Starting phenix.real_space_refine on Wed Mar 4 05:57:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dgs_27428/03_2026/8dgs_27428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dgs_27428/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dgs_27428/03_2026/8dgs_27428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dgs_27428/03_2026/8dgs_27428.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dgs_27428/03_2026/8dgs_27428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dgs_27428/03_2026/8dgs_27428.map" } 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-5986/lib/python3.9/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: 3.00, per 1000 atoms: 0.27 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: 1.04 Conformation dependent library (CDL) restraints added in 664.0 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: 0.26 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: 1.53 Time building geometry restraints manager: 1.37 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: 6488 16.69 - 33.39: 348 33.39 - 50.08: 97 50.08 - 66.77: 30 66.77 - 83.46: 6 Dihedral angle restraints: 6969 sinusoidal: 2918 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 6966 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: 2.510 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: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.720 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 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 : 11.933 83.463 4357 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 covalent geometry : bond 0.00486 (11308) covalent geometry : angle 0.66851 (15301) hydrogen bonds : bond 0.14508 ( 615) hydrogen bonds : angle 5.60505 ( 1794) metal coordination : bond 0.04193 ( 8) metal coordination : angle 4.29950 ( 6) Misc. bond : bond 0.00035 ( 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 : 0.452 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: 0.1217 time to fit residues: 57.2411 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 : 0.451 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3579 r_free = 0.3579 target = 0.081324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.050109 restraints weight = 172424.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.054393 restraints weight = 56931.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.055680 restraints weight = 24160.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.056167 restraints weight = 15997.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.056689 restraints weight = 14545.994| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 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 = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11318 Z= 0.170 Angle : 0.631 7.570 15307 Z= 0.328 Chirality : 0.043 0.210 1697 Planarity : 0.004 0.055 1952 Dihedral : 6.655 55.380 1605 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.41 % Allowed : 2.49 % Favored : 97.10 % 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: 1.56 (0.23), residues: 1360 helix: 2.00 (0.19), residues: 736 sheet: 0.38 (0.47), residues: 125 loop : -0.21 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 127 TYR 0.041 0.002 TYR E 157 PHE 0.040 0.002 PHE D 174 TRP 0.022 0.001 TRP B 247 HIS 0.006 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00364 (11308) covalent geometry : angle 0.62622 (15301) hydrogen bonds : bond 0.04757 ( 615) hydrogen bonds : angle 4.72387 ( 1794) metal coordination : bond 0.01271 ( 8) metal coordination : angle 4.14633 ( 6) Misc. bond : bond 0.00525 ( 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 225 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.430 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: A 249 ASP cc_start: 0.8560 (m-30) cc_final: 0.8256 (t70) REVERT: A 255 LEU cc_start: 0.9375 (tp) cc_final: 0.9001 (tp) REVERT: A 555 ASP cc_start: 0.9360 (t0) cc_final: 0.9087 (t0) REVERT: A 594 ASP cc_start: 0.8011 (t0) cc_final: 0.7399 (t0) REVERT: A 604 TRP cc_start: 0.8385 (m-10) cc_final: 0.8119 (m-10) REVERT: A 617 ILE cc_start: 0.9442 (pt) cc_final: 0.9136 (pt) REVERT: A 668 MET cc_start: 0.8944 (tpp) cc_final: 0.8159 (tpp) REVERT: A 695 GLU cc_start: 0.9435 (mt-10) cc_final: 0.8568 (tt0) REVERT: A 698 LYS cc_start: 0.9103 (mmtp) cc_final: 0.8819 (mtpt) REVERT: B 143 MET cc_start: 0.9135 (ptp) cc_final: 0.8756 (pmm) REVERT: B 146 MET cc_start: 0.8488 (mmm) cc_final: 0.7849 (mmt) REVERT: B 230 MET cc_start: 0.7996 (tpp) cc_final: 0.7667 (tpp) REVERT: B 316 TYR cc_start: 0.9250 (t80) cc_final: 0.9045 (t80) REVERT: B 345 ASN cc_start: 0.8932 (t0) cc_final: 0.8520 (t0) REVERT: C 121 MET cc_start: 0.9380 (mtp) cc_final: 0.9142 (mtp) REVERT: C 202 GLU cc_start: 0.8559 (mp0) cc_final: 0.8342 (mp0) REVERT: C 208 GLU cc_start: 0.8922 (tt0) cc_final: 0.8647 (tm-30) REVERT: D 14 GLU cc_start: 0.9541 (tm-30) cc_final: 0.9267 (tm-30) REVERT: D 50 ASN cc_start: 0.9411 (m110) cc_final: 0.9059 (m-40) REVERT: D 95 TYR cc_start: 0.9057 (m-10) cc_final: 0.8768 (m-10) REVERT: D 100 LEU cc_start: 0.9261 (tt) cc_final: 0.8725 (mt) REVERT: D 121 MET cc_start: 0.9632 (mtp) cc_final: 0.9027 (mmm) REVERT: D 147 LYS cc_start: 0.9629 (mttt) cc_final: 0.9207 (tppt) REVERT: D 149 TYR cc_start: 0.8838 (m-10) cc_final: 0.8489 (m-80) REVERT: D 153 PHE cc_start: 0.9367 (t80) cc_final: 0.8968 (t80) REVERT: D 218 MET cc_start: 0.9290 (mtm) cc_final: 0.8975 (mtm) REVERT: D 219 GLN cc_start: 0.8907 (tp40) cc_final: 0.8631 (tm-30) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.1023 time to fit residues: 32.4357 Evaluate side-chains 155 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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: 5.9990 chunk 18 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 ASN ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.046558 restraints weight = 185820.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.049845 restraints weight = 56475.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.052060 restraints weight = 29393.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.053452 restraints weight = 19080.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.054361 restraints weight = 14271.885| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11318 Z= 0.238 Angle : 0.672 10.145 15307 Z= 0.350 Chirality : 0.044 0.172 1697 Planarity : 0.005 0.048 1952 Dihedral : 6.616 58.045 1605 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.50 % Allowed : 3.57 % Favored : 95.93 % 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: 1.19 (0.23), residues: 1360 helix: 1.68 (0.19), residues: 735 sheet: 0.23 (0.43), residues: 130 loop : -0.36 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 166 TYR 0.035 0.002 TYR E 157 PHE 0.034 0.003 PHE D 153 TRP 0.013 0.001 TRP B 247 HIS 0.007 0.001 HIS A 542 Details of bonding type rmsd covalent geometry : bond 0.00489 (11308) covalent geometry : angle 0.66531 (15301) hydrogen bonds : bond 0.04422 ( 615) hydrogen bonds : angle 4.77202 ( 1794) metal coordination : bond 0.01966 ( 8) metal coordination : angle 4.85569 ( 6) Misc. bond : bond 0.00689 ( 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 191 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.396 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 195 CYS cc_start: 0.4046 (m) cc_final: 0.3409 (m) REVERT: A 210 TRP cc_start: 0.3785 (m100) cc_final: 0.2905 (m100) REVERT: A 242 PHE cc_start: 0.9153 (m-80) cc_final: 0.8950 (m-80) REVERT: A 268 PHE cc_start: 0.8684 (p90) cc_final: 0.8423 (p90) REVERT: A 555 ASP cc_start: 0.9295 (t0) cc_final: 0.9016 (t0) REVERT: A 594 ASP cc_start: 0.8251 (t0) cc_final: 0.7552 (t0) REVERT: A 604 TRP cc_start: 0.8334 (m-10) cc_final: 0.8062 (m-10) REVERT: A 617 ILE cc_start: 0.9407 (pt) cc_final: 0.9202 (pt) REVERT: A 668 MET cc_start: 0.9034 (tpp) cc_final: 0.8212 (tpp) REVERT: A 698 LYS cc_start: 0.9093 (mmtp) cc_final: 0.8801 (mtpt) REVERT: B 143 MET cc_start: 0.9132 (ptp) cc_final: 0.8719 (pmm) REVERT: B 146 MET cc_start: 0.8937 (mmm) cc_final: 0.8391 (mmt) REVERT: B 214 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8874 (tm-30) REVERT: B 308 MET cc_start: 0.8413 (tpt) cc_final: 0.8169 (tpt) REVERT: B 312 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8779 (mt-10) REVERT: B 345 ASN cc_start: 0.8871 (t0) cc_final: 0.8519 (t0) REVERT: C 14 GLU cc_start: 0.9281 (pp20) cc_final: 0.8894 (pp20) REVERT: C 22 MET cc_start: 0.9018 (ttm) cc_final: 0.8755 (ttp) REVERT: C 121 MET cc_start: 0.9389 (mtp) cc_final: 0.9105 (mtp) REVERT: C 194 GLN cc_start: 0.9175 (tp-100) cc_final: 0.8918 (tp-100) REVERT: C 202 GLU cc_start: 0.8550 (mp0) cc_final: 0.8340 (mp0) REVERT: D 95 TYR cc_start: 0.9108 (m-10) cc_final: 0.8793 (m-10) REVERT: D 121 MET cc_start: 0.9669 (mtp) cc_final: 0.9034 (mmm) REVERT: D 147 LYS cc_start: 0.9602 (mttt) cc_final: 0.9198 (tppt) REVERT: D 150 GLN cc_start: 0.9069 (mt0) cc_final: 0.8620 (tp-100) REVERT: D 167 ARG cc_start: 0.9131 (ttt180) cc_final: 0.8862 (ttt90) REVERT: D 218 MET cc_start: 0.9332 (mtm) cc_final: 0.9023 (mtm) REVERT: D 219 GLN cc_start: 0.8984 (tp40) cc_final: 0.8637 (tm-30) REVERT: D 221 LEU cc_start: 0.9751 (mt) cc_final: 0.9543 (mt) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.0973 time to fit residues: 27.1631 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 : 0.463 ------------------------------------------------------------------------------- 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: 0.0970 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.078935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.046957 restraints weight = 202266.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.050299 restraints weight = 57450.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.052572 restraints weight = 29453.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.054038 restraints weight = 18962.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.054958 restraints weight = 14079.243| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11318 Z= 0.166 Angle : 0.602 10.156 15307 Z= 0.312 Chirality : 0.042 0.220 1697 Planarity : 0.004 0.040 1952 Dihedral : 6.429 59.405 1605 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.41 % Allowed : 2.41 % Favored : 97.18 % 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: 1.23 (0.23), residues: 1360 helix: 1.77 (0.19), residues: 734 sheet: 0.04 (0.43), residues: 132 loop : -0.36 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 222 TYR 0.027 0.002 TYR E 157 PHE 0.040 0.002 PHE E 156 TRP 0.016 0.001 TRP B 247 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00350 (11308) covalent geometry : angle 0.59530 (15301) hydrogen bonds : bond 0.04067 ( 615) hydrogen bonds : angle 4.55538 ( 1794) metal coordination : bond 0.01213 ( 8) metal coordination : angle 4.62787 ( 6) Misc. bond : bond 0.00521 ( 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 186 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.473 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 187 MET cc_start: 0.8355 (mpp) cc_final: 0.8087 (mmp) REVERT: A 242 PHE cc_start: 0.9077 (m-80) cc_final: 0.8819 (m-80) REVERT: A 255 LEU cc_start: 0.9342 (tp) cc_final: 0.8856 (tp) REVERT: A 268 PHE cc_start: 0.8578 (p90) cc_final: 0.8350 (p90) REVERT: A 555 ASP cc_start: 0.9237 (t0) cc_final: 0.8943 (t0) REVERT: A 604 TRP cc_start: 0.8354 (m-10) cc_final: 0.8141 (m-10) REVERT: A 668 MET cc_start: 0.9020 (tpp) cc_final: 0.8194 (tpp) REVERT: A 689 MET cc_start: 0.8443 (ttm) cc_final: 0.8158 (ttm) REVERT: A 698 LYS cc_start: 0.9113 (mmtp) cc_final: 0.8796 (mtpt) REVERT: B 143 MET cc_start: 0.9145 (ptp) cc_final: 0.8667 (pmm) REVERT: B 146 MET cc_start: 0.9090 (mmm) cc_final: 0.8419 (mmt) REVERT: B 214 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8939 (tm-30) REVERT: B 230 MET cc_start: 0.8101 (tpp) cc_final: 0.7899 (tpp) REVERT: B 308 MET cc_start: 0.8383 (tpt) cc_final: 0.8162 (tpp) REVERT: B 316 TYR cc_start: 0.9229 (t80) cc_final: 0.8535 (t80) REVERT: B 345 ASN cc_start: 0.8858 (t0) cc_final: 0.8517 (t0) REVERT: C 14 GLU cc_start: 0.9223 (pp20) cc_final: 0.8906 (pp20) REVERT: C 22 MET cc_start: 0.8957 (ttm) cc_final: 0.8614 (ttp) REVERT: C 121 MET cc_start: 0.9370 (mtp) cc_final: 0.9102 (mtp) REVERT: C 194 GLN cc_start: 0.9152 (tp-100) cc_final: 0.8906 (tp-100) REVERT: C 202 GLU cc_start: 0.8570 (mp0) cc_final: 0.8350 (mp0) REVERT: D 14 GLU cc_start: 0.9494 (tm-30) cc_final: 0.9216 (tm-30) REVERT: D 26 MET cc_start: 0.9297 (mmm) cc_final: 0.8974 (mmm) REVERT: D 95 TYR cc_start: 0.9092 (m-10) cc_final: 0.8792 (m-10) REVERT: D 121 MET cc_start: 0.9638 (mtp) cc_final: 0.9011 (mmm) REVERT: D 147 LYS cc_start: 0.9638 (mttt) cc_final: 0.9187 (tppt) REVERT: D 167 ARG cc_start: 0.9082 (ttt180) cc_final: 0.8858 (ttt90) REVERT: D 217 ILE cc_start: 0.9567 (mm) cc_final: 0.8983 (tp) REVERT: D 218 MET cc_start: 0.9301 (mtm) cc_final: 0.8982 (mtm) REVERT: D 219 GLN cc_start: 0.8998 (tp40) cc_final: 0.8656 (tm-30) REVERT: D 221 LEU cc_start: 0.9753 (mt) cc_final: 0.9539 (mt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.0867 time to fit residues: 24.1912 Evaluate side-chains 150 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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: 7.9990 chunk 19 optimal weight: 8.9990 chunk 80 optimal weight: 0.4980 chunk 90 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS C 8 GLN ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.046670 restraints weight = 194672.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.050006 restraints weight = 56895.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.052254 restraints weight = 29483.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.053665 restraints weight = 19008.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.054695 restraints weight = 14167.565| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11318 Z= 0.171 Angle : 0.593 9.519 15307 Z= 0.309 Chirality : 0.042 0.204 1697 Planarity : 0.004 0.039 1952 Dihedral : 6.425 59.279 1605 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.41 % Allowed : 2.41 % Favored : 97.18 % 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: 1.23 (0.23), residues: 1360 helix: 1.80 (0.19), residues: 734 sheet: -0.02 (0.42), residues: 132 loop : -0.38 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.023 0.002 TYR E 157 PHE 0.035 0.002 PHE E 156 TRP 0.013 0.001 TRP B 247 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00360 (11308) covalent geometry : angle 0.58271 (15301) hydrogen bonds : bond 0.03980 ( 615) hydrogen bonds : angle 4.53843 ( 1794) metal coordination : bond 0.01555 ( 8) metal coordination : angle 5.46120 ( 6) Misc. bond : bond 0.00224 ( 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 189 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 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: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8566 (mpp) cc_final: 0.8088 (mmt) REVERT: A 242 PHE cc_start: 0.9086 (m-80) cc_final: 0.8861 (m-80) REVERT: A 249 ASP cc_start: 0.8545 (t0) cc_final: 0.7961 (t0) REVERT: A 255 LEU cc_start: 0.9335 (tp) cc_final: 0.8909 (tp) REVERT: A 268 PHE cc_start: 0.8536 (p90) cc_final: 0.8316 (p90) REVERT: A 555 ASP cc_start: 0.9258 (t0) cc_final: 0.8965 (t0) REVERT: A 604 TRP cc_start: 0.8346 (m-10) cc_final: 0.8126 (m-10) REVERT: A 668 MET cc_start: 0.9037 (tpp) cc_final: 0.8255 (tpp) REVERT: A 689 MET cc_start: 0.8472 (ttm) cc_final: 0.8091 (ttm) REVERT: A 698 LYS cc_start: 0.9101 (mmtp) cc_final: 0.8806 (mtpt) REVERT: B 143 MET cc_start: 0.9000 (ptp) cc_final: 0.8537 (pmm) REVERT: B 146 MET cc_start: 0.9119 (mmm) cc_final: 0.8539 (mmt) REVERT: B 214 GLN cc_start: 0.9196 (tm-30) cc_final: 0.8936 (tm-30) REVERT: B 308 MET cc_start: 0.8427 (tpt) cc_final: 0.7946 (tpp) REVERT: B 312 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8680 (mt-10) REVERT: B 313 LEU cc_start: 0.9518 (mt) cc_final: 0.9241 (mt) REVERT: B 345 ASN cc_start: 0.8859 (t0) cc_final: 0.8517 (t0) REVERT: C 22 MET cc_start: 0.9012 (ttm) cc_final: 0.8630 (ttp) REVERT: C 121 MET cc_start: 0.9380 (mtp) cc_final: 0.9083 (mtp) REVERT: C 146 GLN cc_start: 0.9385 (tp-100) cc_final: 0.9151 (tp-100) REVERT: C 194 GLN cc_start: 0.9158 (tp-100) cc_final: 0.8906 (tp-100) REVERT: C 202 GLU cc_start: 0.8575 (mp0) cc_final: 0.8368 (mp0) REVERT: C 223 ASP cc_start: 0.9411 (m-30) cc_final: 0.9050 (m-30) REVERT: D 14 GLU cc_start: 0.9495 (tm-30) cc_final: 0.9151 (tm-30) REVERT: D 26 MET cc_start: 0.9283 (mmm) cc_final: 0.8975 (mmm) REVERT: D 95 TYR cc_start: 0.9087 (m-10) cc_final: 0.8694 (m-10) REVERT: D 121 MET cc_start: 0.9651 (mtp) cc_final: 0.9017 (mmm) REVERT: D 147 LYS cc_start: 0.9631 (mttt) cc_final: 0.9156 (tppt) REVERT: D 150 GLN cc_start: 0.9110 (mt0) cc_final: 0.8653 (tp-100) REVERT: D 174 PHE cc_start: 0.9030 (t80) cc_final: 0.8781 (t80) REVERT: D 217 ILE cc_start: 0.9575 (mm) cc_final: 0.8976 (tp) REVERT: D 218 MET cc_start: 0.9316 (mtm) cc_final: 0.8991 (mtm) REVERT: D 219 GLN cc_start: 0.8996 (tp40) cc_final: 0.8373 (tp-100) REVERT: D 221 LEU cc_start: 0.9752 (mt) cc_final: 0.9532 (mt) REVERT: E 4 TYR cc_start: 0.6698 (m-80) cc_final: 0.6472 (m-80) REVERT: E 111 MET cc_start: 0.4348 (mtt) cc_final: 0.3580 (tpp) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.0875 time to fit residues: 24.4797 Evaluate side-chains 146 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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: 0.0370 chunk 101 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.080276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.048008 restraints weight = 196631.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.051468 restraints weight = 55942.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.053793 restraints weight = 28612.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.055380 restraints weight = 18363.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.056310 restraints weight = 13443.532| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 11318 Z= 0.116 Angle : 0.558 9.974 15307 Z= 0.288 Chirality : 0.042 0.194 1697 Planarity : 0.003 0.042 1952 Dihedral : 6.316 59.593 1605 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.41 % Allowed : 1.83 % Favored : 97.76 % 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: 1.45 (0.23), residues: 1360 helix: 2.00 (0.19), residues: 734 sheet: 0.14 (0.45), residues: 121 loop : -0.34 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 626 TYR 0.023 0.001 TYR E 157 PHE 0.027 0.002 PHE E 156 TRP 0.015 0.001 TRP B 247 HIS 0.006 0.001 HIS A 585 Details of bonding type rmsd covalent geometry : bond 0.00242 (11308) covalent geometry : angle 0.55323 (15301) hydrogen bonds : bond 0.03748 ( 615) hydrogen bonds : angle 4.34862 ( 1794) metal coordination : bond 0.00753 ( 8) metal coordination : angle 3.81786 ( 6) Misc. bond : bond 0.00039 ( 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 193 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.445 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 242 PHE cc_start: 0.9033 (m-80) cc_final: 0.8775 (m-80) REVERT: A 255 LEU cc_start: 0.9270 (tp) cc_final: 0.8939 (tp) REVERT: A 555 ASP cc_start: 0.9300 (t0) cc_final: 0.9020 (t70) REVERT: A 565 ASP cc_start: 0.8970 (t70) cc_final: 0.8722 (t70) REVERT: A 617 ILE cc_start: 0.9343 (pt) cc_final: 0.8529 (pt) REVERT: A 620 MET cc_start: 0.8315 (mtt) cc_final: 0.7764 (mtt) REVERT: A 627 MET cc_start: 0.8832 (mmm) cc_final: 0.8544 (mmt) REVERT: A 668 MET cc_start: 0.9010 (tpp) cc_final: 0.8209 (tpp) REVERT: A 674 LEU cc_start: 0.9328 (tp) cc_final: 0.9121 (tp) REVERT: A 689 MET cc_start: 0.8484 (ttm) cc_final: 0.8079 (ttm) REVERT: A 698 LYS cc_start: 0.9098 (mmtp) cc_final: 0.8783 (mtpt) REVERT: A 699 LYS cc_start: 0.8783 (mttp) cc_final: 0.8504 (tmtt) REVERT: B 115 LEU cc_start: 0.9794 (mt) cc_final: 0.9502 (pp) REVERT: B 143 MET cc_start: 0.9029 (ptp) cc_final: 0.8585 (pmm) REVERT: B 146 MET cc_start: 0.9150 (mmm) cc_final: 0.8580 (mmt) REVERT: B 214 GLN cc_start: 0.9175 (tm-30) cc_final: 0.8909 (tm-30) REVERT: B 308 MET cc_start: 0.8419 (tpt) cc_final: 0.7969 (tpp) REVERT: B 312 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8653 (mt-10) REVERT: B 316 TYR cc_start: 0.9223 (t80) cc_final: 0.8506 (t80) REVERT: C 14 GLU cc_start: 0.9090 (pp20) cc_final: 0.8799 (pp20) REVERT: C 22 MET cc_start: 0.8924 (ttm) cc_final: 0.8517 (ttp) REVERT: C 121 MET cc_start: 0.9398 (mtp) cc_final: 0.9118 (mtp) REVERT: C 194 GLN cc_start: 0.9144 (tp-100) cc_final: 0.8869 (tp-100) REVERT: C 202 GLU cc_start: 0.8565 (mp0) cc_final: 0.8348 (mp0) REVERT: C 217 ILE cc_start: 0.9789 (mm) cc_final: 0.9550 (mm) REVERT: D 26 MET cc_start: 0.9270 (mmm) cc_final: 0.8904 (mmm) REVERT: D 95 TYR cc_start: 0.8969 (m-10) cc_final: 0.8681 (m-10) REVERT: D 121 MET cc_start: 0.9628 (mtp) cc_final: 0.8972 (mmm) REVERT: D 147 LYS cc_start: 0.9620 (mttt) cc_final: 0.9101 (tppt) REVERT: D 174 PHE cc_start: 0.8992 (t80) cc_final: 0.8757 (t80) REVERT: D 217 ILE cc_start: 0.9544 (mm) cc_final: 0.8952 (tp) REVERT: D 218 MET cc_start: 0.9322 (mtm) cc_final: 0.8998 (mtm) REVERT: D 219 GLN cc_start: 0.9002 (tp40) cc_final: 0.8584 (tm-30) REVERT: E 4 TYR cc_start: 0.6611 (m-80) cc_final: 0.6308 (m-80) REVERT: E 111 MET cc_start: 0.4254 (mtt) cc_final: 0.3455 (tpp) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.0944 time to fit residues: 26.3172 Evaluate side-chains 154 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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: 8.9990 chunk 108 optimal weight: 9.9990 chunk 73 optimal weight: 0.3980 chunk 9 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN B 100 HIS C 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.075981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.044702 restraints weight = 213262.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.047837 restraints weight = 60656.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.049857 restraints weight = 31370.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.051314 restraints weight = 20628.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.052131 restraints weight = 15377.661| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 11318 Z= 0.337 Angle : 0.786 13.309 15307 Z= 0.412 Chirality : 0.046 0.182 1697 Planarity : 0.005 0.050 1952 Dihedral : 6.941 59.886 1605 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.41 % Allowed : 1.83 % Favored : 97.76 % 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: 0.47 (0.22), residues: 1360 helix: 1.13 (0.18), residues: 736 sheet: -0.08 (0.40), residues: 134 loop : -0.75 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 74 TYR 0.032 0.003 TYR C 82 PHE 0.020 0.003 PHE C 174 TRP 0.057 0.003 TRP A 604 HIS 0.009 0.003 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00687 (11308) covalent geometry : angle 0.77389 (15301) hydrogen bonds : bond 0.04454 ( 615) hydrogen bonds : angle 4.98936 ( 1794) metal coordination : bond 0.02276 ( 8) metal coordination : angle 6.90699 ( 6) Misc. bond : bond 0.00392 ( 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 168 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8441 (mpp) cc_final: 0.7990 (mmt) REVERT: A 195 CYS cc_start: 0.4499 (m) cc_final: 0.3713 (m) REVERT: A 210 TRP cc_start: 0.4183 (m100) cc_final: 0.3075 (m100) REVERT: A 255 LEU cc_start: 0.9392 (tp) cc_final: 0.9076 (tp) REVERT: A 555 ASP cc_start: 0.9321 (t0) cc_final: 0.9040 (t0) REVERT: A 594 ASP cc_start: 0.8975 (m-30) cc_final: 0.8649 (m-30) REVERT: A 668 MET cc_start: 0.9071 (tpp) cc_final: 0.8285 (tpp) REVERT: A 689 MET cc_start: 0.8432 (ttm) cc_final: 0.8095 (ttm) REVERT: B 143 MET cc_start: 0.8869 (ptp) cc_final: 0.8464 (pmm) REVERT: B 308 MET cc_start: 0.8467 (tpt) cc_final: 0.8043 (tpt) REVERT: B 312 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8823 (mt-10) REVERT: B 313 LEU cc_start: 0.9543 (mt) cc_final: 0.9323 (mt) REVERT: B 345 ASN cc_start: 0.9099 (t0) cc_final: 0.8714 (p0) REVERT: C 14 GLU cc_start: 0.9153 (pp20) cc_final: 0.8837 (pp20) REVERT: C 22 MET cc_start: 0.9025 (ttm) cc_final: 0.8584 (ttp) REVERT: C 50 ASN cc_start: 0.9593 (m-40) cc_final: 0.9242 (t0) REVERT: C 121 MET cc_start: 0.9389 (mtp) cc_final: 0.9124 (mtp) REVERT: C 194 GLN cc_start: 0.9147 (tp-100) cc_final: 0.8931 (tp-100) REVERT: C 202 GLU cc_start: 0.8655 (mp0) cc_final: 0.8342 (mp0) REVERT: C 223 ASP cc_start: 0.9426 (m-30) cc_final: 0.9091 (m-30) REVERT: D 14 GLU cc_start: 0.9457 (tm-30) cc_final: 0.9221 (tm-30) REVERT: D 26 MET cc_start: 0.9310 (mmm) cc_final: 0.9022 (mmm) REVERT: D 95 TYR cc_start: 0.8917 (m-10) cc_final: 0.8576 (m-10) REVERT: D 121 MET cc_start: 0.9702 (mtp) cc_final: 0.9046 (mmm) REVERT: D 147 LYS cc_start: 0.9659 (mttt) cc_final: 0.9248 (tppt) REVERT: D 150 GLN cc_start: 0.9123 (mt0) cc_final: 0.8656 (tp-100) REVERT: D 217 ILE cc_start: 0.9609 (mm) cc_final: 0.9075 (tp) REVERT: D 218 MET cc_start: 0.9390 (mtm) cc_final: 0.9102 (mtm) REVERT: D 219 GLN cc_start: 0.9102 (tp40) cc_final: 0.8500 (tp40) REVERT: D 221 LEU cc_start: 0.9730 (mt) cc_final: 0.9472 (mt) REVERT: E 111 MET cc_start: 0.4229 (mtt) cc_final: 0.3424 (tpp) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0873 time to fit residues: 21.8294 Evaluate side-chains 135 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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: 7.9990 chunk 12 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 128 optimal weight: 40.0000 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.078489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.047655 restraints weight = 227797.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.051270 restraints weight = 64890.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.052845 restraints weight = 30119.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.054396 restraints weight = 17395.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.054449 restraints weight = 14346.947| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 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 = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4853 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= 0.132 Angle : 0.604 9.941 15307 Z= 0.316 Chirality : 0.043 0.171 1697 Planarity : 0.004 0.039 1952 Dihedral : 6.748 59.725 1605 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.41 % Allowed : 1.16 % Favored : 98.42 % 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: 0.96 (0.23), residues: 1360 helix: 1.57 (0.19), residues: 735 sheet: 0.11 (0.44), residues: 121 loop : -0.58 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 149 TYR 0.049 0.002 TYR E 157 PHE 0.023 0.002 PHE D 177 TRP 0.081 0.003 TRP A 604 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00280 (11308) covalent geometry : angle 0.59525 (15301) hydrogen bonds : bond 0.03936 ( 615) hydrogen bonds : angle 4.56235 ( 1794) metal coordination : bond 0.01158 ( 8) metal coordination : angle 5.26563 ( 6) Misc. bond : bond 0.00097 ( 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 175 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.432 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 255 LEU cc_start: 0.9256 (tp) cc_final: 0.8975 (tp) REVERT: A 555 ASP cc_start: 0.9332 (t0) cc_final: 0.9041 (t0) REVERT: A 565 ASP cc_start: 0.8955 (t70) cc_final: 0.8578 (t70) REVERT: A 594 ASP cc_start: 0.8877 (m-30) cc_final: 0.8565 (m-30) REVERT: A 668 MET cc_start: 0.9016 (tpp) cc_final: 0.8216 (tpp) REVERT: A 674 LEU cc_start: 0.9335 (tp) cc_final: 0.9094 (tp) REVERT: A 689 MET cc_start: 0.8552 (ttm) cc_final: 0.8243 (ttm) REVERT: A 713 SER cc_start: 0.9474 (m) cc_final: 0.9230 (m) REVERT: B 146 MET cc_start: 0.9136 (mmm) cc_final: 0.8540 (mmt) REVERT: B 308 MET cc_start: 0.8409 (tpt) cc_final: 0.7987 (tpt) REVERT: B 312 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8851 (mt-10) REVERT: B 313 LEU cc_start: 0.9534 (mt) cc_final: 0.9321 (mt) REVERT: B 345 ASN cc_start: 0.9076 (t0) cc_final: 0.8690 (p0) REVERT: C 22 MET cc_start: 0.9016 (ttm) cc_final: 0.8589 (ttp) REVERT: C 121 MET cc_start: 0.9389 (mtp) cc_final: 0.9052 (mtp) REVERT: C 194 GLN cc_start: 0.9177 (tp-100) cc_final: 0.8878 (tp-100) REVERT: C 202 GLU cc_start: 0.8614 (mp0) cc_final: 0.8386 (mp0) REVERT: D 14 GLU cc_start: 0.9411 (tm-30) cc_final: 0.9188 (tm-30) REVERT: D 95 TYR cc_start: 0.8927 (m-10) cc_final: 0.8621 (m-10) REVERT: D 100 LEU cc_start: 0.9244 (tt) cc_final: 0.8520 (mt) REVERT: D 121 MET cc_start: 0.9649 (mtp) cc_final: 0.9001 (mmm) REVERT: D 147 LYS cc_start: 0.9627 (mttt) cc_final: 0.9190 (tppt) REVERT: D 150 GLN cc_start: 0.9118 (mt0) cc_final: 0.8735 (tp-100) REVERT: D 217 ILE cc_start: 0.9577 (mm) cc_final: 0.8988 (tp) REVERT: D 218 MET cc_start: 0.9291 (mtm) cc_final: 0.8996 (mtm) REVERT: D 219 GLN cc_start: 0.9041 (tp40) cc_final: 0.8564 (tm-30) REVERT: D 221 LEU cc_start: 0.9738 (mt) cc_final: 0.9504 (mt) REVERT: E 72 MET cc_start: 0.5980 (ptm) cc_final: 0.5743 (ptm) REVERT: E 111 MET cc_start: 0.4001 (mtt) cc_final: 0.3312 (tpp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.0864 time to fit residues: 22.5600 Evaluate side-chains 135 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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: 9.9990 chunk 74 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.078459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.046824 restraints weight = 202325.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.050145 restraints weight = 57772.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.052358 restraints weight = 29860.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.053778 restraints weight = 19394.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.054839 restraints weight = 14413.291| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4985 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= 0.148 Angle : 0.612 9.959 15307 Z= 0.320 Chirality : 0.043 0.172 1697 Planarity : 0.004 0.039 1952 Dihedral : 6.658 59.989 1605 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.41 % Allowed : 0.58 % Favored : 99.00 % 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: 1.01 (0.23), residues: 1360 helix: 1.63 (0.19), residues: 735 sheet: 0.04 (0.45), residues: 121 loop : -0.57 (0.29), residues: 504 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 0.022 0.002 PHE D 174 TRP 0.055 0.002 TRP A 604 HIS 0.004 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00314 (11308) covalent geometry : angle 0.60573 (15301) hydrogen bonds : bond 0.03850 ( 615) hydrogen bonds : angle 4.54951 ( 1794) metal coordination : bond 0.01017 ( 8) metal coordination : angle 4.46961 ( 6) Misc. bond : bond 0.00400 ( 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 167 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.432 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: 0.8370 (mpp) cc_final: 0.8118 (mpp) REVERT: A 255 LEU cc_start: 0.9292 (tp) cc_final: 0.9007 (tp) REVERT: A 555 ASP cc_start: 0.9307 (t0) cc_final: 0.9003 (t0) REVERT: A 565 ASP cc_start: 0.9067 (t70) cc_final: 0.8736 (t70) REVERT: A 594 ASP cc_start: 0.8871 (m-30) cc_final: 0.8595 (m-30) REVERT: A 668 MET cc_start: 0.9064 (tpp) cc_final: 0.8241 (tpp) REVERT: A 674 LEU cc_start: 0.9381 (tp) cc_final: 0.9116 (tp) REVERT: A 689 MET cc_start: 0.8380 (ttm) cc_final: 0.7909 (ttm) REVERT: A 713 SER cc_start: 0.9486 (m) cc_final: 0.9260 (m) REVERT: B 146 MET cc_start: 0.9167 (mmm) cc_final: 0.8543 (mmt) REVERT: B 230 MET cc_start: 0.8025 (tpp) cc_final: 0.6948 (tmm) REVERT: B 308 MET cc_start: 0.8379 (tpt) cc_final: 0.7948 (tpt) REVERT: B 312 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8855 (mt-10) REVERT: B 313 LEU cc_start: 0.9548 (mt) cc_final: 0.9320 (mt) REVERT: C 22 MET cc_start: 0.8997 (ttm) cc_final: 0.8438 (ttp) REVERT: C 50 ASN cc_start: 0.9509 (m-40) cc_final: 0.9180 (t0) REVERT: C 121 MET cc_start: 0.9425 (mtp) cc_final: 0.9138 (mtp) REVERT: C 194 GLN cc_start: 0.9153 (tp-100) cc_final: 0.8857 (tp-100) REVERT: C 202 GLU cc_start: 0.8595 (mp0) cc_final: 0.8248 (mp0) REVERT: C 223 ASP cc_start: 0.9314 (m-30) cc_final: 0.8940 (m-30) REVERT: D 26 MET cc_start: 0.9188 (mmm) cc_final: 0.8836 (mmm) REVERT: D 95 TYR cc_start: 0.8922 (m-10) cc_final: 0.8629 (m-10) REVERT: D 100 LEU cc_start: 0.9267 (tt) cc_final: 0.8541 (mt) REVERT: D 121 MET cc_start: 0.9658 (mtp) cc_final: 0.8989 (mmm) REVERT: D 147 LYS cc_start: 0.9619 (mttt) cc_final: 0.9150 (tppt) REVERT: D 150 GLN cc_start: 0.9196 (mt0) cc_final: 0.8815 (tp-100) REVERT: D 217 ILE cc_start: 0.9587 (mm) cc_final: 0.8994 (tp) REVERT: D 218 MET cc_start: 0.9338 (mtm) cc_final: 0.9027 (mtm) REVERT: D 219 GLN cc_start: 0.9041 (tp40) cc_final: 0.8375 (tp-100) REVERT: D 221 LEU cc_start: 0.9734 (mt) cc_final: 0.9503 (mt) REVERT: E 72 MET cc_start: 0.5776 (ptm) cc_final: 0.5543 (ptm) REVERT: E 111 MET cc_start: 0.3960 (mtt) cc_final: 0.3290 (tpp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.0805 time to fit residues: 20.5524 Evaluate side-chains 132 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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: 0.7980 chunk 55 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 111 optimal weight: 0.4980 chunk 48 optimal weight: 0.2980 chunk 34 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.080191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.048107 restraints weight = 208580.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.051545 restraints weight = 58856.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.053763 restraints weight = 30136.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.055364 restraints weight = 19455.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.056344 restraints weight = 14391.587| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11318 Z= 0.110 Angle : 0.584 9.499 15307 Z= 0.301 Chirality : 0.043 0.182 1697 Planarity : 0.003 0.043 1952 Dihedral : 6.330 59.432 1605 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.41 % Allowed : 0.91 % Favored : 98.67 % 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: 1.21 (0.23), residues: 1360 helix: 1.88 (0.19), residues: 730 sheet: 0.01 (0.45), residues: 127 loop : -0.57 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 626 TYR 0.043 0.002 TYR E 157 PHE 0.023 0.001 PHE D 174 TRP 0.036 0.002 TRP A 604 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00226 (11308) covalent geometry : angle 0.58091 (15301) hydrogen bonds : bond 0.03607 ( 615) hydrogen bonds : angle 4.37853 ( 1794) metal coordination : bond 0.01166 ( 8) metal coordination : angle 3.13910 ( 6) Misc. bond : bond 0.00100 ( 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 177 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.252 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 195 CYS cc_start: 0.4053 (m) cc_final: 0.3759 (m) REVERT: A 255 LEU cc_start: 0.9216 (tp) cc_final: 0.8948 (tp) REVERT: A 555 ASP cc_start: 0.9318 (t0) cc_final: 0.9020 (t0) REVERT: A 594 ASP cc_start: 0.8785 (m-30) cc_final: 0.8459 (m-30) REVERT: A 640 TYR cc_start: 0.9459 (t80) cc_final: 0.9123 (t80) REVERT: A 668 MET cc_start: 0.9006 (tpp) cc_final: 0.8201 (tpp) REVERT: A 674 LEU cc_start: 0.9408 (tp) cc_final: 0.9144 (tp) REVERT: A 689 MET cc_start: 0.8376 (ttm) cc_final: 0.7845 (ttm) REVERT: A 693 MET cc_start: 0.9119 (mtp) cc_final: 0.8768 (mtm) REVERT: A 713 SER cc_start: 0.9460 (m) cc_final: 0.9238 (m) REVERT: B 100 HIS cc_start: 0.7928 (t70) cc_final: 0.7618 (t-90) REVERT: B 115 LEU cc_start: 0.9794 (mt) cc_final: 0.9530 (pp) REVERT: B 146 MET cc_start: 0.9105 (mmm) cc_final: 0.8571 (mmt) REVERT: B 230 MET cc_start: 0.8034 (tpp) cc_final: 0.6978 (tmm) REVERT: B 308 MET cc_start: 0.8324 (tpt) cc_final: 0.7926 (tpt) REVERT: B 312 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8885 (mt-10) REVERT: B 345 ASN cc_start: 0.9088 (t0) cc_final: 0.8703 (p0) REVERT: C 14 GLU cc_start: 0.9050 (pp20) cc_final: 0.8790 (pp20) REVERT: C 194 GLN cc_start: 0.9124 (tp-100) cc_final: 0.8811 (tp-100) REVERT: C 202 GLU cc_start: 0.8578 (mp0) cc_final: 0.8358 (mp0) REVERT: C 223 ASP cc_start: 0.9267 (m-30) cc_final: 0.8883 (m-30) REVERT: D 20 ASP cc_start: 0.9110 (m-30) cc_final: 0.8869 (p0) REVERT: D 26 MET cc_start: 0.9073 (mmm) cc_final: 0.8742 (mmm) REVERT: D 95 TYR cc_start: 0.8959 (m-10) cc_final: 0.8697 (m-10) REVERT: D 100 LEU cc_start: 0.9180 (tt) cc_final: 0.8487 (mt) REVERT: D 121 MET cc_start: 0.9618 (mtp) cc_final: 0.8896 (mmm) REVERT: D 147 LYS cc_start: 0.9617 (mttt) cc_final: 0.9122 (tppt) REVERT: D 173 ASN cc_start: 0.9290 (m110) cc_final: 0.8822 (m110) REVERT: D 218 MET cc_start: 0.9293 (mtm) cc_final: 0.8961 (mtm) REVERT: D 219 GLN cc_start: 0.9019 (tp40) cc_final: 0.8543 (tm-30) REVERT: E 111 MET cc_start: 0.3691 (mtt) cc_final: 0.3033 (tpp) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.0858 time to fit residues: 22.8062 Evaluate side-chains 146 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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: 6.9990 chunk 6 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 116 optimal weight: 0.3980 chunk 110 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 98 optimal weight: 0.0060 chunk 118 optimal weight: 20.0000 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.079566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.047617 restraints weight = 199245.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.051012 restraints weight = 58065.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.053281 restraints weight = 30030.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.054768 restraints weight = 19405.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.055819 restraints weight = 14374.487| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- 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: 25 | |-----------------------------------------------------------------------------| |-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: 25 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11318 Z= 0.118 Angle : 0.598 9.577 15307 Z= 0.313 Chirality : 0.043 0.180 1697 Planarity : 0.003 0.042 1952 Dihedral : 6.269 58.753 1605 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.41 % Allowed : 0.58 % Favored : 99.00 % 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: 1.20 (0.23), residues: 1360 helix: 1.83 (0.19), residues: 730 sheet: 0.03 (0.46), residues: 121 loop : -0.50 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 626 TYR 0.042 0.002 TYR E 157 PHE 0.024 0.001 PHE E 156 TRP 0.030 0.002 TRP A 604 HIS 0.003 0.001 HIS B 145 Details of bonding type rmsd covalent geometry : bond 0.00246 (11308) covalent geometry : angle 0.59486 (15301) hydrogen bonds : bond 0.03697 ( 615) hydrogen bonds : angle 4.43194 ( 1794) metal coordination : bond 0.00542 ( 8) metal coordination : angle 3.09098 ( 6) Misc. bond : bond 0.00034 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2309.92 seconds wall clock time: 40 minutes 33.34 seconds (2433.34 seconds total)