Starting phenix.real_space_refine on Thu Sep 18 00:52:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uav_63996/09_2025/9uav_63996.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uav_63996/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9uav_63996/09_2025/9uav_63996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uav_63996/09_2025/9uav_63996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uav_63996/09_2025/9uav_63996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uav_63996/09_2025/9uav_63996.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'PHE:plan': 26, 'ARG:plan': 12, 'GLN:plan1': 4, 'GLU:plan': 9, 'HIS:plan': 7, 'TRP:plan': 4, 'TYR:plan': 8, 'ASP:plan': 8, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 428 Chain: "B" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 1423 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PTRANS': 7, 'TRANS': 258} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 808 Unresolved non-hydrogen angles: 1038 Unresolved non-hydrogen dihedrals: 701 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'PHE:plan': 26, 'ARG:plan': 12, 'GLN:plan1': 5, 'GLU:plan': 9, 'HIS:plan': 7, 'TRP:plan': 4, 'TYR:plan': 8, 'ASP:plan': 8, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 432 Chain: "C" Number of atoms: 3276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 436, 3275 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 6, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 113 Conformer: "B" Number of residues, atoms: 436, 3275 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 6, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 113 bond proxies already assigned to first conformer: 3343 Chain: "D" Number of atoms: 3267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 438, 3266 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 6, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 7, 'GLU:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 139 Conformer: "B" Number of residues, atoms: 438, 3266 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 6, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 7, 'GLU:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 139 bond proxies already assigned to first conformer: 3330 Chain: "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: {'PHE:plan': 2, 'ASP:plan': 2, 'GLU:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLN:plan1': 2} 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: {'GLU:plan': 19, 'PHE:plan': 3, 'ASP:plan': 2, 'TYR:plan': 10, 'ASN:plan1': 7, 'ARG:plan': 6, 'GLN:plan1': 5, 'HIS:plan': 7} 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: 4.44, per 1000 atoms: 0.35 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: 1.28 Conformation dependent library (CDL) restraints added in 862.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.33 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: 1.84 Time building geometry restraints manager: 1.55 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 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.270 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.320 ------------------------------------------------------------------------------- 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 : 9.27 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (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 ARG 0.033 0.001 ARG E 250 TYR 0.049 0.002 TYR D 563 PHE 0.061 0.003 PHE C 690 TRP 0.023 0.002 TRP F 47 HIS 0.013 0.002 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00745 (13046) covalent geometry : angle 1.12966 (17824) SS BOND : bond 0.00517 ( 9) SS BOND : angle 1.93167 ( 18) hydrogen bonds : bond 0.12088 ( 925) hydrogen bonds : angle 5.62170 ( 2740) link_ALPHA1-3 : bond 0.01243 ( 2) link_ALPHA1-3 : angle 2.99733 ( 6) 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_NAG-ASN : bond 0.00935 ( 8) link_NAG-ASN : angle 5.27489 ( 24) *********************** 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 : 0.468 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: 0.1049 time to fit residues: 34.7281 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 : 0.484 ------------------------------------------------------------------------------- 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 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0000 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 8.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN C 323 ASN ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 577 GLN ** C 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 GLN ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5039 r_free = 0.5039 target = 0.254313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.237306 restraints weight = 22451.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.235481 restraints weight = 33310.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.234018 restraints weight = 32217.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.233355 restraints weight = 30118.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.232882 restraints weight = 26610.399| |-----------------------------------------------------------------------------| r_work (final): 0.4847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4847 r_free = 0.4847 target_work(ls_wunit_k1) = 0.232 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4847 r_free = 0.4847 target_work(ls_wunit_k1) = 0.232 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5531 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13075 Z= 0.143 Angle : 0.756 12.787 17902 Z= 0.362 Chirality : 0.045 0.417 2140 Planarity : 0.005 0.072 2336 Dihedral : 11.292 110.059 2402 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.78 % Favored : 96.06 % Rotamer: Outliers : 3.94 % Allowed : 30.85 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.20), residues: 1853 helix: 1.75 (0.15), residues: 1146 sheet: -1.17 (0.41), residues: 166 loop : -1.75 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 689 TYR 0.023 0.001 TYR D 654 PHE 0.024 0.001 PHE E 251 TRP 0.012 0.001 TRP C 302 HIS 0.003 0.001 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00303 (13046) covalent geometry : angle 0.71817 (17824) SS BOND : bond 0.00381 ( 9) SS BOND : angle 1.44176 ( 18) hydrogen bonds : bond 0.03612 ( 925) hydrogen bonds : angle 4.16778 ( 2740) link_ALPHA1-3 : bond 0.02213 ( 2) link_ALPHA1-3 : angle 4.36109 ( 6) link_ALPHA1-4 : bond 0.01442 ( 4) link_ALPHA1-4 : angle 2.97440 ( 12) link_ALPHA1-6 : bond 0.01413 ( 4) link_ALPHA1-6 : angle 2.13538 ( 12) link_BETA1-4 : bond 0.01398 ( 2) link_BETA1-4 : angle 7.02908 ( 6) link_NAG-ASN : bond 0.00814 ( 8) link_NAG-ASN : angle 4.23962 ( 24) *********************** 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 269 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 0.413 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: symmetry clash REVERT: C 282 TYR cc_start: 0.5728 (OUTLIER) cc_final: 0.5522 (m-10) REVERT: C 500 LYS cc_start: 0.3938 (mptt) cc_final: 0.2879 (mptt) REVERT: D 556 SER cc_start: 0.8279 (m) cc_final: 0.7821 (t) REVERT: D 693 MET cc_start: 0.5761 (ptt) cc_final: 0.5419 (ptt) outliers start: 36 outliers final: 16 residues processed: 255 average time/residue: 0.1073 time to fit residues: 40.7259 Evaluate side-chains 231 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 TYR 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 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 E residue 122 THR Chi-restraints excluded: chain E residue 123 TYR 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 73 optimal weight: 3.9990 chunk 95 optimal weight: 30.0000 chunk 157 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 86 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 144 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 511 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 518 HIS ** D 527 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** E 221 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.249768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.231311 restraints weight = 22383.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.230344 restraints weight = 32847.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.229266 restraints weight = 30008.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.228793 restraints weight = 28445.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.228409 restraints weight = 26331.990| |-----------------------------------------------------------------------------| r_work (final): 0.4813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4807 r_free = 0.4807 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 = 0.4807 r_free = 0.4807 target_work(ls_wunit_k1) = 0.228 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5640 moved from start: 0.1485 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= 0.200 Angle : 0.768 11.221 17902 Z= 0.370 Chirality : 0.046 0.398 2140 Planarity : 0.004 0.058 2336 Dihedral : 10.157 109.821 2402 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 5.03 % Allowed : 31.07 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.20), residues: 1853 helix: 1.69 (0.15), residues: 1153 sheet: -1.20 (0.41), residues: 167 loop : -1.78 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 689 TYR 0.025 0.002 TYR D 654 PHE 0.030 0.002 PHE E 251 TRP 0.010 0.001 TRP C 302 HIS 0.009 0.001 HIS C 653 Details of bonding type rmsd covalent geometry : bond 0.00444 (13046) covalent geometry : angle 0.73091 (17824) SS BOND : bond 0.00525 ( 9) SS BOND : angle 2.02250 ( 18) hydrogen bonds : bond 0.03672 ( 925) hydrogen bonds : angle 4.08344 ( 2740) link_ALPHA1-3 : bond 0.01930 ( 2) link_ALPHA1-3 : angle 4.25426 ( 6) link_ALPHA1-4 : bond 0.01201 ( 4) link_ALPHA1-4 : angle 2.84330 ( 12) link_ALPHA1-6 : bond 0.01330 ( 4) link_ALPHA1-6 : angle 2.24492 ( 12) link_BETA1-4 : bond 0.01227 ( 2) link_BETA1-4 : angle 7.09885 ( 6) link_NAG-ASN : bond 0.00863 ( 8) link_NAG-ASN : angle 4.04633 ( 24) *********************** 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 264 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 0.550 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: -0.0298 (ppp) cc_final: -0.0842 (tmm) REVERT: C 500 LYS cc_start: 0.3644 (mptt) cc_final: 0.2641 (mptt) REVERT: D 693 MET cc_start: 0.5919 (OUTLIER) cc_final: 0.5707 (ptt) REVERT: F 66 TYR cc_start: 0.2462 (p90) cc_final: 0.2235 (p90) outliers start: 46 outliers final: 28 residues processed: 246 average time/residue: 0.1028 time to fit residues: 37.9097 Evaluate side-chains 237 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 305 ILE 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 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 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 345 GLU Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 693 MET Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain E residue 45 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 239 LEU Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain F residue 80 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 69 optimal weight: 0.0170 chunk 99 optimal weight: 0.9990 chunk 178 optimal weight: 30.0000 chunk 143 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 148 optimal weight: 0.0770 chunk 149 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 130 optimal weight: 0.0000 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 577 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** ** 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 = 0.5029 r_free = 0.5029 target = 0.252811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.235224 restraints weight = 22530.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.234544 restraints weight = 33544.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.234383 restraints weight = 29730.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.233922 restraints weight = 24608.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.232730 restraints weight = 26116.525| |-----------------------------------------------------------------------------| r_work (final): 0.4850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4850 r_free = 0.4850 target_work(ls_wunit_k1) = 0.232 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4850 r_free = 0.4850 target_work(ls_wunit_k1) = 0.232 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5531 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13075 Z= 0.134 Angle : 0.734 11.322 17902 Z= 0.347 Chirality : 0.045 0.400 2140 Planarity : 0.004 0.053 2336 Dihedral : 9.520 108.587 2402 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.89 % Favored : 95.95 % Rotamer: Outliers : 3.50 % Allowed : 32.39 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.20), residues: 1853 helix: 1.94 (0.15), residues: 1154 sheet: -1.19 (0.42), residues: 164 loop : -1.65 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 132 TYR 0.031 0.001 TYR C 523 PHE 0.030 0.001 PHE D 706 TRP 0.008 0.001 TRP D 302 HIS 0.004 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00276 (13046) covalent geometry : angle 0.69834 (17824) SS BOND : bond 0.00434 ( 9) SS BOND : angle 1.85756 ( 18) hydrogen bonds : bond 0.03158 ( 925) hydrogen bonds : angle 3.83190 ( 2740) link_ALPHA1-3 : bond 0.02265 ( 2) link_ALPHA1-3 : angle 4.32664 ( 6) link_ALPHA1-4 : bond 0.01414 ( 4) link_ALPHA1-4 : angle 2.74953 ( 12) link_ALPHA1-6 : bond 0.01705 ( 4) link_ALPHA1-6 : angle 2.00709 ( 12) link_BETA1-4 : bond 0.01278 ( 2) link_BETA1-4 : angle 6.63455 ( 6) link_NAG-ASN : bond 0.00830 ( 8) link_NAG-ASN : angle 3.91622 ( 24) *********************** 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 249 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.401 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 216 MET cc_start: -0.0182 (ppp) cc_final: -0.0587 (tmm) REVERT: C 500 LYS cc_start: 0.3497 (mptt) cc_final: 0.2561 (mptt) REVERT: C 673 MET cc_start: 0.1865 (mmm) cc_final: 0.1633 (mmm) outliers start: 32 outliers final: 21 residues processed: 236 average time/residue: 0.1007 time to fit residues: 36.0563 Evaluate side-chains 226 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 464 GLN Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 548 ASN Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 611 TYR Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 287 LEU 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 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 277 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 81 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 11 optimal weight: 30.0000 chunk 176 optimal weight: 40.0000 chunk 110 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 ASN C 466 ASN ** 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 E 246 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.245248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.226139 restraints weight = 22303.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.225116 restraints weight = 32682.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.224277 restraints weight = 30247.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.223485 restraints weight = 29263.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.222887 restraints weight = 29965.511| |-----------------------------------------------------------------------------| r_work (final): 0.4761 ------------------------------------------------------------------------------- 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: 0.5782 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 13075 Z= 0.295 Angle : 0.849 10.701 17902 Z= 0.413 Chirality : 0.049 0.374 2140 Planarity : 0.005 0.054 2336 Dihedral : 9.531 111.151 2402 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.97 % Favored : 94.92 % Rotamer: Outliers : 5.69 % Allowed : 30.85 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.20), residues: 1853 helix: 1.51 (0.15), residues: 1148 sheet: -1.28 (0.44), residues: 136 loop : -1.67 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 341 TYR 0.022 0.002 TYR C 299 PHE 0.024 0.002 PHE D 706 TRP 0.012 0.002 TRP D 302 HIS 0.008 0.002 HIS C 529 Details of bonding type rmsd covalent geometry : bond 0.00661 (13046) covalent geometry : angle 0.81624 (17824) SS BOND : bond 0.00909 ( 9) SS BOND : angle 2.07883 ( 18) hydrogen bonds : bond 0.04008 ( 925) hydrogen bonds : angle 4.31195 ( 2740) link_ALPHA1-3 : bond 0.02014 ( 2) link_ALPHA1-3 : angle 4.82719 ( 6) link_ALPHA1-4 : bond 0.01131 ( 4) link_ALPHA1-4 : angle 2.78947 ( 12) link_ALPHA1-6 : bond 0.01404 ( 4) link_ALPHA1-6 : angle 2.26077 ( 12) link_BETA1-4 : bond 0.01053 ( 2) link_BETA1-4 : angle 7.00246 ( 6) link_NAG-ASN : bond 0.00816 ( 8) link_NAG-ASN : angle 3.93881 ( 24) *********************** 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 272 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 220 time to evaluate : 0.477 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: symmetry clash REVERT: C 331 LEU cc_start: 0.8449 (mt) cc_final: 0.8168 (mt) outliers start: 52 outliers final: 38 residues processed: 252 average time/residue: 0.1026 time to fit residues: 38.5257 Evaluate side-chains 249 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL 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 588 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 628 VAL 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 330 SER Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 535 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 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 154 MET 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 71 THR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 264 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 88 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 chunk 56 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 169 optimal weight: 20.0000 chunk 176 optimal weight: 50.0000 chunk 57 optimal weight: 5.9990 chunk 125 optimal weight: 0.5980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS C 237 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.247110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.228471 restraints weight = 22110.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.227367 restraints weight = 30165.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 75)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.226345 restraints weight = 27059.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.225437 restraints weight = 27979.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.225136 restraints weight = 25290.201| |-----------------------------------------------------------------------------| r_work (final): 0.4772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4770 r_free = 0.4770 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 = 0.4770 r_free = 0.4770 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5753 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 13075 Z= 0.217 Angle : 0.797 13.390 17902 Z= 0.384 Chirality : 0.046 0.387 2140 Planarity : 0.004 0.050 2336 Dihedral : 9.185 111.104 2402 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.38 % Favored : 95.52 % Rotamer: Outliers : 4.16 % Allowed : 32.39 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.20), residues: 1853 helix: 1.68 (0.15), residues: 1152 sheet: -1.21 (0.44), residues: 138 loop : -1.71 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 205 TYR 0.027 0.002 TYR C 282 PHE 0.018 0.002 PHE D 706 TRP 0.011 0.001 TRP D 302 HIS 0.005 0.001 HIS C 529 Details of bonding type rmsd covalent geometry : bond 0.00486 (13046) covalent geometry : angle 0.76418 (17824) SS BOND : bond 0.00465 ( 9) SS BOND : angle 2.14239 ( 18) hydrogen bonds : bond 0.03531 ( 925) hydrogen bonds : angle 4.09099 ( 2740) link_ALPHA1-3 : bond 0.02257 ( 2) link_ALPHA1-3 : angle 4.78283 ( 6) link_ALPHA1-4 : bond 0.01251 ( 4) link_ALPHA1-4 : angle 2.76649 ( 12) link_ALPHA1-6 : bond 0.01491 ( 4) link_ALPHA1-6 : angle 2.00092 ( 12) link_BETA1-4 : bond 0.01067 ( 2) link_BETA1-4 : angle 6.70280 ( 6) link_NAG-ASN : bond 0.00800 ( 8) link_NAG-ASN : angle 3.73640 ( 24) *********************** 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 259 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.501 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: 0.5563 (pp) cc_final: 0.5097 (mt) REVERT: C 331 LEU cc_start: 0.8390 (mt) cc_final: 0.8166 (mt) REVERT: C 500 LYS cc_start: 0.4120 (mmtt) cc_final: 0.2408 (mptt) REVERT: F 43 PHE cc_start: 0.3583 (m-80) cc_final: 0.3379 (m-80) REVERT: F 63 GLU cc_start: 0.3846 (pm20) cc_final: 0.3644 (pm20) outliers start: 38 outliers final: 27 residues processed: 247 average time/residue: 0.0970 time to fit residues: 36.1227 Evaluate side-chains 238 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 229 LEU 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 541 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 287 LEU 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 154 MET Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 231 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 71 THR 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 117 optimal weight: 4.9990 chunk 51 optimal weight: 50.0000 chunk 175 optimal weight: 50.0000 chunk 160 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 7 optimal weight: 40.0000 chunk 74 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4955 r_free = 0.4955 target = 0.243687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.224730 restraints weight = 22009.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.224416 restraints weight = 33820.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.222333 restraints weight = 31042.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.220965 restraints weight = 30719.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.220664 restraints weight = 29570.132| |-----------------------------------------------------------------------------| r_work (final): 0.4738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4740 r_free = 0.4740 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4740 r_free = 0.4740 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 13075 Z= 0.266 Angle : 0.844 11.268 17902 Z= 0.410 Chirality : 0.048 0.376 2140 Planarity : 0.004 0.050 2336 Dihedral : 9.033 111.238 2402 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.08 % Favored : 94.81 % Rotamer: Outliers : 4.92 % Allowed : 32.60 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.20), residues: 1853 helix: 1.55 (0.15), residues: 1149 sheet: -1.59 (0.41), residues: 154 loop : -1.63 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 250 TYR 0.037 0.002 TYR C 282 PHE 0.024 0.002 PHE C 651 TRP 0.012 0.002 TRP D 302 HIS 0.008 0.001 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00596 (13046) covalent geometry : angle 0.80993 (17824) SS BOND : bond 0.01161 ( 9) SS BOND : angle 3.06758 ( 18) hydrogen bonds : bond 0.03870 ( 925) hydrogen bonds : angle 4.29865 ( 2740) link_ALPHA1-3 : bond 0.02395 ( 2) link_ALPHA1-3 : angle 5.09329 ( 6) link_ALPHA1-4 : bond 0.01211 ( 4) link_ALPHA1-4 : angle 2.82905 ( 12) link_ALPHA1-6 : bond 0.01313 ( 4) link_ALPHA1-6 : angle 2.03857 ( 12) link_BETA1-4 : bond 0.01020 ( 2) link_BETA1-4 : angle 6.82515 ( 6) link_NAG-ASN : bond 0.00904 ( 8) link_NAG-ASN : angle 3.53828 ( 24) *********************** 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 270 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 0.507 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: 0.5682 (pp) cc_final: 0.5176 (mt) REVERT: C 281 TYR cc_start: 0.6195 (OUTLIER) cc_final: 0.5902 (t80) REVERT: C 626 TYR cc_start: 0.6301 (t80) cc_final: 0.5922 (t80) REVERT: D 220 LYS cc_start: 0.7168 (tttm) cc_final: 0.6950 (ttpp) REVERT: F 43 PHE cc_start: 0.3982 (m-80) cc_final: 0.3449 (m-80) outliers start: 45 outliers final: 37 residues processed: 255 average time/residue: 0.1094 time to fit residues: 41.9734 Evaluate side-chains 251 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 281 TYR 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 541 THR 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 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 330 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 535 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 154 MET Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 214 ILE 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 67 VAL Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 275 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 39 optimal weight: 6.9990 chunk 6 optimal weight: 50.0000 chunk 52 optimal weight: 90.0000 chunk 138 optimal weight: 0.1980 chunk 107 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 11 optimal weight: 30.0000 chunk 58 optimal weight: 10.0000 chunk 134 optimal weight: 0.2980 chunk 38 optimal weight: 9.9990 chunk 180 optimal weight: 50.0000 overall best weight: 1.7582 ------------------------------------------------------------------------------- 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 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 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** D 685 HIS ** 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 = 0.4967 r_free = 0.4967 target = 0.245284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.227044 restraints weight = 22154.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.225273 restraints weight = 29763.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.223706 restraints weight = 26952.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.223348 restraints weight = 26173.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 72)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.222720 restraints weight = 23611.833| |-----------------------------------------------------------------------------| r_work (final): 0.4757 ------------------------------------------------------------------------------- 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: 0.5795 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13075 Z= 0.191 Angle : 0.805 12.010 17902 Z= 0.386 Chirality : 0.047 0.392 2140 Planarity : 0.005 0.160 2336 Dihedral : 8.747 109.755 2402 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.21 % Favored : 95.68 % Rotamer: Outliers : 4.70 % Allowed : 33.04 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.20), residues: 1853 helix: 1.73 (0.15), residues: 1151 sheet: -1.63 (0.41), residues: 157 loop : -1.55 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 554 TYR 0.022 0.001 TYR C 282 PHE 0.032 0.002 PHE C 651 TRP 0.011 0.001 TRP D 302 HIS 0.009 0.001 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00424 (13046) covalent geometry : angle 0.77394 (17824) SS BOND : bond 0.00797 ( 9) SS BOND : angle 2.04668 ( 18) hydrogen bonds : bond 0.03426 ( 925) hydrogen bonds : angle 4.04359 ( 2740) link_ALPHA1-3 : bond 0.02686 ( 2) link_ALPHA1-3 : angle 5.09604 ( 6) link_ALPHA1-4 : bond 0.01287 ( 4) link_ALPHA1-4 : angle 2.82812 ( 12) link_ALPHA1-6 : bond 0.01457 ( 4) link_ALPHA1-6 : angle 1.81981 ( 12) link_BETA1-4 : bond 0.01049 ( 2) link_BETA1-4 : angle 6.59326 ( 6) link_NAG-ASN : bond 0.00782 ( 8) link_NAG-ASN : angle 3.55887 ( 24) *********************** 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 259 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 0.471 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: 0.5554 (pp) cc_final: 0.5033 (mt) REVERT: C 281 TYR cc_start: 0.6104 (OUTLIER) cc_final: 0.5851 (t80) REVERT: C 626 TYR cc_start: 0.6224 (t80) cc_final: 0.5872 (t80) REVERT: D 220 LYS cc_start: 0.7038 (tttm) cc_final: 0.6834 (ttpp) REVERT: E 228 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7527 (mt-10) outliers start: 43 outliers final: 37 residues processed: 247 average time/residue: 0.1003 time to fit residues: 37.3089 Evaluate side-chains 247 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 281 TYR 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 541 THR 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 690 PHE Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 535 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 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 154 MET Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 228 GLU 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 81 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 275 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 147 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 7 optimal weight: 30.0000 chunk 36 optimal weight: 50.0000 chunk 130 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 50.0000 chunk 77 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 ** 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 = 0.4956 r_free = 0.4956 target = 0.243758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.225381 restraints weight = 22198.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.223614 restraints weight = 31031.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 82)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.222067 restraints weight = 28825.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.221467 restraints weight = 28187.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.221090 restraints weight = 24842.571| |-----------------------------------------------------------------------------| r_work (final): 0.4744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4750 r_free = 0.4750 target_work(ls_wunit_k1) = 0.221 | | 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) = 0.221 | | 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: 0.5831 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13075 Z= 0.224 Angle : 0.828 15.215 17902 Z= 0.397 Chirality : 0.047 0.390 2140 Planarity : 0.004 0.058 2336 Dihedral : 8.579 109.754 2402 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.24 % Favored : 94.65 % Rotamer: Outliers : 4.81 % Allowed : 32.71 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.20), residues: 1853 helix: 1.74 (0.15), residues: 1151 sheet: -1.64 (0.41), residues: 153 loop : -1.56 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 552 TYR 0.025 0.002 TYR C 509 PHE 0.031 0.002 PHE D 706 TRP 0.012 0.002 TRP D 302 HIS 0.009 0.001 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00500 (13046) covalent geometry : angle 0.79668 (17824) SS BOND : bond 0.00826 ( 9) SS BOND : angle 2.17170 ( 18) hydrogen bonds : bond 0.03591 ( 925) hydrogen bonds : angle 4.12998 ( 2740) link_ALPHA1-3 : bond 0.02523 ( 2) link_ALPHA1-3 : angle 5.14853 ( 6) link_ALPHA1-4 : bond 0.01212 ( 4) link_ALPHA1-4 : angle 2.85840 ( 12) link_ALPHA1-6 : bond 0.01301 ( 4) link_ALPHA1-6 : angle 1.88831 ( 12) link_BETA1-4 : bond 0.01042 ( 2) link_BETA1-4 : angle 6.64860 ( 6) link_NAG-ASN : bond 0.00855 ( 8) link_NAG-ASN : angle 3.51582 ( 24) *********************** 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 258 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 214 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 LEU cc_start: 0.5566 (pp) cc_final: 0.5016 (mt) REVERT: C 626 TYR cc_start: 0.6395 (t80) cc_final: 0.6082 (t80) REVERT: E 214 ILE cc_start: 0.6695 (mm) cc_final: 0.6046 (mm) REVERT: E 252 ARG cc_start: 0.6456 (mmp-170) cc_final: 0.6211 (mmm160) REVERT: F 43 PHE cc_start: 0.3497 (m-80) cc_final: 0.3124 (m-80) outliers start: 44 outliers final: 40 residues processed: 245 average time/residue: 0.1026 time to fit residues: 37.9441 Evaluate side-chains 252 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 229 LEU 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 541 THR Chi-restraints excluded: chain C residue 560 MET 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 690 PHE 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 330 SER Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 535 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 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 154 MET Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 220 LYS 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 81 LEU Chi-restraints excluded: chain F residue 259 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 15 optimal weight: 70.0000 chunk 27 optimal weight: 50.0000 chunk 66 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 82 optimal weight: 0.5980 chunk 22 optimal weight: 30.0000 chunk 62 optimal weight: 6.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- 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 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 HIS ** D 237 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** ** 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 = 0.4969 r_free = 0.4969 target = 0.245189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.227016 restraints weight = 22336.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.224294 restraints weight = 30795.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.222965 restraints weight = 29489.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.222317 restraints weight = 31752.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.221596 restraints weight = 28028.973| |-----------------------------------------------------------------------------| r_work (final): 0.4751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4753 r_free = 0.4753 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4753 r_free = 0.4753 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5825 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13075 Z= 0.183 Angle : 0.811 13.358 17902 Z= 0.389 Chirality : 0.046 0.379 2140 Planarity : 0.005 0.127 2336 Dihedral : 8.404 108.667 2402 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.59 % Favored : 95.25 % Rotamer: Outliers : 3.94 % Allowed : 33.81 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.20), residues: 1853 helix: 1.84 (0.15), residues: 1149 sheet: -1.65 (0.40), residues: 153 loop : -1.55 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 554 TYR 0.024 0.001 TYR C 523 PHE 0.043 0.002 PHE C 651 TRP 0.012 0.001 TRP C 482 HIS 0.009 0.001 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00407 (13046) covalent geometry : angle 0.78094 (17824) SS BOND : bond 0.00335 ( 9) SS BOND : angle 1.78094 ( 18) hydrogen bonds : bond 0.03381 ( 925) hydrogen bonds : angle 4.00380 ( 2740) link_ALPHA1-3 : bond 0.02843 ( 2) link_ALPHA1-3 : angle 5.19164 ( 6) link_ALPHA1-4 : bond 0.01287 ( 4) link_ALPHA1-4 : angle 2.87115 ( 12) link_ALPHA1-6 : bond 0.01386 ( 4) link_ALPHA1-6 : angle 1.75744 ( 12) link_BETA1-4 : bond 0.01079 ( 2) link_BETA1-4 : angle 6.52161 ( 6) link_NAG-ASN : bond 0.00780 ( 8) link_NAG-ASN : angle 3.49564 ( 24) ********************** 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 257 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 LEU cc_start: 0.5655 (pp) cc_final: 0.5084 (mt) REVERT: C 626 TYR cc_start: 0.6439 (t80) cc_final: 0.6107 (t80) REVERT: E 214 ILE cc_start: 0.6670 (mm) cc_final: 0.6019 (mm) outliers start: 36 outliers final: 34 residues processed: 246 average time/residue: 0.1013 time to fit residues: 37.8066 Evaluate side-chains 250 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 541 THR Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 690 PHE 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 330 SER Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 535 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 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 154 MET Chi-restraints excluded: chain E residue 186 THR 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 Chi-restraints excluded: chain F residue 260 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 46 optimal weight: 50.0000 chunk 161 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 90.0000 chunk 71 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 165 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 237 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** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 GLN ** 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 = 0.4966 r_free = 0.4966 target = 0.245156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.226804 restraints weight = 22262.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.225128 restraints weight = 31420.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.223581 restraints weight = 30238.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.222840 restraints weight = 30280.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.222168 restraints weight = 26123.584| |-----------------------------------------------------------------------------| r_work (final): 0.4753 ------------------------------------------------------------------------------- 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: 0.5805 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13075 Z= 0.175 Angle : 0.791 12.063 17902 Z= 0.378 Chirality : 0.046 0.364 2140 Planarity : 0.004 0.061 2336 Dihedral : 8.105 107.725 2402 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.13 % Favored : 94.71 % Rotamer: Outliers : 4.05 % Allowed : 33.37 % Favored : 62.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.20), residues: 1853 helix: 1.91 (0.15), residues: 1150 sheet: -1.49 (0.40), residues: 156 loop : -1.53 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 501 TYR 0.023 0.001 TYR C 281 PHE 0.048 0.002 PHE C 651 TRP 0.012 0.001 TRP C 482 HIS 0.008 0.001 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00385 (13046) covalent geometry : angle 0.76131 (17824) SS BOND : bond 0.00446 ( 9) SS BOND : angle 1.59590 ( 18) hydrogen bonds : bond 0.03309 ( 925) hydrogen bonds : angle 3.96357 ( 2740) link_ALPHA1-3 : bond 0.02785 ( 2) link_ALPHA1-3 : angle 5.15261 ( 6) link_ALPHA1-4 : bond 0.01241 ( 4) link_ALPHA1-4 : angle 2.91139 ( 12) link_ALPHA1-6 : bond 0.01421 ( 4) link_ALPHA1-6 : angle 1.71250 ( 12) link_BETA1-4 : bond 0.01081 ( 2) link_BETA1-4 : angle 6.47544 ( 6) link_NAG-ASN : bond 0.00778 ( 8) link_NAG-ASN : angle 3.44870 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2625.28 seconds wall clock time: 45 minutes 56.90 seconds (2756.90 seconds total)