Starting phenix.real_space_refine on Wed Jul 30 20:04:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uav_63996/07_2025/9uav_63996.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uav_63996/07_2025/9uav_63996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uav_63996/07_2025/9uav_63996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uav_63996/07_2025/9uav_63996.map" model { file = "/net/cci-nas-00/data/ceres_data/9uav_63996/07_2025/9uav_63996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uav_63996/07_2025/9uav_63996.cif" } resolution = 3.7 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= 0.002 sd= 0.061 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 8036 2.51 5 N 2272 2.21 5 O 2473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 12831 Number of models: 1 Model: "" Number of chains: 12 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: "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: "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: "E" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1745 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 19, 'TRANS': 212} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "F" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1407 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PTRANS': 19, 'TRANS': 211} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 501 Unresolved non-hydrogen angles: 641 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 7, 'TYR:plan': 10, 'ASN:plan1': 7, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 19, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 276 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: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} 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: "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 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 Time building chain proxies: 11.65, per 1000 atoms: 0.91 Number of scatterers: 12831 At special positions: 0 Unit cell: (132.68, 125.19, 164.78, 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 2473 8.00 N 2272 7.00 C 8036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS C 311 " - pdb=" SG CYS C 539 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 79 " - pdb=" SG CYS F 261 " distance=2.04 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 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3512 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 10 sheets defined 65.0% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 1 through 26 removed outlier: 3.578A 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 66 Processing helix chain 'A' and resid 73 through 96 Processing helix chain 'A' and resid 103 through 129 removed outlier: 3.759A pdb=" N ARG A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 167 removed outlier: 3.582A pdb=" N SER A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 201 removed outlier: 3.640A pdb=" N PHE A 174 " --> pdb=" O VAL A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 233 removed outlier: 3.657A pdb=" N ILE A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 266 removed outlier: 3.730A pdb=" N MET A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 30 through 39 removed outlier: 3.584A pdb=" N VAL B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 66 removed outlier: 4.664A pdb=" N VAL B 45 " --> pdb=" O PRO B 41 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR B 47 " --> pdb=" O MET B 43 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 95 removed outlier: 4.477A pdb=" N HIS B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 129 removed outlier: 4.064A pdb=" N ARG B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 166 removed outlier: 3.555A pdb=" N HIS B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 201 removed outlier: 3.568A pdb=" N PHE B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 237 removed outlier: 4.295A pdb=" N ALA B 209 " --> pdb=" O TRP B 205 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 266 removed outlier: 4.046A pdb=" N ASP B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 197 Processing helix chain 'C' and resid 199 through 215 Processing helix chain 'C' and resid 218 through 230 removed outlier: 3.918A pdb=" N ALA C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 253 removed outlier: 3.816A pdb=" N LYS C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 267 removed outlier: 3.921A pdb=" N ALA C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 267 " --> pdb=" O PHE C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 removed outlier: 3.777A pdb=" N ALA C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 303 Processing helix chain 'C' and resid 311 through 333 removed outlier: 3.584A pdb=" N VAL C 321 " --> pdb=" O HIS C 317 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 331 " --> pdb=" O SER C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 482 Processing helix chain 'C' and resid 496 through 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'C' and resid 499 through 531 removed outlier: 3.600A pdb=" N SER C 531 " --> pdb=" O GLN C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 553 Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.545A pdb=" N THR C 561 " --> pdb=" O GLU C 557 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 565 " --> pdb=" O THR C 561 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP C 568 " --> pdb=" O ASN C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 585 removed outlier: 3.721A pdb=" N ALA C 574 " --> pdb=" O ASP C 570 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL C 575 " --> pdb=" O TYR C 571 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 580 " --> pdb=" O ILE C 576 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 599 removed outlier: 3.609A pdb=" N GLN C 599 " --> pdb=" O PHE C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 624 Processing helix chain 'C' and resid 626 through 640 removed outlier: 3.879A pdb=" N ARG C 630 " --> pdb=" O TYR C 626 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 631 " --> pdb=" O THR C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 662 removed outlier: 3.540A pdb=" N ALA C 650 " --> pdb=" O ASP C 646 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 660 " --> pdb=" O LEU C 656 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 677 removed outlier: 3.615A pdb=" N MET C 667 " --> pdb=" O SER C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 698 removed outlier: 3.627A pdb=" N SER C 698 " --> pdb=" O ALA C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 723 removed outlier: 4.015A pdb=" N VAL C 705 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 706 " --> pdb=" O GLN C 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 197 Processing helix chain 'D' and resid 199 through 216 removed outlier: 3.851A pdb=" N MET D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 230 removed outlier: 4.477A pdb=" N ALA D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 253 removed outlier: 3.639A pdb=" N ALA D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS D 248 " --> pdb=" O GLU D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 removed outlier: 3.698A pdb=" N GLN D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR D 259 " --> pdb=" O PRO D 255 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 removed outlier: 3.643A pdb=" N GLY D 288 " --> pdb=" O PHE D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 303 Processing helix chain 'D' and resid 311 through 333 removed outlier: 4.418A pdb=" N VAL D 321 " --> pdb=" O HIS D 317 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS D 324 " --> pdb=" O LEU D 320 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 331 " --> pdb=" O SER D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 481 removed outlier: 3.775A pdb=" N GLN D 464 " --> pdb=" O GLY D 460 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY D 481 " --> pdb=" O ALA D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 532 removed outlier: 3.622A pdb=" N GLY D 532 " --> pdb=" O MET D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 552 removed outlier: 4.144A pdb=" N ARG D 552 " --> pdb=" O ASN D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 555 No H-bonds generated for 'chain 'D' and resid 553 through 555' Processing helix chain 'D' and resid 556 through 567 removed outlier: 4.173A pdb=" N MET D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER D 565 " --> pdb=" O THR D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 574 removed outlier: 6.927A pdb=" N TYR D 571 " --> pdb=" O ASP D 568 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN D 572 " --> pdb=" O GLY D 569 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA D 573 " --> pdb=" O ASP D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 585 removed outlier: 3.860A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 599 removed outlier: 3.809A pdb=" N GLN D 599 " --> pdb=" O PHE D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 624 removed outlier: 4.380A pdb=" N HIS D 617 " --> pdb=" O ARG D 613 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN D 624 " --> pdb=" O ARG D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 640 Processing helix chain 'D' and resid 646 through 660 Processing helix chain 'D' and resid 663 through 676 Processing helix chain 'D' and resid 685 through 698 removed outlier: 3.658A 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 99 through 111 removed outlier: 3.941A pdb=" N LEU E 103 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 104 " --> pdb=" O PRO E 100 " (cutoff:3.500A) Proline residue: E 106 - end of helix removed outlier: 4.159A pdb=" N SER E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.764A pdb=" N GLN E 203 " --> pdb=" O SER E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 246 removed outlier: 3.515A pdb=" N HIS E 246 " --> pdb=" O LEU E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 285 removed outlier: 3.760A pdb=" N GLN E 279 " --> pdb=" O ARG E 275 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 111 Processing helix chain 'F' and resid 242 through 246 removed outlier: 3.556A pdb=" N SER F 245 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS F 246 " --> pdb=" O LEU F 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 242 through 246' Processing helix chain 'F' and resid 272 through 284 removed outlier: 4.492A pdb=" N GLN F 276 " --> pdb=" O LEU F 272 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 43 through 49 removed outlier: 4.572A pdb=" N PHE E 43 " --> pdb=" O ASN E 257 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE E 259 " --> pdb=" O PHE E 43 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL E 45 " --> pdb=" O ILE E 259 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N CYS E 261 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N TRP E 47 " --> pdb=" O CYS E 261 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER E 263 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY E 49 " --> pdb=" O SER E 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 122 through 126 removed outlier: 3.810A pdb=" N TYR E 134 " --> pdb=" O THR E 122 " (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 Processing sheet with id=AA5, first strand: chain 'E' and resid 189 through 191 removed outlier: 7.335A pdb=" N GLU E 233 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL E 229 " --> pdb=" O GLU E 233 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 44 through 46 removed outlier: 5.794A pdb=" N ARG F 44 " --> pdb=" O ILE F 259 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N CYS F 261 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASN F 46 " --> pdb=" O CYS F 261 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N SER F 263 " --> pdb=" O ASN F 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 114 through 117 removed outlier: 4.310A pdb=" N SER F 114 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL F 125 " --> pdb=" O SER F 114 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG F 116 " --> pdb=" O TYR F 123 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR F 123 " --> pdb=" O ARG F 116 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE F 131 " --> pdb=" O LEU F 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 178 through 181 Processing sheet with id=AA9, first strand: chain 'F' and resid 198 through 199 removed outlier: 3.580A pdb=" N CYS F 199 " --> pdb=" O ARG F 205 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG F 205 " --> pdb=" O CYS F 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 210 through 214 removed outlier: 3.948A pdb=" N THR F 210 " --> pdb=" O TYR F 234 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLU F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER F 225 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU F 239 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE F 223 " --> pdb=" O LEU F 239 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2740 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: 3.69 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: 1.02 - 1.18: 1 1.18 - 1.34: 4363 1.34 - 1.51: 3651 1.51 - 1.67: 4954 1.67 - 1.83: 77 Bond restraints: 13046 Sorted by residual: bond pdb=" CG PRO E 217 " pdb=" CD PRO E 217 " ideal model delta sigma weight residual 1.503 1.018 0.485 3.40e-02 8.65e+02 2.03e+02 bond pdb=" N PRO E 217 " pdb=" CD PRO E 217 " ideal model delta sigma weight residual 1.473 1.565 -0.092 1.40e-02 5.10e+03 4.35e+01 bond pdb=" CG PRO F 271 " pdb=" CD PRO F 271 " ideal model delta sigma weight residual 1.503 1.333 0.170 3.40e-02 8.65e+02 2.50e+01 bond pdb=" C5 MAN J 3 " pdb=" O5 MAN J 3 " ideal model delta sigma weight residual 1.418 1.490 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" N PRO F 271 " pdb=" CD PRO F 271 " ideal model delta sigma weight residual 1.473 1.518 -0.045 1.40e-02 5.10e+03 1.01e+01 ... (remaining 13041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 17622 4.37 - 8.75: 169 8.75 - 13.12: 21 13.12 - 17.49: 8 17.49 - 21.86: 4 Bond angle restraints: 17824 Sorted by residual: angle pdb=" N PRO E 217 " pdb=" CD PRO E 217 " pdb=" CG PRO E 217 " ideal model delta sigma weight residual 103.20 81.34 21.86 1.50e+00 4.44e-01 2.12e+02 angle pdb=" CA PRO E 217 " pdb=" N PRO E 217 " pdb=" CD PRO E 217 " ideal model delta sigma weight residual 112.00 94.96 17.04 1.40e+00 5.10e-01 1.48e+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 96.35 15.65 1.40e+00 5.10e-01 1.25e+02 angle pdb=" CA PRO E 217 " pdb=" CB PRO E 217 " pdb=" CG PRO E 217 " ideal model delta sigma weight residual 104.50 88.04 16.46 1.90e+00 2.77e-01 7.50e+01 angle pdb=" CA PRO F 265 " pdb=" N PRO F 265 " pdb=" CD PRO F 265 " ideal model delta sigma weight residual 112.00 101.35 10.65 1.40e+00 5.10e-01 5.79e+01 ... (remaining 17819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.89: 7200 23.89 - 47.78: 615 47.78 - 71.67: 74 71.67 - 95.56: 36 95.56 - 119.45: 13 Dihedral angle restraints: 7938 sinusoidal: 2474 harmonic: 5464 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 -1.89 -84.11 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS F 79 " pdb=" SG CYS F 79 " pdb=" SG CYS F 261 " pdb=" CB CYS F 261 " ideal model delta sinusoidal sigma weight residual -86.00 -26.35 -59.65 1 1.00e+01 1.00e-02 4.75e+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 38.78 54.22 1 1.00e+01 1.00e-02 3.99e+01 ... (remaining 7935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2010 0.110 - 0.220: 113 0.220 - 0.330: 11 0.330 - 0.441: 4 0.441 - 0.551: 2 Chirality restraints: 2140 Sorted by residual: chirality pdb=" CG LEU D 520 " pdb=" CB LEU D 520 " pdb=" CD1 LEU D 520 " pdb=" CD2 LEU D 520 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.58e+00 chirality pdb=" C1 NAG C 801 " pdb=" ND2 ASN C 217 " pdb=" C2 NAG C 801 " pdb=" O5 NAG C 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.91e+00 chirality pdb=" CA PRO E 217 " pdb=" N PRO E 217 " pdb=" C PRO E 217 " pdb=" CB PRO E 217 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.53e+00 ... (remaining 2137 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 216 " 0.117 5.00e-02 4.00e+02 1.60e-01 4.11e+01 pdb=" N PRO E 217 " -0.276 5.00e-02 4.00e+02 pdb=" CA PRO E 217 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO E 217 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 264 " -0.095 5.00e-02 4.00e+02 1.37e-01 3.01e+01 pdb=" N PRO F 265 " 0.237 5.00e-02 4.00e+02 pdb=" CA PRO F 265 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO F 265 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 270 " -0.091 5.00e-02 4.00e+02 1.25e-01 2.49e+01 pdb=" N PRO F 271 " 0.215 5.00e-02 4.00e+02 pdb=" CA PRO F 271 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO F 271 " -0.066 5.00e-02 4.00e+02 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 413 2.71 - 3.26: 13131 3.26 - 3.80: 21095 3.80 - 4.35: 23193 4.35 - 4.90: 38987 Nonbonded interactions: 96819 Sorted by model distance: nonbonded pdb=" OD1 ASN D 323 " pdb=" OH TYR D 523 " model vdw 2.161 3.040 nonbonded pdb=" OG SER D 556 " pdb=" OH TYR D 586 " model vdw 2.166 3.040 nonbonded pdb=" OD1 ASP D 635 " pdb=" OH TYR D 654 " model vdw 2.215 3.040 nonbonded pdb=" OG SER B 39 " pdb=" OG SER B 42 " model vdw 2.216 3.040 nonbonded pdb=" OE2 GLU D 223 " pdb=" OG SER D 254 " model vdw 2.219 3.040 ... (remaining 96814 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: 1.550 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: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 36.090 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5585 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 : 0.007 0.485 13075 Z= 0.308 Angle : 1.165 21.865 17902 Z= 0.590 Chirality : 0.059 0.551 2140 Planarity : 0.008 0.160 2336 Dihedral : 18.875 119.445 4399 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.05 % Favored : 95.84 % Rotamer: Outliers : 0.66 % Allowed : 34.79 % Favored : 64.55 % Cbeta Deviations : 0.06 % 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: 0.46 (0.20), residues: 1853 helix: 1.51 (0.16), residues: 1140 sheet: -0.99 (0.42), residues: 166 loop : -1.86 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 47 HIS 0.013 0.002 HIS E 216 PHE 0.061 0.003 PHE C 690 TYR 0.049 0.002 TYR D 563 ARG 0.033 0.001 ARG E 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00935 ( 8) link_NAG-ASN : angle 5.27489 ( 24) link_ALPHA1-4 : bond 0.00660 ( 4) link_ALPHA1-4 : angle 3.26203 ( 12) link_ALPHA1-6 : bond 0.00938 ( 4) link_ALPHA1-6 : angle 1.61777 ( 12) link_BETA1-4 : bond 0.02146 ( 2) link_BETA1-4 : angle 10.03177 ( 6) link_ALPHA1-3 : bond 0.01243 ( 2) link_ALPHA1-3 : angle 2.99733 ( 6) hydrogen bonds : bond 0.12088 ( 925) hydrogen bonds : angle 5.62170 ( 2740) SS BOND : bond 0.00517 ( 9) SS BOND : angle 1.93167 ( 18) covalent geometry : bond 0.00745 (13046) covalent geometry : angle 1.12966 (17824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 220 time to evaluate : 1.411 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: C 338 GLN cc_start: 0.4866 (mm-40) cc_final: 0.4552 (mm-40) REVERT: F 279 GLN cc_start: 0.6325 (mp10) cc_final: 0.6004 (mp10) outliers start: 6 outliers final: 1 residues processed: 223 average time/residue: 0.2446 time to fit residues: 79.5399 Evaluate side-chains 209 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 217 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.8980 chunk 139 optimal weight: 0.0370 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 107 optimal weight: 0.5980 chunk 167 optimal weight: 50.0000 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 577 GLN ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 685 HIS E 65 ASN E 221 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.252527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.234197 restraints weight = 22370.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.233986 restraints weight = 31825.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.233622 restraints weight = 30333.431| |-----------------------------------------------------------------------------| r_work (final): 0.4854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4854 r_free = 0.4854 target_work(ls_wunit_k1) = 0.233 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4854 r_free = 0.4854 target_work(ls_wunit_k1) = 0.233 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5493 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13075 Z= 0.164 Angle : 0.773 13.314 17902 Z= 0.372 Chirality : 0.046 0.421 2140 Planarity : 0.005 0.072 2336 Dihedral : 11.727 111.009 2402 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.11 % Favored : 95.79 % Rotamer: Outliers : 4.38 % Allowed : 30.85 % 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: 0.67 (0.20), residues: 1853 helix: 1.69 (0.15), residues: 1144 sheet: -1.14 (0.41), residues: 166 loop : -1.76 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 302 HIS 0.003 0.001 HIS D 540 PHE 0.027 0.001 PHE E 251 TYR 0.024 0.001 TYR D 654 ARG 0.004 0.001 ARG D 600 Details of bonding type rmsd link_NAG-ASN : bond 0.00802 ( 8) link_NAG-ASN : angle 4.30988 ( 24) link_ALPHA1-4 : bond 0.01406 ( 4) link_ALPHA1-4 : angle 2.97644 ( 12) link_ALPHA1-6 : bond 0.01267 ( 4) link_ALPHA1-6 : angle 2.18397 ( 12) link_BETA1-4 : bond 0.01465 ( 2) link_BETA1-4 : angle 7.23810 ( 6) link_ALPHA1-3 : bond 0.01970 ( 2) link_ALPHA1-3 : angle 4.09451 ( 6) hydrogen bonds : bond 0.03828 ( 925) hydrogen bonds : angle 4.32477 ( 2740) SS BOND : bond 0.00433 ( 9) SS BOND : angle 1.58297 ( 18) covalent geometry : bond 0.00358 (13046) covalent geometry : angle 0.73504 (17824) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 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: C 500 LYS cc_start: 0.3623 (mptt) cc_final: 0.2670 (mptt) REVERT: C 511 ASN cc_start: 0.7303 (t0) cc_final: 0.7093 (t0) REVERT: D 556 SER cc_start: 0.8311 (m) cc_final: 0.7935 (t) outliers start: 40 outliers final: 20 residues processed: 247 average time/residue: 0.2448 time to fit residues: 89.5521 Evaluate side-chains 229 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 611 TYR Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 65 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 130 optimal weight: 0.0670 chunk 178 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 174 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 overall best weight: 5.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 GLN C 290 ASN ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 ASN C 524 ASN ** C 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 HIS ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.241203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.221752 restraints weight = 21931.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.221622 restraints weight = 33187.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.221555 restraints weight = 30282.642| |-----------------------------------------------------------------------------| r_work (final): 0.4756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4757 r_free = 0.4757 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4757 r_free = 0.4757 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5800 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.113 13075 Z= 0.456 Angle : 1.035 13.766 17902 Z= 0.515 Chirality : 0.055 0.382 2140 Planarity : 0.006 0.073 2336 Dihedral : 11.125 112.903 2402 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.94 % Favored : 93.95 % Rotamer: Outliers : 8.10 % Allowed : 29.32 % Favored : 62.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.28 (0.20), residues: 1853 helix: 0.90 (0.15), residues: 1151 sheet: -1.49 (0.40), residues: 160 loop : -2.09 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 302 HIS 0.011 0.002 HIS C 529 PHE 0.030 0.003 PHE E 251 TYR 0.032 0.003 TYR D 281 ARG 0.008 0.001 ARG D 552 Details of bonding type rmsd link_NAG-ASN : bond 0.00885 ( 8) link_NAG-ASN : angle 4.25032 ( 24) link_ALPHA1-4 : bond 0.00899 ( 4) link_ALPHA1-4 : angle 3.07285 ( 12) link_ALPHA1-6 : bond 0.01435 ( 4) link_ALPHA1-6 : angle 2.76549 ( 12) link_BETA1-4 : bond 0.01280 ( 2) link_BETA1-4 : angle 7.86555 ( 6) link_ALPHA1-3 : bond 0.01555 ( 2) link_ALPHA1-3 : angle 5.03355 ( 6) hydrogen bonds : bond 0.05092 ( 925) hydrogen bonds : angle 5.07593 ( 2740) SS BOND : bond 0.02156 ( 9) SS BOND : angle 2.71190 ( 18) covalent geometry : bond 0.01027 (13046) covalent geometry : angle 1.00147 (17824) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 219 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 216 MET cc_start: 0.0155 (ppp) cc_final: -0.0867 (tmm) REVERT: C 309 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7248 (tt0) REVERT: C 630 ARG cc_start: 0.5582 (OUTLIER) cc_final: 0.3195 (tpm170) REVERT: C 673 MET cc_start: 0.2071 (mmm) cc_final: 0.1856 (mmm) REVERT: E 182 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6849 (pp20) outliers start: 74 outliers final: 45 residues processed: 266 average time/residue: 0.2276 time to fit residues: 89.0656 Evaluate side-chains 254 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 611 TYR Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 555 TRP Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 182 GLU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 95 optimal weight: 30.0000 chunk 30 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 19 optimal weight: 20.0000 chunk 166 optimal weight: 0.0170 chunk 85 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 ASN ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS ** D 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.248687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.230225 restraints weight = 22165.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.229326 restraints weight = 31551.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.228114 restraints weight = 27833.039| |-----------------------------------------------------------------------------| r_work (final): 0.4811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4810 r_free = 0.4810 target_work(ls_wunit_k1) = 0.228 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4810 r_free = 0.4810 target_work(ls_wunit_k1) = 0.228 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5648 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13075 Z= 0.150 Angle : 0.768 10.788 17902 Z= 0.372 Chirality : 0.045 0.398 2140 Planarity : 0.004 0.075 2336 Dihedral : 10.133 111.743 2402 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.89 % Favored : 96.00 % Rotamer: Outliers : 4.16 % Allowed : 32.49 % Favored : 63.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.54 (0.20), residues: 1853 helix: 1.62 (0.15), residues: 1153 sheet: -1.35 (0.44), residues: 137 loop : -1.91 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 302 HIS 0.005 0.001 HIS C 637 PHE 0.029 0.002 PHE E 251 TYR 0.025 0.002 TYR C 282 ARG 0.005 0.001 ARG C 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00809 ( 8) link_NAG-ASN : angle 4.02142 ( 24) link_ALPHA1-4 : bond 0.01422 ( 4) link_ALPHA1-4 : angle 2.88546 ( 12) link_ALPHA1-6 : bond 0.01410 ( 4) link_ALPHA1-6 : angle 2.19181 ( 12) link_BETA1-4 : bond 0.01134 ( 2) link_BETA1-4 : angle 6.80208 ( 6) link_ALPHA1-3 : bond 0.02332 ( 2) link_ALPHA1-3 : angle 4.28246 ( 6) hydrogen bonds : bond 0.03534 ( 925) hydrogen bonds : angle 4.10086 ( 2740) SS BOND : bond 0.00406 ( 9) SS BOND : angle 2.27321 ( 18) covalent geometry : bond 0.00318 (13046) covalent geometry : angle 0.73163 (17824) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 216 MET cc_start: 0.0429 (ppp) cc_final: -0.0197 (tmm) REVERT: C 500 LYS cc_start: 0.4052 (mmtt) cc_final: 0.2360 (mppt) REVERT: C 630 ARG cc_start: 0.5181 (OUTLIER) cc_final: 0.3070 (tpm170) REVERT: D 320 LEU cc_start: 0.8460 (tt) cc_final: 0.7688 (mt) REVERT: D 556 SER cc_start: 0.8369 (m) cc_final: 0.8077 (t) REVERT: D 583 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7318 (mm-30) REVERT: F 43 PHE cc_start: 0.3277 (m-80) cc_final: 0.3052 (m-80) outliers start: 38 outliers final: 24 residues processed: 245 average time/residue: 0.2212 time to fit residues: 80.8885 Evaluate side-chains 231 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 596 ILE Chi-restraints excluded: chain C residue 611 TYR Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 674 HIS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 33 optimal weight: 50.0000 chunk 6 optimal weight: 50.0000 chunk 94 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 26 optimal weight: 50.0000 chunk 150 optimal weight: 0.4980 chunk 159 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.247862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.230854 restraints weight = 22264.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.229934 restraints weight = 33834.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.228189 restraints weight = 31607.135| |-----------------------------------------------------------------------------| r_work (final): 0.4813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4809 r_free = 0.4809 target_work(ls_wunit_k1) = 0.228 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4809 r_free = 0.4809 target_work(ls_wunit_k1) = 0.228 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5626 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13075 Z= 0.155 Angle : 0.755 10.629 17902 Z= 0.361 Chirality : 0.045 0.394 2140 Planarity : 0.004 0.053 2336 Dihedral : 9.476 109.659 2402 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.21 % Favored : 95.62 % Rotamer: Outliers : 3.83 % Allowed : 34.46 % Favored : 61.71 % 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: 0.71 (0.20), residues: 1853 helix: 1.76 (0.15), residues: 1157 sheet: -1.29 (0.45), residues: 135 loop : -1.88 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 555 HIS 0.009 0.001 HIS D 685 PHE 0.019 0.002 PHE C 690 TYR 0.026 0.001 TYR C 523 ARG 0.004 0.000 ARG C 689 Details of bonding type rmsd link_NAG-ASN : bond 0.00814 ( 8) link_NAG-ASN : angle 3.87017 ( 24) link_ALPHA1-4 : bond 0.01326 ( 4) link_ALPHA1-4 : angle 2.76834 ( 12) link_ALPHA1-6 : bond 0.01570 ( 4) link_ALPHA1-6 : angle 2.02895 ( 12) link_BETA1-4 : bond 0.01157 ( 2) link_BETA1-4 : angle 6.69321 ( 6) link_ALPHA1-3 : bond 0.02346 ( 2) link_ALPHA1-3 : angle 4.44905 ( 6) hydrogen bonds : bond 0.03347 ( 925) hydrogen bonds : angle 3.92956 ( 2740) SS BOND : bond 0.00347 ( 9) SS BOND : angle 1.89375 ( 18) covalent geometry : bond 0.00335 (13046) covalent geometry : angle 0.72091 (17824) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 LEU cc_start: 0.5578 (pp) cc_final: 0.4984 (mt) REVERT: C 216 MET cc_start: 0.0401 (ppp) cc_final: 0.0050 (tmm) REVERT: C 281 TYR cc_start: 0.5614 (OUTLIER) cc_final: 0.5409 (t80) REVERT: C 305 ILE cc_start: 0.7994 (mt) cc_final: 0.7760 (mt) REVERT: C 500 LYS cc_start: 0.4109 (mmtt) cc_final: 0.2407 (mptt) REVERT: C 630 ARG cc_start: 0.5460 (OUTLIER) cc_final: 0.4965 (mmt180) REVERT: C 673 MET cc_start: 0.2023 (mmm) cc_final: 0.1665 (mmm) REVERT: D 556 SER cc_start: 0.8381 (m) cc_final: 0.8131 (t) REVERT: D 583 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7536 (mm-30) REVERT: F 43 PHE cc_start: 0.3380 (m-80) cc_final: 0.2995 (m-80) REVERT: F 66 TYR cc_start: 0.2794 (p90) cc_final: 0.2522 (p90) outliers start: 35 outliers final: 29 residues processed: 242 average time/residue: 0.2239 time to fit residues: 81.4260 Evaluate side-chains 236 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 464 GLN Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 611 TYR Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 674 HIS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 81 optimal weight: 0.6980 chunk 153 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 145 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 50.0000 chunk 48 optimal weight: 50.0000 chunk 180 optimal weight: 50.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 685 HIS ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.242511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.224378 restraints weight = 22279.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.223228 restraints weight = 35439.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.222148 restraints weight = 31208.974| |-----------------------------------------------------------------------------| r_work (final): 0.4751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4750 r_free = 0.4750 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4750 r_free = 0.4750 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5795 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 13075 Z= 0.303 Angle : 0.876 13.451 17902 Z= 0.425 Chirality : 0.049 0.371 2140 Planarity : 0.005 0.078 2336 Dihedral : 9.591 111.523 2402 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.02 % Favored : 94.87 % Rotamer: Outliers : 4.70 % Allowed : 33.26 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.32 (0.20), residues: 1853 helix: 1.44 (0.15), residues: 1153 sheet: -1.74 (0.40), residues: 156 loop : -1.85 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 302 HIS 0.009 0.001 HIS D 685 PHE 0.035 0.002 PHE C 690 TYR 0.040 0.002 TYR C 282 ARG 0.011 0.001 ARG C 689 Details of bonding type rmsd link_NAG-ASN : bond 0.00801 ( 8) link_NAG-ASN : angle 3.92484 ( 24) link_ALPHA1-4 : bond 0.01188 ( 4) link_ALPHA1-4 : angle 2.81975 ( 12) link_ALPHA1-6 : bond 0.01294 ( 4) link_ALPHA1-6 : angle 2.29082 ( 12) link_BETA1-4 : bond 0.00999 ( 2) link_BETA1-4 : angle 6.99459 ( 6) link_ALPHA1-3 : bond 0.02129 ( 2) link_ALPHA1-3 : angle 4.88777 ( 6) hydrogen bonds : bond 0.04102 ( 925) hydrogen bonds : angle 4.41656 ( 2740) SS BOND : bond 0.00534 ( 9) SS BOND : angle 2.12271 ( 18) covalent geometry : bond 0.00684 (13046) covalent geometry : angle 0.84396 (17824) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 LEU cc_start: 0.5573 (pp) cc_final: 0.5125 (mt) REVERT: C 309 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: C 626 TYR cc_start: 0.6318 (t80) cc_final: 0.5893 (t80) REVERT: C 630 ARG cc_start: 0.5629 (OUTLIER) cc_final: 0.3471 (tpm170) REVERT: D 583 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7404 (mm-30) REVERT: E 214 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.5893 (mm) REVERT: F 43 PHE cc_start: 0.3859 (m-80) cc_final: 0.3272 (m-80) outliers start: 43 outliers final: 33 residues processed: 245 average time/residue: 0.2389 time to fit residues: 87.0743 Evaluate side-chains 247 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 464 GLN Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 596 ILE Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 674 HIS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 112 optimal weight: 4.9990 chunk 80 optimal weight: 0.3980 chunk 132 optimal weight: 0.9980 chunk 22 optimal weight: 30.0000 chunk 149 optimal weight: 0.2980 chunk 178 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 122 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 ASN ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 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 = 0.4976 r_free = 0.4976 target = 0.246051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.228420 restraints weight = 22238.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.226275 restraints weight = 32889.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.224486 restraints weight = 35101.207| |-----------------------------------------------------------------------------| r_work (final): 0.4775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4776 r_free = 0.4776 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4776 r_free = 0.4776 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5736 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13075 Z= 0.156 Angle : 0.783 11.582 17902 Z= 0.375 Chirality : 0.046 0.384 2140 Planarity : 0.004 0.054 2336 Dihedral : 9.069 109.407 2402 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.38 % Favored : 95.46 % Rotamer: Outliers : 3.61 % Allowed : 33.59 % Favored : 62.80 % 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: 0.68 (0.20), residues: 1853 helix: 1.71 (0.15), residues: 1154 sheet: -1.60 (0.41), residues: 155 loop : -1.68 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 302 HIS 0.006 0.001 HIS D 294 PHE 0.035 0.002 PHE C 690 TYR 0.025 0.001 TYR C 523 ARG 0.003 0.001 ARG E 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00748 ( 8) link_NAG-ASN : angle 3.82020 ( 24) link_ALPHA1-4 : bond 0.01350 ( 4) link_ALPHA1-4 : angle 2.78837 ( 12) link_ALPHA1-6 : bond 0.01600 ( 4) link_ALPHA1-6 : angle 1.74303 ( 12) link_BETA1-4 : bond 0.01092 ( 2) link_BETA1-4 : angle 6.57527 ( 6) link_ALPHA1-3 : bond 0.02357 ( 2) link_ALPHA1-3 : angle 4.53678 ( 6) hydrogen bonds : bond 0.03345 ( 925) hydrogen bonds : angle 3.96657 ( 2740) SS BOND : bond 0.00378 ( 9) SS BOND : angle 1.67846 ( 18) covalent geometry : bond 0.00340 (13046) covalent geometry : angle 0.75178 (17824) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 LEU cc_start: 0.5673 (pp) cc_final: 0.5194 (mt) REVERT: C 630 ARG cc_start: 0.5481 (OUTLIER) cc_final: 0.3131 (tpm170) REVERT: D 556 SER cc_start: 0.8370 (m) cc_final: 0.8120 (t) REVERT: D 583 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7245 (mm-30) REVERT: E 214 ILE cc_start: 0.6473 (mm) cc_final: 0.5747 (mm) outliers start: 33 outliers final: 29 residues processed: 249 average time/residue: 0.2338 time to fit residues: 86.0027 Evaluate side-chains 248 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 464 GLN Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 674 HIS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 141 optimal weight: 6.9990 chunk 89 optimal weight: 0.4980 chunk 86 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 25 optimal weight: 50.0000 chunk 52 optimal weight: 50.0000 chunk 116 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.242454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.224485 restraints weight = 22145.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.223048 restraints weight = 34671.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.222092 restraints weight = 34255.948| |-----------------------------------------------------------------------------| r_work (final): 0.4754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4755 r_free = 0.4755 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4755 r_free = 0.4755 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5795 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13075 Z= 0.273 Angle : 0.861 12.097 17902 Z= 0.418 Chirality : 0.049 0.375 2140 Planarity : 0.005 0.118 2336 Dihedral : 9.158 110.426 2402 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.19 % Favored : 94.71 % Rotamer: Outliers : 4.05 % Allowed : 34.14 % Favored : 61.82 % 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: 0.52 (0.20), residues: 1853 helix: 1.55 (0.15), residues: 1152 sheet: -1.66 (0.41), residues: 155 loop : -1.65 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 555 HIS 0.009 0.001 HIS D 294 PHE 0.054 0.002 PHE C 651 TYR 0.036 0.002 TYR D 299 ARG 0.009 0.001 ARG D 243 Details of bonding type rmsd link_NAG-ASN : bond 0.00842 ( 8) link_NAG-ASN : angle 3.77670 ( 24) link_ALPHA1-4 : bond 0.01221 ( 4) link_ALPHA1-4 : angle 2.84298 ( 12) link_ALPHA1-6 : bond 0.01253 ( 4) link_ALPHA1-6 : angle 2.09749 ( 12) link_BETA1-4 : bond 0.01032 ( 2) link_BETA1-4 : angle 6.81548 ( 6) link_ALPHA1-3 : bond 0.02140 ( 2) link_ALPHA1-3 : angle 4.80752 ( 6) hydrogen bonds : bond 0.03871 ( 925) hydrogen bonds : angle 4.30247 ( 2740) SS BOND : bond 0.00554 ( 9) SS BOND : angle 2.03903 ( 18) covalent geometry : bond 0.00616 (13046) covalent geometry : angle 0.83077 (17824) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 1.381 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: B 46 LEU cc_start: 0.5575 (pp) cc_final: 0.5101 (mt) REVERT: C 626 TYR cc_start: 0.6316 (t80) cc_final: 0.6002 (t80) REVERT: C 630 ARG cc_start: 0.5508 (OUTLIER) cc_final: 0.3210 (tpm170) REVERT: C 667 MET cc_start: 0.4530 (tmm) cc_final: 0.4209 (tmm) REVERT: C 673 MET cc_start: 0.1311 (mmm) cc_final: 0.0893 (mmm) REVERT: D 583 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7404 (mm-30) REVERT: E 214 ILE cc_start: 0.6777 (mm) cc_final: 0.6139 (mm) outliers start: 37 outliers final: 33 residues processed: 243 average time/residue: 0.2363 time to fit residues: 85.3469 Evaluate side-chains 247 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 464 GLN Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 674 HIS Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 674 HIS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 97 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 41 optimal weight: 90.0000 chunk 52 optimal weight: 50.0000 chunk 57 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 30.0000 chunk 163 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.246228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.228344 restraints weight = 22208.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.226375 restraints weight = 33316.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.224370 restraints weight = 32342.883| |-----------------------------------------------------------------------------| r_work (final): 0.4767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4769 r_free = 0.4769 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4769 r_free = 0.4769 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13075 Z= 0.152 Angle : 0.797 12.478 17902 Z= 0.381 Chirality : 0.046 0.389 2140 Planarity : 0.004 0.059 2336 Dihedral : 8.812 108.274 2402 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.21 % Favored : 95.62 % Rotamer: Outliers : 3.61 % Allowed : 34.35 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.87 (0.20), residues: 1853 helix: 1.83 (0.15), residues: 1154 sheet: -1.58 (0.41), residues: 157 loop : -1.51 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 482 HIS 0.006 0.001 HIS D 294 PHE 0.054 0.002 PHE C 651 TYR 0.034 0.001 TYR D 299 ARG 0.019 0.001 ARG E 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00855 ( 8) link_NAG-ASN : angle 3.67256 ( 24) link_ALPHA1-4 : bond 0.01347 ( 4) link_ALPHA1-4 : angle 2.82792 ( 12) link_ALPHA1-6 : bond 0.01600 ( 4) link_ALPHA1-6 : angle 1.71698 ( 12) link_BETA1-4 : bond 0.01094 ( 2) link_BETA1-4 : angle 6.50805 ( 6) link_ALPHA1-3 : bond 0.02429 ( 2) link_ALPHA1-3 : angle 4.54584 ( 6) hydrogen bonds : bond 0.03278 ( 925) hydrogen bonds : angle 3.93881 ( 2740) SS BOND : bond 0.00411 ( 9) SS BOND : angle 1.64224 ( 18) covalent geometry : bond 0.00326 (13046) covalent geometry : angle 0.76681 (17824) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 1.640 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: B 46 LEU cc_start: 0.5573 (pp) cc_final: 0.5067 (mt) REVERT: C 282 TYR cc_start: 0.6784 (m-80) cc_final: 0.6541 (m-80) REVERT: C 309 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.7054 (tt0) REVERT: C 630 ARG cc_start: 0.5550 (OUTLIER) cc_final: 0.3311 (tpm170) REVERT: C 667 MET cc_start: 0.4413 (tmm) cc_final: 0.4046 (tmm) REVERT: C 673 MET cc_start: 0.1222 (mmm) cc_final: 0.0736 (mmm) REVERT: D 583 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7368 (mm-30) REVERT: D 706 PHE cc_start: 0.7547 (t80) cc_final: 0.7316 (t80) REVERT: E 214 ILE cc_start: 0.6582 (mm) cc_final: 0.5920 (mm) outliers start: 33 outliers final: 27 residues processed: 251 average time/residue: 0.2594 time to fit residues: 96.0837 Evaluate side-chains 246 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 464 GLN Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 674 HIS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 16 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 162 optimal weight: 30.0000 chunk 180 optimal weight: 5.9990 chunk 47 optimal weight: 100.0000 chunk 107 optimal weight: 0.9990 chunk 8 optimal weight: 40.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS C 466 ASN ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 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 = 0.4973 r_free = 0.4973 target = 0.245595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.227309 restraints weight = 22258.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.224379 restraints weight = 30641.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 75)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.223177 restraints weight = 27659.007| |-----------------------------------------------------------------------------| r_work (final): 0.4763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4762 r_free = 0.4762 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4762 r_free = 0.4762 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5774 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13075 Z= 0.159 Angle : 0.796 12.648 17902 Z= 0.379 Chirality : 0.046 0.386 2140 Planarity : 0.004 0.083 2336 Dihedral : 8.646 107.247 2402 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.54 % Favored : 95.30 % Rotamer: Outliers : 3.39 % Allowed : 34.46 % Favored : 62.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.98 (0.20), residues: 1853 helix: 1.90 (0.15), residues: 1158 sheet: -1.46 (0.41), residues: 155 loop : -1.49 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 482 HIS 0.008 0.001 HIS D 294 PHE 0.055 0.002 PHE C 651 TYR 0.031 0.001 TYR D 299 ARG 0.014 0.001 ARG E 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00800 ( 8) link_NAG-ASN : angle 3.54828 ( 24) link_ALPHA1-4 : bond 0.01276 ( 4) link_ALPHA1-4 : angle 2.85142 ( 12) link_ALPHA1-6 : bond 0.01522 ( 4) link_ALPHA1-6 : angle 1.69776 ( 12) link_BETA1-4 : bond 0.01141 ( 2) link_BETA1-4 : angle 6.46743 ( 6) link_ALPHA1-3 : bond 0.02437 ( 2) link_ALPHA1-3 : angle 4.60677 ( 6) hydrogen bonds : bond 0.03234 ( 925) hydrogen bonds : angle 3.86311 ( 2740) SS BOND : bond 0.00447 ( 9) SS BOND : angle 1.54331 ( 18) covalent geometry : bond 0.00351 (13046) covalent geometry : angle 0.76746 (17824) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 1.659 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: B 46 LEU cc_start: 0.5582 (pp) cc_final: 0.5032 (mt) REVERT: C 309 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: C 626 TYR cc_start: 0.6382 (t80) cc_final: 0.6124 (t80) REVERT: C 630 ARG cc_start: 0.5560 (OUTLIER) cc_final: 0.3224 (tpm170) REVERT: C 667 MET cc_start: 0.4315 (tmm) cc_final: 0.3927 (tmm) REVERT: C 673 MET cc_start: 0.1367 (mmm) cc_final: 0.0828 (mmm) REVERT: D 583 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7253 (mm-30) REVERT: D 706 PHE cc_start: 0.7621 (t80) cc_final: 0.7397 (t80) REVERT: E 214 ILE cc_start: 0.6735 (mm) cc_final: 0.6055 (mm) outliers start: 31 outliers final: 28 residues processed: 246 average time/residue: 0.2338 time to fit residues: 85.7050 Evaluate side-chains 246 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 464 GLN Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 674 HIS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 275 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 179 optimal weight: 50.0000 chunk 155 optimal weight: 0.4980 chunk 90 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 54 optimal weight: 50.0000 chunk 115 optimal weight: 50.0000 chunk 45 optimal weight: 50.0000 chunk 38 optimal weight: 20.0000 chunk 145 optimal weight: 9.9990 chunk 41 optimal weight: 90.0000 chunk 104 optimal weight: 0.0020 overall best weight: 5.4996 ------------------------------------------------------------------------------- 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 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 HIS ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 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 = 0.4904 r_free = 0.4904 target = 0.237894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.220179 restraints weight = 21772.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.218534 restraints weight = 29719.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.217554 restraints weight = 30205.262| |-----------------------------------------------------------------------------| r_work (final): 0.4706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4707 r_free = 0.4707 target_work(ls_wunit_k1) = 0.217 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4707 r_free = 0.4707 target_work(ls_wunit_k1) = 0.217 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.105 13075 Z= 0.434 Angle : 1.026 15.667 17902 Z= 0.502 Chirality : 0.055 0.355 2140 Planarity : 0.006 0.078 2336 Dihedral : 9.361 112.614 2402 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.32 % Favored : 93.52 % Rotamer: Outliers : 3.83 % Allowed : 34.35 % Favored : 61.82 % 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: 0.20 (0.20), residues: 1853 helix: 1.25 (0.16), residues: 1151 sheet: -1.55 (0.40), residues: 157 loop : -1.75 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 302 HIS 0.009 0.002 HIS C 529 PHE 0.065 0.003 PHE C 651 TYR 0.026 0.003 TYR A 30 ARG 0.017 0.001 ARG E 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00884 ( 8) link_NAG-ASN : angle 3.77669 ( 24) link_ALPHA1-4 : bond 0.01101 ( 4) link_ALPHA1-4 : angle 3.04092 ( 12) link_ALPHA1-6 : bond 0.01150 ( 4) link_ALPHA1-6 : angle 2.52488 ( 12) link_BETA1-4 : bond 0.00978 ( 2) link_BETA1-4 : angle 7.22307 ( 6) link_ALPHA1-3 : bond 0.01874 ( 2) link_ALPHA1-3 : angle 5.26747 ( 6) hydrogen bonds : bond 0.04686 ( 925) hydrogen bonds : angle 4.81654 ( 2740) SS BOND : bond 0.00689 ( 9) SS BOND : angle 2.32513 ( 18) covalent geometry : bond 0.00977 (13046) covalent geometry : angle 0.99780 (17824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5360.44 seconds wall clock time: 95 minutes 38.02 seconds (5738.02 seconds total)