Starting phenix.real_space_refine on Fri Jul 3 01:19:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dgs_27428/07_2026/8dgs_27428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dgs_27428/07_2026/8dgs_27428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dgs_27428/07_2026/8dgs_27428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dgs_27428/07_2026/8dgs_27428.map" model { file = "/net/cci-nas-00/data/ceres_data/8dgs_27428/07_2026/8dgs_27428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dgs_27428/07_2026/8dgs_27428.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dgs_27428/07_2026/8dgs_27428.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dgs_27428/07_2026/8dgs_27428.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.045 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: 9 Type Number sf(0) Gaussians I 1 10.91 5 Zn 2 6.06 5 P 11 5.49 5 Mg 2 5.21 5 S 66 5.16 5 C 6995 2.51 5 N 1905 2.21 5 O 2106 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11089 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3424 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 406} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2465 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2459 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 314, 2459 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 2498 Chain: "C" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1846 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 5, 'TRANS': 223} Chain: "D" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1833 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 223} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 1398 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1324 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 162} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 167, 1324 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 162} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1257 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' ZN': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' MG': 1, 'AGS': 1, 'LCJ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 733 SG CYS A 248 53.497 61.150 43.069 1.00 85.78 S ATOM 758 SG CYS A 251 56.058 63.787 42.201 1.00107.33 S ATOM 940 SG CYS A 272 57.047 60.027 41.972 1.00121.87 S ATOM 846 SG CYS A 261 43.870 52.039 42.561 1.00106.38 S ATOM 868 SG CYS A 264 43.355 53.941 45.755 1.00115.33 S ATOM 998 SG CYS A 280 43.643 50.219 46.131 1.00172.39 S Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N MET E 1 " occ=0.76 ... (3 atoms not shown) pdb=" CB MET E 1 " occ=0.76 residue: pdb=" N MET E 67 " occ=0.94 ... (6 atoms not shown) pdb=" CE MET E 67 " occ=0.94 residue: pdb=" N GLN E 70 " occ=0.97 ... (7 atoms not shown) pdb=" NE2 GLN E 70 " occ=0.97 residue: pdb=" N TYR E 71 " occ=0.84 ... (10 atoms not shown) pdb=" OH TYR E 71 " occ=0.84 residue: pdb=" N AGLN E 99 " occ=0.58 ... (16 atoms not shown) pdb=" NE2BGLN E 99 " occ=0.42 residue: pdb=" N GLU E 107 " occ=0.82 ... (7 atoms not shown) pdb=" OE2 GLU E 107 " occ=0.82 residue: pdb=" N GLN E 150 " occ=0.97 ... (7 atoms not shown) pdb=" NE2 GLN E 150 " occ=0.97 Time building chain proxies: 2.92, per 1000 atoms: 0.26 Number of scatterers: 11089 At special positions: 0 Unit cell: (83.3, 115.6, 129.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) I 1 52.95 Zn 2 29.99 S 66 16.00 P 11 15.00 Mg 2 11.99 F 1 9.00 O 2106 8.00 N 1905 7.00 C 6995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 442.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" ND1 HIS A 269 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 251 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 248 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 272 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" ND1 HIS A 235 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 261 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 264 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 280 " Number of angles added : 6 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2612 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 7 sheets defined 58.3% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 176 through 188 removed outlier: 4.622A pdb=" N LYS A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ALA A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.514A pdb=" N TRP A 216 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 removed outlier: 4.880A pdb=" N THR A 274 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 507 removed outlier: 3.948A pdb=" N LYS A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 543 removed outlier: 3.574A pdb=" N HIS A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 570 removed outlier: 3.542A pdb=" N MET A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 566 " --> pdb=" O GLN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 634 through 652 removed outlier: 3.629A pdb=" N ASP A 638 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 671 Processing helix chain 'A' and resid 686 through 697 removed outlier: 3.545A pdb=" N LYS A 690 " --> pdb=" O PRO A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 720 removed outlier: 3.547A pdb=" N ILE A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 removed outlier: 3.820A pdb=" N ILE A 724 " --> pdb=" O SER A 720 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 720 through 725' Processing helix chain 'B' and resid 43 through 59 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.622A pdb=" N GLN B 116 " --> pdb=" O ILE B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 151 through 159 Processing helix chain 'B' and resid 162 through 184 removed outlier: 3.567A pdb=" N LYS B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 212 through 221 removed outlier: 4.184A pdb=" N ASN B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 241 through 259 removed outlier: 4.318A pdb=" N ASP B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 309 through 319 Processing helix chain 'B' and resid 331 through 342 Processing helix chain 'B' and resid 351 through 357 removed outlier: 3.505A pdb=" N VAL B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 Processing helix chain 'B' and resid 370 through 380 Processing helix chain 'C' and resid 3 through 17 removed outlier: 3.626A pdb=" N GLN C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 32 removed outlier: 3.702A pdb=" N MET C 22 " --> pdb=" O ARG C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 70 removed outlier: 3.552A pdb=" N ARG C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 105 removed outlier: 4.236A pdb=" N GLN C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 131 Processing helix chain 'C' and resid 135 through 160 Processing helix chain 'C' and resid 164 through 182 Processing helix chain 'C' and resid 184 through 202 removed outlier: 3.733A pdb=" N GLU C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 229 Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 19 through 33 removed outlier: 4.020A pdb=" N GLY D 33 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 69 removed outlier: 3.567A pdb=" N LEU D 43 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR D 69 " --> pdb=" O ILE D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 104 removed outlier: 4.200A pdb=" N MET D 78 " --> pdb=" O ARG D 74 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 133 removed outlier: 4.034A pdb=" N VAL D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 160 removed outlier: 3.585A pdb=" N ARG D 138 " --> pdb=" O THR D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 181 Processing helix chain 'D' and resid 184 through 202 Processing helix chain 'D' and resid 208 through 211 removed outlier: 3.615A pdb=" N TYR D 211 " --> pdb=" O GLU D 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 208 through 211' Processing helix chain 'D' and resid 212 through 230 removed outlier: 4.352A pdb=" N SER D 230 " --> pdb=" O THR D 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing helix chain 'E' and resid 64 through 75 removed outlier: 3.626A pdb=" N THR E 74 " --> pdb=" O GLN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 92 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 151 through 167 Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 170 removed outlier: 4.783A pdb=" N VAL A 197 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 241 removed outlier: 3.769A pdb=" N LYS A 240 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY A 258 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 461 through 465 removed outlier: 6.921A pdb=" N ARG A 462 " --> pdb=" O LYS A 473 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS A 473 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY A 464 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 526 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 520 " --> pdb=" O ALA A 526 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 518 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLN A 530 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N PHE A 516 " --> pdb=" O GLN A 530 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 582 through 585 Processing sheet with id=AA5, first strand: chain 'B' and resid 68 through 76 removed outlier: 6.420A pdb=" N LYS B 84 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLU B 73 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL B 82 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLY B 75 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N GLY B 80 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.681A pdb=" N GLY B 149 " --> pdb=" O VAL B 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 37 through 46 removed outlier: 6.425A pdb=" N THR E 2 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASP E 54 " --> pdb=" O THR E 2 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR E 4 " --> pdb=" O ASP E 54 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU E 56 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU E 6 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N THR E 58 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL E 8 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE E 78 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL E 114 " --> pdb=" O PHE E 78 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N CYS E 80 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASN E 116 " --> pdb=" O CYS E 80 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE E 82 " --> pdb=" O ASN E 116 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ILE E 142 " --> pdb=" O MET E 111 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU E 113 " --> pdb=" O ILE E 142 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1794 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: 1.28 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 3718 1.37 - 1.55: 7464 1.55 - 1.74: 20 1.74 - 1.92: 103 1.92 - 2.11: 3 Bond restraints: 11308 Sorted by residual: bond pdb=" C18 LCJ B 803 " pdb=" N09 LCJ B 803 " ideal model delta sigma weight residual 1.349 1.451 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O2P SEP A 729 " pdb=" P SEP A 729 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" O3P SEP A 729 " pdb=" P SEP A 729 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" O1P SEP A 729 " pdb=" P SEP A 729 " ideal model delta sigma weight residual 1.610 1.512 0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" N3B GNP E 202 " pdb=" PG GNP E 202 " ideal model delta sigma weight residual 1.801 1.711 0.090 2.00e-02 2.50e+03 2.02e+01 ... (remaining 11303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 15132 2.61 - 5.23: 149 5.23 - 7.84: 15 7.84 - 10.45: 2 10.45 - 13.07: 3 Bond angle restraints: 15301 Sorted by residual: angle pdb=" CB GLN E 150 " pdb=" CG GLN E 150 " pdb=" CD GLN E 150 " ideal model delta sigma weight residual 112.60 123.32 -10.72 1.70e+00 3.46e-01 3.98e+01 angle pdb=" C HIS A 235 " pdb=" N ASN A 236 " pdb=" CA ASN A 236 " ideal model delta sigma weight residual 122.41 115.09 7.32 1.47e+00 4.63e-01 2.48e+01 angle pdb=" CA HIS A 235 " pdb=" CB HIS A 235 " pdb=" CG HIS A 235 " ideal model delta sigma weight residual 113.80 118.41 -4.61 1.00e+00 1.00e+00 2.12e+01 angle pdb=" C21 LCJ B 803 " pdb=" C23 LCJ B 803 " pdb=" I01 LCJ B 803 " ideal model delta sigma weight residual 119.32 132.39 -13.07 3.00e+00 1.11e-01 1.90e+01 angle pdb=" CA HIS A 235 " pdb=" C HIS A 235 " pdb=" O HIS A 235 " ideal model delta sigma weight residual 121.58 116.81 4.77 1.16e+00 7.43e-01 1.69e+01 ... (remaining 15296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 6448 16.69 - 33.39: 341 33.39 - 50.08: 97 50.08 - 66.77: 27 66.77 - 83.46: 6 Dihedral angle restraints: 6919 sinusoidal: 2868 harmonic: 4051 Sorted by residual: dihedral pdb=" C HIS A 235 " pdb=" N HIS A 235 " pdb=" CA HIS A 235 " pdb=" CB HIS A 235 " ideal model delta harmonic sigma weight residual -122.60 -112.74 -9.86 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" CA THR E 35 " pdb=" C THR E 35 " pdb=" N ILE E 36 " pdb=" CA ILE E 36 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA THR E 144 " pdb=" C THR E 144 " pdb=" N SER E 145 " pdb=" CA SER E 145 " ideal model delta harmonic sigma weight residual 180.00 162.91 17.09 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 6916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1511 0.075 - 0.151: 169 0.151 - 0.226: 14 0.226 - 0.302: 2 0.302 - 0.377: 1 Chirality restraints: 1697 Sorted by residual: chirality pdb=" CA HIS A 235 " pdb=" N HIS A 235 " pdb=" C HIS A 235 " pdb=" CB HIS A 235 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA CYS E 51 " pdb=" N CYS E 51 " pdb=" C CYS E 51 " pdb=" CB CYS E 51 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ARG E 149 " pdb=" N ARG E 149 " pdb=" C ARG E 149 " pdb=" CB ARG E 149 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1694 not shown) Planarity restraints: 1952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 78 " -0.026 2.00e-02 2.50e+03 1.60e-02 4.51e+00 pdb=" CG PHE E 78 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE E 78 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE E 78 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE E 78 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE E 78 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE E 78 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 707 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO A 708 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 708 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 708 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 235 " 0.019 2.00e-02 2.50e+03 1.57e-02 3.72e+00 pdb=" CG HIS A 235 " -0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS A 235 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS A 235 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS A 235 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS A 235 " 0.001 2.00e-02 2.50e+03 ... (remaining 1949 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.56: 136 2.56 - 3.16: 9541 3.16 - 3.76: 18438 3.76 - 4.36: 25049 4.36 - 4.96: 40404 Nonbonded interactions: 93568 Sorted by model distance: nonbonded pdb=" OD1 ASN A 163 " pdb=" NH1 ARG E 41 " model vdw 1.957 3.120 nonbonded pdb=" O3B AGS B 801 " pdb="MG MG B 802 " model vdw 1.978 2.170 nonbonded pdb=" O2A AGS B 801 " pdb="MG MG B 802 " model vdw 1.996 2.170 nonbonded pdb="MG MG E 201 " pdb=" O2G GNP E 202 " model vdw 2.027 2.170 nonbonded pdb="MG MG E 201 " pdb=" O2B GNP E 202 " model vdw 2.031 2.170 ... (remaining 93563 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 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG )) or resid 6 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 through 201 or (resid \ 202 and (name N or name CA or name C or name O or name CB )) or resid 203 throug \ h 230)) selection = chain 'D' } 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=0.16 max=1.00 mean=0.99 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: 2.440 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.260 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 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 : 0.005 0.111 11318 Z= 0.254 Angle : 0.674 13.066 15307 Z= 0.372 Chirality : 0.048 0.377 1697 Planarity : 0.003 0.049 1952 Dihedral : 11.848 83.463 4307 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.73 % Allowed : 6.64 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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 are not related in a simple way. whole: 1.74 (0.23), residues: 1360 helix: 2.41 (0.19), residues: 729 sheet: 0.09 (0.44), residues: 140 loop : -0.45 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 161 TYR 0.024 0.002 TYR E 96 PHE 0.026 0.002 PHE E 78 TRP 0.008 0.001 TRP A 531 HIS 0.010 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.25 (11308) covalent geometry : angle 0.66851 / 0.37 (15301) hydrogen bonds : bond 0.14508 / 9.89 ( 615) hydrogen bonds : angle 5.60505 / 3.95 ( 1794) metal coordination : bond 0.04193 / 2.67 ( 8) metal coordination : angle 4.29950 / 3.04 ( 6) Misc. bond : bond 0.00035 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 320 time to evaluate : 0.321 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 195 CYS cc_start: 0.4824 (m) cc_final: 0.3453 (m) REVERT: A 249 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7817 (t0) REVERT: A 255 LEU cc_start: 0.9085 (tp) cc_final: 0.8665 (tp) REVERT: A 517 MET cc_start: 0.8415 (mmm) cc_final: 0.8026 (mmm) REVERT: A 594 ASP cc_start: 0.8171 (t0) cc_final: 0.7777 (t0) REVERT: A 604 TRP cc_start: 0.8383 (m-10) cc_final: 0.8146 (m-10) REVERT: A 695 GLU cc_start: 0.8592 (mt-10) cc_final: 0.7891 (tt0) REVERT: B 115 LEU cc_start: 0.9783 (mt) cc_final: 0.9517 (pp) REVERT: B 157 LYS cc_start: 0.9559 (mttt) cc_final: 0.9310 (ptpp) REVERT: B 187 MET cc_start: 0.5603 (OUTLIER) cc_final: 0.4999 (ptm) REVERT: B 188 HIS cc_start: 0.5123 (t-90) cc_final: 0.4290 (t-170) REVERT: B 342 LEU cc_start: 0.8843 (mt) cc_final: 0.8551 (mt) REVERT: C 68 LYS cc_start: 0.9536 (OUTLIER) cc_final: 0.9323 (tptp) REVERT: C 93 ILE cc_start: 0.9672 (mt) cc_final: 0.9414 (pt) REVERT: C 150 GLN cc_start: 0.9526 (mm-40) cc_final: 0.9035 (mm-40) REVERT: C 190 GLN cc_start: 0.9338 (tt0) cc_final: 0.8999 (mt0) REVERT: C 207 ASN cc_start: 0.9524 (OUTLIER) cc_final: 0.9158 (p0) REVERT: C 215 THR cc_start: 0.9181 (t) cc_final: 0.8968 (p) REVERT: C 220 LEU cc_start: 0.9748 (mt) cc_final: 0.9525 (mt) REVERT: D 15 GLN cc_start: 0.9300 (mm-40) cc_final: 0.9090 (mm-40) REVERT: D 22 MET cc_start: 0.8917 (ttp) cc_final: 0.8700 (ttp) REVERT: D 50 ASN cc_start: 0.9280 (m110) cc_final: 0.8978 (m-40) REVERT: D 62 ILE cc_start: 0.9496 (mm) cc_final: 0.9287 (tt) REVERT: D 94 CYS cc_start: 0.9175 (m) cc_final: 0.8914 (p) REVERT: D 95 TYR cc_start: 0.8903 (m-10) cc_final: 0.8457 (m-10) REVERT: D 100 LEU cc_start: 0.9386 (tt) cc_final: 0.8947 (mt) REVERT: D 121 MET cc_start: 0.9541 (mtp) cc_final: 0.9096 (mmm) REVERT: D 147 LYS cc_start: 0.9640 (mttt) cc_final: 0.9023 (tppt) REVERT: D 150 GLN cc_start: 0.9133 (mt0) cc_final: 0.8903 (mm-40) REVERT: D 178 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.9001 (m-10) REVERT: D 218 MET cc_start: 0.8968 (mtm) cc_final: 0.8736 (mtm) REVERT: D 221 LEU cc_start: 0.9748 (mt) cc_final: 0.9490 (mt) REVERT: D 222 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7891 (ttp-170) outliers start: 42 outliers final: 12 residues processed: 348 average time/residue: 0.0996 time to fit residues: 47.4008 Evaluate side-chains 202 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 78 ASN B 236 GLN D 224 ASN E 70 GLN E 99 GLN A Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.081397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.048858 restraints weight = 173657.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.052205 restraints weight = 55921.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.054372 restraints weight = 29734.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.055844 restraints weight = 19571.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.056755 restraints weight = 14762.019| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (11 function evaluations) r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11318 Z= 0.166 Angle : 0.639 7.273 15307 Z= 0.332 Chirality : 0.044 0.199 1697 Planarity : 0.004 0.043 1952 Dihedral : 6.149 55.982 1555 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.50 % Allowed : 2.57 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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 are not related in a simple way. whole: 1.47 (0.23), residues: 1360 helix: 1.94 (0.19), residues: 735 sheet: 0.31 (0.48), residues: 122 loop : -0.25 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 127 TYR 0.042 0.002 TYR E 157 PHE 0.039 0.002 PHE B 334 TRP 0.023 0.002 TRP B 247 HIS 0.005 0.001 HIS A 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (11308) covalent geometry : angle 0.63436 / 0.33 (15301) hydrogen bonds : bond 0.04545 / 3.02 ( 615) hydrogen bonds : angle 4.69254 / 3.22 ( 1794) metal coordination : bond 0.01296 / 0.75 ( 8) metal coordination : angle 4.03980 / 2.14 ( 6) Misc. bond : bond 0.00536 / 0.36 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.265 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 CYS cc_start: 0.3504 (m) cc_final: 0.2870 (m) REVERT: A 210 TRP cc_start: 0.3491 (m100) cc_final: 0.2610 (m100) REVERT: A 249 ASP cc_start: 0.8553 (m-30) cc_final: 0.8244 (t70) REVERT: A 255 LEU cc_start: 0.9396 (tp) cc_final: 0.9005 (tp) REVERT: A 268 PHE cc_start: 0.8625 (p90) cc_final: 0.8327 (p90) REVERT: A 555 ASP cc_start: 0.9346 (t0) cc_final: 0.9079 (t0) REVERT: A 594 ASP cc_start: 0.8194 (t0) cc_final: 0.7507 (t0) REVERT: A 604 TRP cc_start: 0.8292 (m-10) cc_final: 0.8015 (m-10) REVERT: A 617 ILE cc_start: 0.9346 (pt) cc_final: 0.9076 (pt) REVERT: A 668 MET cc_start: 0.8957 (tpp) cc_final: 0.8219 (tpp) REVERT: A 695 GLU cc_start: 0.9453 (mt-10) cc_final: 0.8706 (tt0) REVERT: A 698 LYS cc_start: 0.9119 (mmtp) cc_final: 0.8838 (mtpt) REVERT: B 143 MET cc_start: 0.9134 (ptp) cc_final: 0.8730 (pmm) REVERT: B 146 MET cc_start: 0.8575 (mmm) cc_final: 0.7934 (mmt) REVERT: B 230 MET cc_start: 0.8023 (tpp) cc_final: 0.7736 (tpp) REVERT: B 313 LEU cc_start: 0.9572 (mt) cc_final: 0.8905 (mt) REVERT: B 316 TYR cc_start: 0.9244 (t80) cc_final: 0.9036 (t80) REVERT: B 345 ASN cc_start: 0.8921 (t0) cc_final: 0.8507 (t0) REVERT: C 121 MET cc_start: 0.9383 (mtp) cc_final: 0.9149 (mtp) REVERT: C 202 GLU cc_start: 0.8543 (mp0) cc_final: 0.8339 (mp0) REVERT: C 208 GLU cc_start: 0.8901 (tt0) cc_final: 0.8625 (tm-30) REVERT: D 14 GLU cc_start: 0.9532 (tm-30) cc_final: 0.9245 (tm-30) REVERT: D 50 ASN cc_start: 0.9426 (m110) cc_final: 0.9079 (m-40) REVERT: D 95 TYR cc_start: 0.9053 (m-10) cc_final: 0.8760 (m-10) REVERT: D 100 LEU cc_start: 0.9227 (tt) cc_final: 0.8684 (mt) REVERT: D 121 MET cc_start: 0.9622 (mtp) cc_final: 0.9025 (mmm) REVERT: D 147 LYS cc_start: 0.9621 (mttt) cc_final: 0.9154 (tppt) REVERT: D 149 TYR cc_start: 0.8819 (m-10) cc_final: 0.8495 (m-80) REVERT: D 153 PHE cc_start: 0.9331 (t80) cc_final: 0.8918 (t80) REVERT: D 218 MET cc_start: 0.9308 (mtm) cc_final: 0.8980 (mtm) REVERT: D 219 GLN cc_start: 0.8919 (tp40) cc_final: 0.8631 (tm-30) REVERT: E 20 THR cc_start: 0.9159 (m) cc_final: 0.8952 (p) REVERT: E 23 LEU cc_start: 0.8169 (mt) cc_final: 0.7963 (mt) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.0848 time to fit residues: 27.2631 Evaluate side-chains 159 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 49 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.079983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.047713 restraints weight = 187873.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.051072 restraints weight = 56154.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.053257 restraints weight = 29186.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.054777 restraints weight = 19071.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.055696 restraints weight = 14283.522| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (14 function evaluations) r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11318 Z= 0.175 Angle : 0.621 12.302 15307 Z= 0.322 Chirality : 0.043 0.189 1697 Planarity : 0.004 0.040 1952 Dihedral : 6.028 57.874 1555 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.50 % Allowed : 3.07 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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 are not related in a simple way. whole: 1.40 (0.23), residues: 1360 helix: 1.88 (0.19), residues: 738 sheet: 0.14 (0.43), residues: 137 loop : -0.27 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 127 TYR 0.033 0.002 TYR E 157 PHE 0.028 0.002 PHE C 174 TRP 0.015 0.001 TRP B 247 HIS 0.015 0.002 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (11308) covalent geometry : angle 0.61523 / 0.32 (15301) hydrogen bonds : bond 0.04236 / 2.81 ( 615) hydrogen bonds : angle 4.60238 / 3.15 ( 1794) metal coordination : bond 0.01108 / 0.71 ( 8) metal coordination : angle 4.29114 / 2.26 ( 6) Misc. bond : bond 0.00364 / 0.24 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.449 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 ASP cc_start: 0.8597 (m-30) cc_final: 0.8169 (t70) REVERT: A 555 ASP cc_start: 0.9272 (t0) cc_final: 0.8960 (t0) REVERT: A 604 TRP cc_start: 0.8282 (m-10) cc_final: 0.8024 (m-10) REVERT: A 668 MET cc_start: 0.9027 (tpp) cc_final: 0.8200 (tpp) REVERT: A 689 MET cc_start: 0.8607 (ttm) cc_final: 0.8057 (ttt) REVERT: A 698 LYS cc_start: 0.9094 (mmtp) cc_final: 0.8830 (mtpt) REVERT: B 143 MET cc_start: 0.9135 (ptp) cc_final: 0.8752 (pmm) REVERT: B 146 MET cc_start: 0.8755 (mmm) cc_final: 0.8241 (mmt) REVERT: B 214 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8855 (tm-30) REVERT: B 345 ASN cc_start: 0.8876 (t0) cc_final: 0.8503 (t0) REVERT: C 14 GLU cc_start: 0.9248 (pp20) cc_final: 0.8843 (pp20) REVERT: C 22 MET cc_start: 0.9030 (ttm) cc_final: 0.8679 (ttp) REVERT: C 121 MET cc_start: 0.9373 (mtp) cc_final: 0.9140 (mtp) REVERT: C 194 GLN cc_start: 0.9215 (tp-100) cc_final: 0.8980 (tp-100) REVERT: C 202 GLU cc_start: 0.8560 (mp0) cc_final: 0.8333 (mp0) REVERT: C 208 GLU cc_start: 0.8951 (tt0) cc_final: 0.8720 (tm-30) REVERT: D 50 ASN cc_start: 0.9415 (m110) cc_final: 0.9202 (m110) REVERT: D 95 TYR cc_start: 0.9105 (m-10) cc_final: 0.8785 (m-10) REVERT: D 121 MET cc_start: 0.9642 (mtp) cc_final: 0.9022 (mmm) REVERT: D 147 LYS cc_start: 0.9607 (mttt) cc_final: 0.9201 (tppt) REVERT: D 167 ARG cc_start: 0.9091 (ttt180) cc_final: 0.8631 (ttm-80) REVERT: D 174 PHE cc_start: 0.9112 (t80) cc_final: 0.8901 (t80) REVERT: D 218 MET cc_start: 0.9339 (mtm) cc_final: 0.9011 (mtm) REVERT: D 219 GLN cc_start: 0.8927 (tp40) cc_final: 0.8636 (tm-30) REVERT: D 221 LEU cc_start: 0.9748 (mt) cc_final: 0.9547 (mt) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.0879 time to fit residues: 25.5581 Evaluate side-chains 158 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 106 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 47 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 127 optimal weight: 0.3980 overall best weight: 1.6864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 HIS ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.080022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.047564 restraints weight = 203271.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.051045 restraints weight = 57755.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.053403 restraints weight = 29783.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.054910 restraints weight = 19189.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.055904 restraints weight = 14262.861| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11318 Z= 0.138 Angle : 0.580 10.721 15307 Z= 0.301 Chirality : 0.042 0.191 1697 Planarity : 0.004 0.064 1952 Dihedral : 5.917 58.731 1555 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.41 % Allowed : 2.16 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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 are not related in a simple way. whole: 1.42 (0.23), residues: 1360 helix: 1.92 (0.19), residues: 735 sheet: 0.14 (0.43), residues: 130 loop : -0.27 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 167 TYR 0.029 0.002 TYR E 157 PHE 0.041 0.002 PHE E 156 TRP 0.016 0.001 TRP B 247 HIS 0.007 0.001 HIS E 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (11308) covalent geometry : angle 0.57562 / 0.30 (15301) hydrogen bonds : bond 0.03945 / 2.60 ( 615) hydrogen bonds : angle 4.45596 / 3.04 ( 1794) metal coordination : bond 0.00708 / 0.40 ( 8) metal coordination : angle 3.57661 / 1.84 ( 6) Misc. bond : bond 0.00041 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.339 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 ASP cc_start: 0.8332 (m-30) cc_final: 0.8068 (t70) REVERT: A 555 ASP cc_start: 0.9279 (t0) cc_final: 0.8955 (t0) REVERT: A 604 TRP cc_start: 0.8326 (m-10) cc_final: 0.8108 (m-10) REVERT: A 668 MET cc_start: 0.9027 (tpp) cc_final: 0.8193 (tpp) REVERT: A 689 MET cc_start: 0.8551 (ttm) cc_final: 0.8127 (ttm) REVERT: A 698 LYS cc_start: 0.9111 (mmtp) cc_final: 0.8803 (mtpt) REVERT: B 143 MET cc_start: 0.8986 (ptp) cc_final: 0.8513 (pmm) REVERT: B 146 MET cc_start: 0.9093 (mmm) cc_final: 0.8474 (mmt) REVERT: B 187 MET cc_start: 0.6396 (mmp) cc_final: 0.6188 (mmm) REVERT: B 230 MET cc_start: 0.8054 (tpp) cc_final: 0.7792 (tpp) REVERT: B 316 TYR cc_start: 0.9217 (t80) cc_final: 0.8514 (t80) REVERT: B 345 ASN cc_start: 0.8860 (t0) cc_final: 0.8480 (t0) REVERT: C 14 GLU cc_start: 0.9203 (pp20) cc_final: 0.8883 (pp20) REVERT: C 22 MET cc_start: 0.8960 (ttm) cc_final: 0.8513 (ttp) REVERT: C 121 MET cc_start: 0.9368 (mtp) cc_final: 0.9125 (mtp) REVERT: C 194 GLN cc_start: 0.9173 (tp-100) cc_final: 0.8920 (tp-100) REVERT: C 202 GLU cc_start: 0.8580 (mp0) cc_final: 0.8363 (mp0) REVERT: C 208 GLU cc_start: 0.8969 (tt0) cc_final: 0.8715 (tm-30) REVERT: C 218 MET cc_start: 0.9562 (ptp) cc_final: 0.9004 (ttt) REVERT: D 14 GLU cc_start: 0.9509 (tm-30) cc_final: 0.9206 (tm-30) REVERT: D 26 MET cc_start: 0.9278 (mmm) cc_final: 0.8963 (mmm) REVERT: D 50 ASN cc_start: 0.9386 (m110) cc_final: 0.9151 (m110) REVERT: D 95 TYR cc_start: 0.9110 (m-10) cc_final: 0.8792 (m-10) REVERT: D 121 MET cc_start: 0.9625 (mtp) cc_final: 0.9006 (mmm) REVERT: D 147 LYS cc_start: 0.9650 (mttt) cc_final: 0.9132 (tppt) REVERT: D 167 ARG cc_start: 0.8970 (ttt180) cc_final: 0.8674 (ttt90) REVERT: D 174 PHE cc_start: 0.9065 (t80) cc_final: 0.8830 (t80) REVERT: D 218 MET cc_start: 0.9339 (mtm) cc_final: 0.9001 (mtm) REVERT: D 219 GLN cc_start: 0.8942 (tp40) cc_final: 0.8628 (tm-30) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.0855 time to fit residues: 24.0305 Evaluate side-chains 153 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 4 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 HIS ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN C 8 GLN C 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.076848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.045119 restraints weight = 206251.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.048355 restraints weight = 61288.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.050488 restraints weight = 32042.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.051892 restraints weight = 21016.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.052874 restraints weight = 15806.874| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (15 function evaluations) r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11318 Z= 0.268 Angle : 0.713 12.694 15307 Z= 0.372 Chirality : 0.045 0.204 1697 Planarity : 0.005 0.045 1952 Dihedral : 6.184 59.806 1555 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.41 % Allowed : 2.57 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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 are not related in a simple way. whole: 0.81 (0.23), residues: 1360 helix: 1.38 (0.18), residues: 734 sheet: 0.02 (0.43), residues: 132 loop : -0.51 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 575 TYR 0.027 0.002 TYR C 178 PHE 0.027 0.003 PHE E 156 TRP 0.016 0.002 TRP A 450 HIS 0.008 0.002 HIS A 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.27 (11308) covalent geometry : angle 0.70372 / 0.37 (15301) hydrogen bonds : bond 0.04314 / 2.83 ( 615) hydrogen bonds : angle 4.79315 / 3.27 ( 1794) metal coordination : bond 0.01873 / 1.21 ( 8) metal coordination : angle 5.95533 / 3.35 ( 6) Misc. bond : bond 0.00071 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.402 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: A 195 CYS cc_start: 0.4351 (m) cc_final: 0.3731 (m) REVERT: A 210 TRP cc_start: 0.3794 (m100) cc_final: 0.2780 (m100) REVERT: A 555 ASP cc_start: 0.9326 (t0) cc_final: 0.9054 (t0) REVERT: A 594 ASP cc_start: 0.8952 (m-30) cc_final: 0.8643 (m-30) REVERT: A 604 TRP cc_start: 0.8382 (m-10) cc_final: 0.8162 (m-10) REVERT: A 668 MET cc_start: 0.9075 (tpp) cc_final: 0.8269 (tpp) REVERT: A 689 MET cc_start: 0.8491 (ttm) cc_final: 0.8281 (ttm) REVERT: B 143 MET cc_start: 0.8990 (ptp) cc_final: 0.8618 (pmm) REVERT: B 146 MET cc_start: 0.9080 (mmm) cc_final: 0.8491 (mmt) REVERT: B 187 MET cc_start: 0.6423 (mmp) cc_final: 0.6152 (mmm) REVERT: B 308 MET cc_start: 0.8031 (tmm) cc_final: 0.5894 (tpp) REVERT: B 313 LEU cc_start: 0.9561 (mt) cc_final: 0.9263 (mt) REVERT: B 316 TYR cc_start: 0.9228 (t80) cc_final: 0.8553 (t80) REVERT: B 345 ASN cc_start: 0.8792 (t0) cc_final: 0.8452 (t0) REVERT: C 22 MET cc_start: 0.9061 (ttm) cc_final: 0.8703 (ttp) REVERT: C 121 MET cc_start: 0.9360 (mtp) cc_final: 0.9016 (mtp) REVERT: C 194 GLN cc_start: 0.9145 (tp-100) cc_final: 0.8876 (tp-100) REVERT: C 202 GLU cc_start: 0.8631 (mp0) cc_final: 0.8402 (mp0) REVERT: D 14 GLU cc_start: 0.9522 (tm-30) cc_final: 0.9242 (tm-30) REVERT: D 26 MET cc_start: 0.9309 (mmm) cc_final: 0.8605 (mmm) REVERT: D 95 TYR cc_start: 0.9097 (m-10) cc_final: 0.8814 (m-10) REVERT: D 121 MET cc_start: 0.9681 (mtp) cc_final: 0.9039 (mmm) REVERT: D 147 LYS cc_start: 0.9641 (mttt) cc_final: 0.9186 (tppt) REVERT: D 150 GLN cc_start: 0.9248 (mt0) cc_final: 0.8839 (tp-100) REVERT: D 167 ARG cc_start: 0.8996 (ttt180) cc_final: 0.8693 (ttt90) REVERT: D 174 PHE cc_start: 0.9089 (t80) cc_final: 0.8884 (t80) REVERT: D 217 ILE cc_start: 0.9587 (mm) cc_final: 0.9038 (tp) REVERT: D 218 MET cc_start: 0.9376 (mtm) cc_final: 0.9091 (mtm) REVERT: D 219 GLN cc_start: 0.9018 (tp40) cc_final: 0.8454 (tp40) REVERT: D 221 LEU cc_start: 0.9739 (mt) cc_final: 0.9507 (mt) REVERT: E 111 MET cc_start: 0.4098 (mtt) cc_final: 0.3344 (tpp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.0765 time to fit residues: 20.5889 Evaluate side-chains 138 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 80 optimal weight: 0.0010 chunk 101 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 HIS ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.078267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.047481 restraints weight = 202016.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.051568 restraints weight = 62670.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.052952 restraints weight = 27501.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.054084 restraints weight = 17292.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.054249 restraints weight = 15310.279| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11318 Z= 0.184 Angle : 0.643 11.683 15307 Z= 0.330 Chirality : 0.044 0.271 1697 Planarity : 0.004 0.036 1952 Dihedral : 6.100 58.611 1555 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.41 % Allowed : 2.16 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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 are not related in a simple way. whole: 0.97 (0.23), residues: 1360 helix: 1.61 (0.19), residues: 733 sheet: -0.10 (0.42), residues: 132 loop : -0.55 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.023 0.002 TYR E 157 PHE 0.028 0.002 PHE E 156 TRP 0.015 0.001 TRP B 247 HIS 0.009 0.002 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (11308) covalent geometry : angle 0.62943 / 0.33 (15301) hydrogen bonds : bond 0.04094 / 2.73 ( 615) hydrogen bonds : angle 4.61616 / 3.14 ( 1794) metal coordination : bond 0.01463 / 0.86 ( 8) metal coordination : angle 6.68281 / 3.78 ( 6) Misc. bond : bond 0.00402 / 0.27 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.370 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: symmetry clash REVERT: A 187 MET cc_start: 0.8933 (mmp) cc_final: 0.8709 (mmp) REVERT: A 249 ASP cc_start: 0.8280 (t70) cc_final: 0.7843 (t0) REVERT: A 255 LEU cc_start: 0.9383 (tp) cc_final: 0.9107 (tp) REVERT: A 555 ASP cc_start: 0.9329 (t0) cc_final: 0.9027 (t0) REVERT: A 594 ASP cc_start: 0.8842 (m-30) cc_final: 0.8522 (m-30) REVERT: A 627 MET cc_start: 0.8878 (mmm) cc_final: 0.8648 (mmt) REVERT: A 668 MET cc_start: 0.9039 (tpp) cc_final: 0.8245 (tpp) REVERT: A 699 LYS cc_start: 0.8802 (mttp) cc_final: 0.8566 (tmtt) REVERT: A 713 SER cc_start: 0.9478 (m) cc_final: 0.9247 (m) REVERT: B 143 MET cc_start: 0.9032 (ptp) cc_final: 0.8580 (pmm) REVERT: B 146 MET cc_start: 0.9070 (mmm) cc_final: 0.8503 (mmt) REVERT: B 187 MET cc_start: 0.6423 (mmp) cc_final: 0.6156 (mmm) REVERT: B 230 MET cc_start: 0.8066 (tpp) cc_final: 0.7845 (tpp) REVERT: C 22 MET cc_start: 0.9021 (ttm) cc_final: 0.8727 (ttp) REVERT: C 121 MET cc_start: 0.9352 (mtp) cc_final: 0.9002 (mtp) REVERT: C 194 GLN cc_start: 0.9178 (tp-100) cc_final: 0.8895 (tp-100) REVERT: C 202 GLU cc_start: 0.8630 (mp0) cc_final: 0.8421 (mp0) REVERT: D 14 GLU cc_start: 0.9534 (tm-30) cc_final: 0.9253 (tm-30) REVERT: D 26 MET cc_start: 0.9250 (mmm) cc_final: 0.8992 (mmm) REVERT: D 94 CYS cc_start: 0.9255 (m) cc_final: 0.9054 (p) REVERT: D 95 TYR cc_start: 0.9119 (m-10) cc_final: 0.8695 (m-10) REVERT: D 100 LEU cc_start: 0.9340 (tt) cc_final: 0.8612 (mt) REVERT: D 121 MET cc_start: 0.9658 (mtp) cc_final: 0.9010 (mmm) REVERT: D 147 LYS cc_start: 0.9622 (mttt) cc_final: 0.9145 (tppt) REVERT: D 150 GLN cc_start: 0.9248 (mt0) cc_final: 0.8842 (tp-100) REVERT: D 217 ILE cc_start: 0.9575 (mm) cc_final: 0.8996 (tp) REVERT: D 218 MET cc_start: 0.9314 (mtm) cc_final: 0.9038 (mtm) REVERT: D 219 GLN cc_start: 0.9012 (tp40) cc_final: 0.8377 (tp-100) REVERT: D 221 LEU cc_start: 0.9740 (mt) cc_final: 0.9487 (mt) REVERT: E 111 MET cc_start: 0.4088 (mtt) cc_final: 0.3383 (tpp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0846 time to fit residues: 23.2642 Evaluate side-chains 139 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 65 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 HIS ** B 188 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 = 0.3515 r_free = 0.3515 target = 0.078033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.046377 restraints weight = 210420.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.049702 restraints weight = 58196.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.051858 restraints weight = 29891.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.053377 restraints weight = 19494.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.054260 restraints weight = 14526.403| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11318 Z= 0.172 Angle : 0.620 10.441 15307 Z= 0.324 Chirality : 0.043 0.171 1697 Planarity : 0.004 0.037 1952 Dihedral : 6.028 58.423 1555 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.41 % Allowed : 1.66 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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 are not related in a simple way. whole: 1.03 (0.23), residues: 1360 helix: 1.66 (0.19), residues: 733 sheet: 0.07 (0.44), residues: 121 loop : -0.58 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.023 0.002 TYR E 157 PHE 0.020 0.002 PHE D 177 TRP 0.055 0.002 TRP A 604 HIS 0.008 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (11308) covalent geometry : angle 0.60978 / 0.32 (15301) hydrogen bonds : bond 0.03948 / 2.61 ( 615) hydrogen bonds : angle 4.56979 / 3.10 ( 1794) metal coordination : bond 0.01452 / 0.91 ( 8) metal coordination : angle 5.79503 / 3.26 ( 6) Misc. bond : bond 0.00116 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.318 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: A 255 LEU cc_start: 0.9400 (tp) cc_final: 0.9138 (tp) REVERT: A 555 ASP cc_start: 0.9320 (t0) cc_final: 0.9041 (t0) REVERT: A 565 ASP cc_start: 0.9021 (t70) cc_final: 0.8672 (t70) REVERT: A 594 ASP cc_start: 0.8826 (m-30) cc_final: 0.8553 (m-30) REVERT: A 668 MET cc_start: 0.9049 (tpp) cc_final: 0.8260 (tpp) REVERT: A 699 LYS cc_start: 0.8836 (mttp) cc_final: 0.8590 (tmtt) REVERT: A 713 SER cc_start: 0.9502 (m) cc_final: 0.9286 (m) REVERT: B 143 MET cc_start: 0.8841 (ptp) cc_final: 0.8356 (pmm) REVERT: B 187 MET cc_start: 0.6462 (mmp) cc_final: 0.6180 (tpp) REVERT: B 230 MET cc_start: 0.8141 (tpp) cc_final: 0.7925 (tpp) REVERT: B 313 LEU cc_start: 0.9569 (mt) cc_final: 0.9309 (mt) REVERT: B 345 ASN cc_start: 0.9126 (t0) cc_final: 0.8687 (p0) REVERT: C 22 MET cc_start: 0.9000 (ttm) cc_final: 0.8670 (ttp) REVERT: C 50 ASN cc_start: 0.9529 (m-40) cc_final: 0.9219 (t0) REVERT: C 121 MET cc_start: 0.9374 (mtp) cc_final: 0.9074 (mtp) REVERT: C 194 GLN cc_start: 0.9138 (tp-100) cc_final: 0.8835 (tp-100) REVERT: C 202 GLU cc_start: 0.8530 (mp0) cc_final: 0.8288 (mp0) REVERT: D 14 GLU cc_start: 0.9530 (tm-30) cc_final: 0.9277 (tm-30) REVERT: D 26 MET cc_start: 0.9311 (mmm) cc_final: 0.8928 (mmm) REVERT: D 50 ASN cc_start: 0.9469 (m-40) cc_final: 0.9129 (m-40) REVERT: D 95 TYR cc_start: 0.9099 (m-10) cc_final: 0.8657 (m-10) REVERT: D 100 LEU cc_start: 0.9295 (tt) cc_final: 0.8562 (mt) REVERT: D 121 MET cc_start: 0.9650 (mtp) cc_final: 0.9023 (mmm) REVERT: D 147 LYS cc_start: 0.9638 (mttt) cc_final: 0.9183 (tppt) REVERT: D 150 GLN cc_start: 0.9255 (mt0) cc_final: 0.8819 (tp-100) REVERT: D 217 ILE cc_start: 0.9576 (mm) cc_final: 0.8992 (tp) REVERT: D 218 MET cc_start: 0.9328 (mtm) cc_final: 0.9037 (mtm) REVERT: D 219 GLN cc_start: 0.9023 (tp40) cc_final: 0.8370 (tp-100) REVERT: D 221 LEU cc_start: 0.9735 (mt) cc_final: 0.9499 (mt) REVERT: E 111 MET cc_start: 0.3936 (mtt) cc_final: 0.3239 (tpp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0736 time to fit residues: 20.0183 Evaluate side-chains 145 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 47 optimal weight: 10.0000 chunk 12 optimal weight: 0.2980 chunk 88 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 128 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 HIS ** B 188 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 = 0.3551 r_free = 0.3551 target = 0.079753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.047501 restraints weight = 231118.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.050976 restraints weight = 60309.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.053252 restraints weight = 30308.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.054744 restraints weight = 19497.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.055714 restraints weight = 14494.942| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11318 Z= 0.120 Angle : 0.592 8.265 15307 Z= 0.308 Chirality : 0.042 0.176 1697 Planarity : 0.004 0.046 1952 Dihedral : 6.031 59.926 1555 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.41 % Allowed : 1.33 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: 1.16 (0.23), residues: 1360 helix: 1.82 (0.19), residues: 729 sheet: 0.08 (0.45), residues: 121 loop : -0.57 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 626 TYR 0.031 0.002 TYR C 82 PHE 0.025 0.002 PHE C 174 TRP 0.074 0.002 TRP A 604 HIS 0.005 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (11308) covalent geometry : angle 0.58483 / 0.31 (15301) hydrogen bonds : bond 0.03794 / 2.50 ( 615) hydrogen bonds : angle 4.47615 / 3.03 ( 1794) metal coordination : bond 0.00917 / 0.49 ( 8) metal coordination : angle 4.52919 / 2.41 ( 6) Misc. bond : bond 0.00148 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.357 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: A 254 LEU cc_start: 0.9637 (tp) cc_final: 0.9429 (tt) REVERT: A 255 LEU cc_start: 0.9383 (tp) cc_final: 0.9157 (tp) REVERT: A 554 ILE cc_start: 0.9427 (mm) cc_final: 0.9207 (mm) REVERT: A 555 ASP cc_start: 0.9281 (t0) cc_final: 0.9006 (t0) REVERT: A 565 ASP cc_start: 0.8998 (t70) cc_final: 0.8790 (t70) REVERT: A 594 ASP cc_start: 0.8750 (m-30) cc_final: 0.8511 (m-30) REVERT: A 640 TYR cc_start: 0.9490 (t80) cc_final: 0.9273 (t80) REVERT: A 668 MET cc_start: 0.9040 (tpp) cc_final: 0.8256 (tpp) REVERT: A 674 LEU cc_start: 0.9339 (tp) cc_final: 0.9088 (tp) REVERT: A 713 SER cc_start: 0.9435 (m) cc_final: 0.9184 (m) REVERT: B 143 MET cc_start: 0.8786 (ptp) cc_final: 0.8315 (pmm) REVERT: B 146 MET cc_start: 0.9090 (mmm) cc_final: 0.8483 (mmt) REVERT: B 187 MET cc_start: 0.6485 (mmp) cc_final: 0.6223 (tpp) REVERT: B 345 ASN cc_start: 0.9090 (t0) cc_final: 0.8624 (p0) REVERT: C 14 GLU cc_start: 0.9086 (pp20) cc_final: 0.8406 (pp20) REVERT: C 15 GLN cc_start: 0.8998 (pm20) cc_final: 0.8521 (pm20) REVERT: C 22 MET cc_start: 0.9028 (ttm) cc_final: 0.8575 (ttp) REVERT: C 50 ASN cc_start: 0.9481 (m-40) cc_final: 0.9112 (t0) REVERT: C 121 MET cc_start: 0.9360 (mtp) cc_final: 0.9105 (mtp) REVERT: C 150 GLN cc_start: 0.9247 (mm-40) cc_final: 0.9031 (mm110) REVERT: C 194 GLN cc_start: 0.9169 (tp-100) cc_final: 0.8860 (tp-100) REVERT: C 202 GLU cc_start: 0.8631 (mp0) cc_final: 0.8411 (mp0) REVERT: C 217 ILE cc_start: 0.9818 (mm) cc_final: 0.9581 (mm) REVERT: D 14 GLU cc_start: 0.9571 (tm-30) cc_final: 0.9269 (tm-30) REVERT: D 95 TYR cc_start: 0.8949 (m-10) cc_final: 0.8680 (m-10) REVERT: D 100 LEU cc_start: 0.9219 (tt) cc_final: 0.8496 (mt) REVERT: D 121 MET cc_start: 0.9629 (mtp) cc_final: 0.8972 (mmm) REVERT: D 147 LYS cc_start: 0.9617 (mttt) cc_final: 0.9134 (tppt) REVERT: D 150 GLN cc_start: 0.9222 (mt0) cc_final: 0.8789 (tp-100) REVERT: D 167 ARG cc_start: 0.8954 (ttt180) cc_final: 0.8545 (ttt180) REVERT: D 217 ILE cc_start: 0.9555 (mm) cc_final: 0.8939 (tp) REVERT: D 218 MET cc_start: 0.9281 (mtm) cc_final: 0.8992 (mtm) REVERT: D 219 GLN cc_start: 0.9028 (tp40) cc_final: 0.8556 (tm-30) REVERT: D 221 LEU cc_start: 0.9742 (mt) cc_final: 0.9521 (mt) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.0755 time to fit residues: 20.5392 Evaluate side-chains 147 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 HIS ** B 188 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 = 0.3546 r_free = 0.3546 target = 0.079587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.047554 restraints weight = 201284.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.050969 restraints weight = 57156.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.053221 restraints weight = 29372.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.054750 restraints weight = 19031.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.055730 restraints weight = 14066.385| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11318 Z= 0.134 Angle : 0.606 8.976 15307 Z= 0.317 Chirality : 0.043 0.177 1697 Planarity : 0.004 0.039 1952 Dihedral : 5.911 58.120 1555 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.41 % Allowed : 0.83 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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 are not related in a simple way. whole: 1.17 (0.23), residues: 1360 helix: 1.82 (0.19), residues: 734 sheet: 0.05 (0.44), residues: 122 loop : -0.57 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 181 TYR 0.029 0.002 TYR D 178 PHE 0.024 0.002 PHE D 174 TRP 0.055 0.002 TRP A 604 HIS 0.005 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (11308) covalent geometry : angle 0.59998 / 0.32 (15301) hydrogen bonds : bond 0.03818 / 2.52 ( 615) hydrogen bonds : angle 4.42568 / 3.00 ( 1794) metal coordination : bond 0.00674 / 0.32 ( 8) metal coordination : angle 4.18208 / 2.21 ( 6) Misc. bond : bond 0.00161 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.287 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: A 254 LEU cc_start: 0.9654 (tp) cc_final: 0.9418 (tt) REVERT: A 255 LEU cc_start: 0.9368 (tp) cc_final: 0.9045 (tp) REVERT: A 555 ASP cc_start: 0.9277 (t0) cc_final: 0.9006 (t0) REVERT: A 594 ASP cc_start: 0.8758 (m-30) cc_final: 0.8461 (m-30) REVERT: A 640 TYR cc_start: 0.9518 (t80) cc_final: 0.9307 (t80) REVERT: A 668 MET cc_start: 0.9044 (tpp) cc_final: 0.8226 (tpp) REVERT: A 674 LEU cc_start: 0.9370 (tp) cc_final: 0.9097 (tp) REVERT: A 713 SER cc_start: 0.9447 (m) cc_final: 0.9244 (m) REVERT: B 143 MET cc_start: 0.8750 (ptp) cc_final: 0.8295 (pmm) REVERT: B 146 MET cc_start: 0.9152 (mmm) cc_final: 0.8450 (mmt) REVERT: B 187 MET cc_start: 0.6406 (mmp) cc_final: 0.6192 (tpp) REVERT: B 345 ASN cc_start: 0.9090 (t0) cc_final: 0.8859 (t0) REVERT: C 14 GLU cc_start: 0.9031 (pp20) cc_final: 0.8337 (pp20) REVERT: C 15 GLN cc_start: 0.9014 (pm20) cc_final: 0.8427 (pm20) REVERT: C 22 MET cc_start: 0.8980 (ttm) cc_final: 0.8572 (ttp) REVERT: C 50 ASN cc_start: 0.9473 (m-40) cc_final: 0.9103 (t0) REVERT: C 121 MET cc_start: 0.9358 (mtp) cc_final: 0.9075 (mtp) REVERT: C 146 GLN cc_start: 0.9196 (tm-30) cc_final: 0.8921 (tm-30) REVERT: C 150 GLN cc_start: 0.9230 (mm-40) cc_final: 0.9013 (mm110) REVERT: C 194 GLN cc_start: 0.9116 (tp-100) cc_final: 0.8773 (tp-100) REVERT: C 202 GLU cc_start: 0.8578 (mp0) cc_final: 0.8339 (mp0) REVERT: C 223 ASP cc_start: 0.9358 (m-30) cc_final: 0.8994 (m-30) REVERT: D 14 GLU cc_start: 0.9515 (tm-30) cc_final: 0.9310 (tm-30) REVERT: D 22 MET cc_start: 0.9107 (mmm) cc_final: 0.8660 (tpp) REVERT: D 26 MET cc_start: 0.9152 (mmm) cc_final: 0.8710 (mmm) REVERT: D 50 ASN cc_start: 0.9328 (m110) cc_final: 0.9020 (m110) REVERT: D 95 TYR cc_start: 0.8940 (m-10) cc_final: 0.8670 (m-10) REVERT: D 100 LEU cc_start: 0.9226 (tt) cc_final: 0.8502 (mt) REVERT: D 121 MET cc_start: 0.9630 (mtp) cc_final: 0.8968 (mmm) REVERT: D 147 LYS cc_start: 0.9603 (mttt) cc_final: 0.9123 (tppt) REVERT: D 150 GLN cc_start: 0.9241 (mt0) cc_final: 0.8794 (tp-100) REVERT: D 217 ILE cc_start: 0.9571 (mm) cc_final: 0.8962 (tp) REVERT: D 218 MET cc_start: 0.9307 (mtm) cc_final: 0.9013 (mtm) REVERT: D 221 LEU cc_start: 0.9732 (mt) cc_final: 0.9517 (mt) REVERT: E 111 MET cc_start: 0.5711 (mmp) cc_final: 0.5178 (tpp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0774 time to fit residues: 20.4622 Evaluate side-chains 144 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 44 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 0.0170 chunk 54 optimal weight: 0.1980 chunk 64 optimal weight: 4.9990 overall best weight: 1.6424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 HIS ** B 188 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 = 0.3544 r_free = 0.3544 target = 0.079483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.047365 restraints weight = 212905.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.050787 restraints weight = 58951.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.053082 restraints weight = 30024.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.054608 restraints weight = 19370.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.055562 restraints weight = 14380.638| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11318 Z= 0.135 Angle : 0.615 9.330 15307 Z= 0.323 Chirality : 0.043 0.178 1697 Planarity : 0.004 0.039 1952 Dihedral : 5.818 54.343 1555 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.41 % Allowed : 0.83 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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 are not related in a simple way. whole: 1.14 (0.23), residues: 1360 helix: 1.81 (0.19), residues: 734 sheet: -0.02 (0.44), residues: 122 loop : -0.60 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 626 TYR 0.045 0.002 TYR E 157 PHE 0.028 0.002 PHE D 174 TRP 0.044 0.002 TRP A 604 HIS 0.008 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (11308) covalent geometry : angle 0.61002 / 0.32 (15301) hydrogen bonds : bond 0.03747 / 2.46 ( 615) hydrogen bonds : angle 4.42502 / 3.01 ( 1794) metal coordination : bond 0.00632 / 0.29 ( 8) metal coordination : angle 4.09665 / 2.18 ( 6) Misc. bond : bond 0.00350 / 0.23 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.436 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: symmetry clash revert: symmetry clash REVERT: A 254 LEU cc_start: 0.9653 (tp) cc_final: 0.9414 (tt) REVERT: A 255 LEU cc_start: 0.9295 (tp) cc_final: 0.9041 (tp) REVERT: A 555 ASP cc_start: 0.9286 (t0) cc_final: 0.9007 (t0) REVERT: A 594 ASP cc_start: 0.8727 (m-30) cc_final: 0.8467 (m-30) REVERT: A 640 TYR cc_start: 0.9517 (t80) cc_final: 0.9306 (t80) REVERT: A 668 MET cc_start: 0.9035 (tpp) cc_final: 0.8223 (tpp) REVERT: A 674 LEU cc_start: 0.9387 (tp) cc_final: 0.9117 (tp) REVERT: B 143 MET cc_start: 0.8665 (ptp) cc_final: 0.8291 (pmm) REVERT: B 146 MET cc_start: 0.9114 (mmm) cc_final: 0.8456 (mmt) REVERT: B 187 MET cc_start: 0.6581 (mmp) cc_final: 0.6381 (tpp) REVERT: B 230 MET cc_start: 0.7986 (tpp) cc_final: 0.6721 (tmm) REVERT: B 345 ASN cc_start: 0.9071 (t0) cc_final: 0.8661 (p0) REVERT: C 14 GLU cc_start: 0.9014 (pp20) cc_final: 0.8265 (pp20) REVERT: C 15 GLN cc_start: 0.9027 (pm20) cc_final: 0.8435 (pm20) REVERT: C 50 ASN cc_start: 0.9470 (m-40) cc_final: 0.9109 (t0) REVERT: C 121 MET cc_start: 0.9381 (mtp) cc_final: 0.9111 (mtp) REVERT: C 150 GLN cc_start: 0.9224 (mm-40) cc_final: 0.8989 (mm110) REVERT: C 194 GLN cc_start: 0.9154 (tp-100) cc_final: 0.8844 (tp-100) REVERT: C 202 GLU cc_start: 0.8617 (mp0) cc_final: 0.8396 (mp0) REVERT: C 223 ASP cc_start: 0.9310 (m-30) cc_final: 0.8930 (m-30) REVERT: D 22 MET cc_start: 0.9121 (mmm) cc_final: 0.8679 (tpp) REVERT: D 26 MET cc_start: 0.9132 (mmm) cc_final: 0.8683 (mmm) REVERT: D 50 ASN cc_start: 0.9335 (m110) cc_final: 0.9019 (m110) REVERT: D 95 TYR cc_start: 0.8935 (m-10) cc_final: 0.8680 (m-10) REVERT: D 100 LEU cc_start: 0.9246 (tt) cc_final: 0.8499 (mt) REVERT: D 121 MET cc_start: 0.9636 (mtp) cc_final: 0.8964 (mmm) REVERT: D 147 LYS cc_start: 0.9633 (mttt) cc_final: 0.9164 (tppt) REVERT: D 150 GLN cc_start: 0.9227 (mt0) cc_final: 0.8802 (tp-100) REVERT: D 173 ASN cc_start: 0.9295 (m-40) cc_final: 0.9014 (m-40) REVERT: D 218 MET cc_start: 0.9319 (mtm) cc_final: 0.9004 (mtm) REVERT: D 221 LEU cc_start: 0.9727 (mt) cc_final: 0.9523 (mt) REVERT: E 111 MET cc_start: 0.5830 (mmp) cc_final: 0.4701 (tpp) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.0788 time to fit residues: 20.7261 Evaluate side-chains 144 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 109 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 98 optimal weight: 0.0670 chunk 118 optimal weight: 20.0000 chunk 0 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 HIS ** B 188 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 = 0.3543 r_free = 0.3543 target = 0.079542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.047611 restraints weight = 202298.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.051009 restraints weight = 57010.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.053308 restraints weight = 29136.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.054808 restraints weight = 18750.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.055818 restraints weight = 13873.535| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11318 Z= 0.133 Angle : 0.602 8.434 15307 Z= 0.318 Chirality : 0.043 0.163 1697 Planarity : 0.004 0.039 1952 Dihedral : 5.717 52.972 1555 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.41 % Allowed : 0.83 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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 are not related in a simple way. whole: 1.17 (0.23), residues: 1360 helix: 1.82 (0.19), residues: 735 sheet: -0.03 (0.44), residues: 122 loop : -0.56 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 626 TYR 0.044 0.002 TYR E 157 PHE 0.025 0.002 PHE D 174 TRP 0.036 0.002 TRP A 604 HIS 0.005 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (11308) covalent geometry : angle 0.59701 / 0.32 (15301) hydrogen bonds : bond 0.03777 / 2.49 ( 615) hydrogen bonds : angle 4.43817 / 3.02 ( 1794) metal coordination : bond 0.00619 / 0.29 ( 8) metal coordination : angle 4.05298 / 2.16 ( 6) Misc. bond : bond 0.00219 / 0.15 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2021.84 seconds wall clock time: 35 minutes 38.86 seconds (2138.86 seconds total)