 32 optimal weight: 0.0040 chunk 158 optimal weight: 0.1980 chunk 28 optimal weight: 0.0060 chunk 11 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 91 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 160 optimal weight: 70.0000 chunk 120 optimal weight: 8.9990 chunk 155 optimal weight: 30.0000 chunk 138 optimal weight: 2.9990 overall best weight: 0.2208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 258 GLN D 540 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.206512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.149345 restraints weight = 24174.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.153648 restraints weight = 11487.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.156319 restraints weight = 7505.395| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4148 r_free = 0.4148 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 = 0.4148 r_free = 0.4148 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13247 Z= 0.127 Angle : 0.750 15.039 18146 Z= 0.360 Chirality : 0.043 0.260 2174 Planarity : 0.003 0.056 2372 Dihedral : 8.839 113.337 2438 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.39 % Favored : 96.51 % Rotamer: Outliers : 2.63 % Allowed : 33.15 % 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: 1.46 (0.20), residues: 1891 helix: 2.35 (0.15), residues: 1195 sheet: -0.87 (0.42), residues: 167 loop : -1.76 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 618 HIS 0.008 0.001 HIS E 130 PHE 0.021 0.001 PHE C 522 TYR 0.018 0.001 TYR B 47 ARG 0.006 0.001 ARG F 275 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 8) link_NAG-ASN : angle 2.98220 ( 24) link_ALPHA1-4 : bond 0.01217 ( 4) link_ALPHA1-4 : angle 3.03444 ( 12) link_ALPHA1-6 : bond 0.01578 ( 4) link_ALPHA1-6 : angle 1.94580 ( 12) link_BETA1-4 : bond 0.01423 ( 2) link_BETA1-4 : angle 6.85619 ( 6) link_ALPHA1-3 : bond 0.02264 ( 2) link_ALPHA1-3 : angle 4.04801 ( 6) hydrogen bonds : bond 0.02933 ( 898) hydrogen bonds : angle 3.54592 ( 2656) SS BOND : bond 0.00344 ( 9) SS BOND : angle 1.17992 ( 18) covalent geometry : bond 0.00264 (13218) covalent geometry : angle 0.72203 (18068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5836.68 seconds wall clock time: 101 minutes 55.95 seconds (6115.95 seconds total)