Starting phenix.real_space_refine on Tue Jul 29 12:29:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dgs_27428/07_2025/8dgs_27428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dgs_27428/07_2025/8dgs_27428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dgs_27428/07_2025/8dgs_27428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dgs_27428/07_2025/8dgs_27428.map" model { file = "/net/cci-nas-00/data/ceres_data/8dgs_27428/07_2025/8dgs_27428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dgs_27428/07_2025/8dgs_27428.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.045 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.00, per 1000 atoms: 0.81 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: 3.03 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.22 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: 3.63 Time building geometry restraints manager: 3.45 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: 2.330 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: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.190 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (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 TRP 0.008 0.001 TRP A 531 HIS 0.010 0.001 HIS A 235 PHE 0.026 0.002 PHE E 78 TYR 0.024 0.002 TYR E 96 ARG 0.005 0.000 ARG E 161 Details of bonding type rmsd hydrogen bonds : bond 0.14508 ( 615) hydrogen bonds : angle 5.60505 ( 1794) metal coordination : bond 0.04193 ( 8) metal coordination : angle 4.29950 ( 6) covalent geometry : bond 0.00486 (11308) covalent geometry : angle 0.66851 (15301) 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 : 1.368 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: 0.8027 (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: 0.9782 (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: 0.5602 (OUTLIER) cc_final: 0.4999 (ptm) REVERT: B 188 HIS cc_start: 0.5122 (t-90) cc_final: 0.4289 (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: 0.8913 (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: 0.2958 time to fit residues: 137.5478 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 : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.0070 chunk 53 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 GLN D 224 ASN E 70 GLN E 99 GLN A Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.082301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.049456 restraints weight = 185598.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.052888 restraints weight = 57224.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.055175 restraints weight = 30122.242| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11318 Z= 0.142 Angle : 0.613 7.177 15307 Z= 0.318 Chirality : 0.043 0.206 1697 Planarity : 0.004 0.044 1952 Dihedral : 6.574 54.523 1605 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.41 % Allowed : 2.57 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.23), residues: 1360 helix: 2.06 (0.19), residues: 737 sheet: 0.28 (0.45), residues: 135 loop : -0.24 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 247 HIS 0.005 0.001 HIS B 184 PHE 0.037 0.002 PHE B 334 TYR 0.040 0.002 TYR E 157 ARG 0.008 0.001 ARG D 127 Details of bonding type rmsd hydrogen bonds : bond 0.04612 ( 615) hydrogen bonds : angle 4.64129 ( 1794) metal coordination : bond 0.00931 ( 8) metal coordination : angle 3.75969 ( 6) covalent geometry : bond 0.00295 (11308) covalent geometry : angle 0.60848 (15301) Misc. bond : bond 0.00598 ( 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 233 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 1.345 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: A 195 CYS cc_start: 0.3313 (m) cc_final: 0.2685 (m) REVERT: A 210 TRP cc_start: 0.3565 (m100) cc_final: 0.2632 (m100) REVERT: A 249 ASP cc_start: 0.8617 (m-30) cc_final: 0.8166 (t70) REVERT: A 255 LEU cc_start: 0.9388 (tp) cc_final: 0.9032 (tp) REVERT: A 555 ASP cc_start: 0.9383 (t0) cc_final: 0.9111 (t0) REVERT: A 594 ASP cc_start: 0.8188 (t0) cc_final: 0.7489 (t0) REVERT: A 604 TRP cc_start: 0.8365 (m-10) cc_final: 0.8103 (m-10) REVERT: A 668 MET cc_start: 0.8944 (tpp) cc_final: 0.8242 (tpp) REVERT: A 689 MET cc_start: 0.8595 (ttm) cc_final: 0.8311 (ttm) REVERT: A 695 GLU cc_start: 0.9467 (mt-10) cc_final: 0.8570 (tt0) REVERT: A 698 LYS cc_start: 0.9113 (mmtp) cc_final: 0.8842 (mtpt) REVERT: B 143 MET cc_start: 0.9182 (ptp) cc_final: 0.8749 (pmm) REVERT: B 146 MET cc_start: 0.8565 (mmm) cc_final: 0.7931 (mmt) REVERT: B 152 ASP cc_start: 0.9432 (m-30) cc_final: 0.9184 (m-30) REVERT: B 230 MET cc_start: 0.7999 (tpp) cc_final: 0.7725 (tpp) REVERT: B 313 LEU cc_start: 0.9545 (mt) cc_final: 0.8943 (mt) REVERT: B 316 TYR cc_start: 0.9232 (t80) cc_final: 0.8564 (t80) REVERT: B 345 ASN cc_start: 0.8937 (t0) cc_final: 0.8524 (t0) REVERT: C 9 ARG cc_start: 0.9387 (tpt90) cc_final: 0.9027 (tpt170) REVERT: C 26 MET cc_start: 0.9644 (mmp) cc_final: 0.9301 (tpp) REVERT: C 121 MET cc_start: 0.9334 (mtp) cc_final: 0.9101 (mtp) REVERT: C 202 GLU cc_start: 0.8617 (mp0) cc_final: 0.8397 (mp0) REVERT: C 208 GLU cc_start: 0.8934 (tt0) cc_final: 0.8647 (tm-30) REVERT: C 217 ILE cc_start: 0.9760 (mm) cc_final: 0.9395 (tt) REVERT: D 14 GLU cc_start: 0.9522 (tm-30) cc_final: 0.9231 (tm-30) REVERT: D 26 MET cc_start: 0.9225 (mmm) cc_final: 0.8926 (mmm) REVERT: D 50 ASN cc_start: 0.9395 (m110) cc_final: 0.9089 (m-40) REVERT: D 94 CYS cc_start: 0.9227 (m) cc_final: 0.9023 (m) REVERT: D 95 TYR cc_start: 0.9084 (m-10) cc_final: 0.8784 (m-10) REVERT: D 100 LEU cc_start: 0.9208 (tt) cc_final: 0.8685 (mt) REVERT: D 121 MET cc_start: 0.9605 (mtp) cc_final: 0.9039 (mmm) REVERT: D 147 LYS cc_start: 0.9638 (mttt) cc_final: 0.9174 (tppt) REVERT: D 149 TYR cc_start: 0.8730 (m-10) cc_final: 0.8407 (m-80) REVERT: D 153 PHE cc_start: 0.9365 (t80) cc_final: 0.8953 (t80) REVERT: D 218 MET cc_start: 0.9269 (mtm) cc_final: 0.8952 (mtm) REVERT: D 219 GLN cc_start: 0.8821 (tp40) cc_final: 0.8526 (tm-30) REVERT: D 222 ARG cc_start: 0.8262 (mtt180) cc_final: 0.8048 (ttp-170) outliers start: 1 outliers final: 0 residues processed: 233 average time/residue: 0.2553 time to fit residues: 83.0957 Evaluate side-chains 164 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 109 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 39 optimal weight: 0.0060 chunk 111 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN C 15 GLN D 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.078091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.046400 restraints weight = 174906.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.049584 restraints weight = 55280.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.051690 restraints weight = 29416.597| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11318 Z= 0.278 Angle : 0.729 11.265 15307 Z= 0.378 Chirality : 0.044 0.216 1697 Planarity : 0.005 0.040 1952 Dihedral : 6.691 56.508 1605 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.58 % Allowed : 3.65 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.23), residues: 1360 helix: 1.46 (0.18), residues: 734 sheet: 0.08 (0.43), residues: 137 loop : -0.37 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 450 HIS 0.016 0.002 HIS B 188 PHE 0.028 0.003 PHE D 153 TYR 0.035 0.002 TYR E 157 ARG 0.005 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 615) hydrogen bonds : angle 4.85012 ( 1794) metal coordination : bond 0.02543 ( 8) metal coordination : angle 5.40295 ( 6) covalent geometry : bond 0.00575 (11308) covalent geometry : angle 0.72094 (15301) Misc. bond : bond 0.00541 ( 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 193 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 CYS cc_start: 0.3770 (m) cc_final: 0.3154 (m) REVERT: A 210 TRP cc_start: 0.3818 (m100) cc_final: 0.2946 (m100) REVERT: A 555 ASP cc_start: 0.9427 (t0) cc_final: 0.9179 (t0) REVERT: A 594 ASP cc_start: 0.8293 (t0) cc_final: 0.7622 (t0) REVERT: A 604 TRP cc_start: 0.8447 (m-10) cc_final: 0.8190 (m-10) REVERT: A 668 MET cc_start: 0.9101 (tpp) cc_final: 0.8277 (tpp) REVERT: A 689 MET cc_start: 0.8487 (ttm) cc_final: 0.8180 (ttp) REVERT: A 698 LYS cc_start: 0.9098 (mmtp) cc_final: 0.8801 (mtpt) REVERT: B 143 MET cc_start: 0.9153 (ptp) cc_final: 0.8712 (pmm) REVERT: B 146 MET cc_start: 0.8975 (mmm) cc_final: 0.8339 (mmt) REVERT: B 315 ASP cc_start: 0.9149 (t0) cc_final: 0.8755 (p0) REVERT: B 345 ASN cc_start: 0.8838 (t0) cc_final: 0.8509 (t0) REVERT: C 121 MET cc_start: 0.9393 (mtp) cc_final: 0.9071 (mtp) REVERT: C 194 GLN cc_start: 0.9226 (tp-100) cc_final: 0.8994 (tp-100) REVERT: C 202 GLU cc_start: 0.8705 (mp0) cc_final: 0.8472 (mp0) REVERT: C 208 GLU cc_start: 0.9073 (tt0) cc_final: 0.8804 (tm-30) REVERT: D 95 TYR cc_start: 0.9184 (m-10) cc_final: 0.8874 (m-10) REVERT: D 121 MET cc_start: 0.9683 (mtp) cc_final: 0.9064 (mmm) REVERT: D 147 LYS cc_start: 0.9615 (mttt) cc_final: 0.9130 (tppt) REVERT: D 150 GLN cc_start: 0.9134 (mt0) cc_final: 0.8711 (tp-100) REVERT: D 218 MET cc_start: 0.9385 (mtm) cc_final: 0.9061 (mtm) REVERT: D 219 GLN cc_start: 0.8965 (tp40) cc_final: 0.8462 (tp40) REVERT: D 221 LEU cc_start: 0.9746 (mt) cc_final: 0.9539 (mt) REVERT: D 222 ARG cc_start: 0.8247 (mtt180) cc_final: 0.8013 (ttp-170) outliers start: 2 outliers final: 0 residues processed: 193 average time/residue: 0.2299 time to fit residues: 63.9655 Evaluate side-chains 156 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 76 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.078897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.046793 restraints weight = 218001.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.050234 restraints weight = 59853.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.052585 restraints weight = 30388.426| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11318 Z= 0.164 Angle : 0.608 11.064 15307 Z= 0.317 Chirality : 0.043 0.242 1697 Planarity : 0.004 0.072 1952 Dihedral : 6.519 58.297 1605 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.58 % Allowed : 1.99 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.23), residues: 1360 helix: 1.69 (0.19), residues: 733 sheet: -0.01 (0.42), residues: 139 loop : -0.42 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 247 HIS 0.007 0.001 HIS A 269 PHE 0.017 0.002 PHE B 334 TYR 0.029 0.002 TYR E 157 ARG 0.007 0.001 ARG E 68 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 615) hydrogen bonds : angle 4.64166 ( 1794) metal coordination : bond 0.01071 ( 8) metal coordination : angle 4.95381 ( 6) covalent geometry : bond 0.00347 (11308) covalent geometry : angle 0.60018 (15301) Misc. bond : bond 0.00449 ( 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 192 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.335 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: 0.8463 (m-30) cc_final: 0.8121 (t70) REVERT: A 255 LEU cc_start: 0.9347 (tp) cc_final: 0.8937 (tp) REVERT: A 268 PHE cc_start: 0.8560 (p90) cc_final: 0.8358 (p90) REVERT: A 555 ASP cc_start: 0.9454 (t0) cc_final: 0.9191 (t0) REVERT: A 604 TRP cc_start: 0.8474 (m-10) cc_final: 0.8257 (m-10) REVERT: A 620 MET cc_start: 0.8513 (mtt) cc_final: 0.8306 (mtp) REVERT: A 668 MET cc_start: 0.9099 (tpp) cc_final: 0.8305 (tpp) REVERT: A 689 MET cc_start: 0.8597 (ttm) cc_final: 0.8296 (ttt) REVERT: A 698 LYS cc_start: 0.9113 (mmtp) cc_final: 0.8786 (mtpt) REVERT: A 699 LYS cc_start: 0.8721 (mttp) cc_final: 0.8431 (tmtt) REVERT: A 713 SER cc_start: 0.9489 (m) cc_final: 0.9248 (m) REVERT: B 143 MET cc_start: 0.9051 (ptp) cc_final: 0.8626 (pmm) REVERT: B 146 MET cc_start: 0.9083 (mmm) cc_final: 0.8455 (mmt) REVERT: B 230 MET cc_start: 0.8150 (tpp) cc_final: 0.7916 (tpp) REVERT: B 316 TYR cc_start: 0.9239 (t80) cc_final: 0.8526 (t80) REVERT: B 345 ASN cc_start: 0.8851 (t0) cc_final: 0.8510 (t0) REVERT: C 22 MET cc_start: 0.9048 (ttm) cc_final: 0.8676 (ttp) REVERT: C 121 MET cc_start: 0.9409 (mtp) cc_final: 0.9120 (mtp) REVERT: C 146 GLN cc_start: 0.9364 (tp-100) cc_final: 0.8901 (tp-100) REVERT: C 150 GLN cc_start: 0.9357 (mm-40) cc_final: 0.9123 (mm-40) REVERT: C 194 GLN cc_start: 0.9233 (tp-100) cc_final: 0.8997 (tp-100) REVERT: C 202 GLU cc_start: 0.8714 (mp0) cc_final: 0.8476 (mp0) REVERT: C 208 GLU cc_start: 0.9102 (tt0) cc_final: 0.8786 (tm-30) REVERT: D 26 MET cc_start: 0.9352 (mmm) cc_final: 0.9013 (mmm) REVERT: D 95 TYR cc_start: 0.9188 (m-10) cc_final: 0.8808 (m-10) REVERT: D 100 LEU cc_start: 0.9319 (tt) cc_final: 0.8634 (mt) REVERT: D 121 MET cc_start: 0.9667 (mtp) cc_final: 0.9060 (mmm) REVERT: D 147 LYS cc_start: 0.9668 (mttt) cc_final: 0.9203 (tppt) REVERT: D 167 ARG cc_start: 0.8939 (ttt180) cc_final: 0.8670 (ttt90) REVERT: D 217 ILE cc_start: 0.9551 (mm) cc_final: 0.8971 (tp) REVERT: D 218 MET cc_start: 0.9340 (mtm) cc_final: 0.9058 (mtm) REVERT: D 219 GLN cc_start: 0.8971 (tp40) cc_final: 0.8658 (tm-30) REVERT: D 221 LEU cc_start: 0.9755 (mt) cc_final: 0.9545 (mt) REVERT: D 222 ARG cc_start: 0.8226 (mtt180) cc_final: 0.8017 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2408 time to fit residues: 65.7395 Evaluate side-chains 151 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 89 optimal weight: 0.0060 chunk 86 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.079673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.047532 restraints weight = 200533.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.050983 restraints weight = 56864.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.053347 restraints weight = 29192.267| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11318 Z= 0.121 Angle : 0.576 9.712 15307 Z= 0.297 Chirality : 0.042 0.202 1697 Planarity : 0.004 0.044 1952 Dihedral : 6.405 58.585 1605 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.58 % Allowed : 2.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.23), residues: 1360 helix: 1.85 (0.19), residues: 737 sheet: -0.08 (0.42), residues: 140 loop : -0.28 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 247 HIS 0.006 0.001 HIS A 269 PHE 0.029 0.002 PHE C 174 TYR 0.026 0.002 TYR E 157 ARG 0.005 0.000 ARG A 626 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 615) hydrogen bonds : angle 4.42374 ( 1794) metal coordination : bond 0.00776 ( 8) metal coordination : angle 4.42791 ( 6) covalent geometry : bond 0.00253 (11308) covalent geometry : angle 0.56964 (15301) Misc. bond : bond 0.00048 ( 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 194 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8480 (mmp) cc_final: 0.8197 (mmt) REVERT: A 254 LEU cc_start: 0.9595 (tp) cc_final: 0.9359 (tt) REVERT: A 255 LEU cc_start: 0.9313 (tp) cc_final: 0.9082 (tp) REVERT: A 555 ASP cc_start: 0.9449 (t0) cc_final: 0.9159 (t0) REVERT: A 604 TRP cc_start: 0.8413 (m-10) cc_final: 0.8212 (m-10) REVERT: A 617 ILE cc_start: 0.9375 (pt) cc_final: 0.8683 (pt) REVERT: A 620 MET cc_start: 0.8271 (mtt) cc_final: 0.7972 (mtt) REVERT: A 627 MET cc_start: 0.8889 (mmm) cc_final: 0.8597 (mmt) REVERT: A 668 MET cc_start: 0.9053 (tpp) cc_final: 0.8218 (tpp) REVERT: A 689 MET cc_start: 0.8504 (ttm) cc_final: 0.8063 (ttp) REVERT: A 698 LYS cc_start: 0.9107 (mmtp) cc_final: 0.8831 (mtpt) REVERT: A 713 SER cc_start: 0.9478 (m) cc_final: 0.9261 (m) REVERT: B 143 MET cc_start: 0.9028 (ptp) cc_final: 0.8611 (pmm) REVERT: B 146 MET cc_start: 0.9148 (mmm) cc_final: 0.8440 (mmt) REVERT: B 308 MET cc_start: 0.8034 (tmm) cc_final: 0.7482 (tmm) REVERT: B 312 GLU cc_start: 0.9342 (mt-10) cc_final: 0.8976 (mt-10) REVERT: B 316 TYR cc_start: 0.9235 (t80) cc_final: 0.8537 (t80) REVERT: B 345 ASN cc_start: 0.8857 (t0) cc_final: 0.8512 (t0) REVERT: C 14 GLU cc_start: 0.9284 (pp20) cc_final: 0.9033 (pp20) REVERT: C 22 MET cc_start: 0.9005 (ttm) cc_final: 0.8599 (ttp) REVERT: C 121 MET cc_start: 0.9379 (mtp) cc_final: 0.9121 (mtp) REVERT: C 146 GLN cc_start: 0.9375 (tp-100) cc_final: 0.9157 (tp-100) REVERT: C 194 GLN cc_start: 0.9207 (tp-100) cc_final: 0.8956 (tp-100) REVERT: C 202 GLU cc_start: 0.8665 (mp0) cc_final: 0.8428 (mp0) REVERT: C 208 GLU cc_start: 0.9075 (tt0) cc_final: 0.8764 (tm-30) REVERT: D 26 MET cc_start: 0.9326 (mmm) cc_final: 0.8991 (mmm) REVERT: D 100 LEU cc_start: 0.9261 (tt) cc_final: 0.8559 (mt) REVERT: D 121 MET cc_start: 0.9654 (mtp) cc_final: 0.9033 (mmm) REVERT: D 147 LYS cc_start: 0.9653 (mttt) cc_final: 0.9134 (tppt) REVERT: D 150 GLN cc_start: 0.9185 (mt0) cc_final: 0.8767 (tp-100) REVERT: D 174 PHE cc_start: 0.9048 (t80) cc_final: 0.8801 (t80) REVERT: D 217 ILE cc_start: 0.9539 (mm) cc_final: 0.8943 (tp) REVERT: D 218 MET cc_start: 0.9315 (mtm) cc_final: 0.9044 (mtm) REVERT: D 219 GLN cc_start: 0.8962 (tp40) cc_final: 0.8632 (tm-30) REVERT: D 221 LEU cc_start: 0.9754 (mt) cc_final: 0.9545 (mt) REVERT: E 72 MET cc_start: 0.7206 (ptt) cc_final: 0.6672 (ptt) REVERT: E 78 PHE cc_start: 0.3171 (m-80) cc_final: 0.2261 (m-80) REVERT: E 111 MET cc_start: 0.5564 (mmp) cc_final: 0.4415 (tpp) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3056 time to fit residues: 85.0786 Evaluate side-chains 152 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 121 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 127 optimal weight: 0.0870 chunk 26 optimal weight: 6.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.078803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.047075 restraints weight = 176142.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.050305 restraints weight = 54585.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.052447 restraints weight = 28777.033| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11318 Z= 0.167 Angle : 0.603 10.377 15307 Z= 0.315 Chirality : 0.043 0.271 1697 Planarity : 0.004 0.038 1952 Dihedral : 6.494 57.114 1605 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.66 % Allowed : 1.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1360 helix: 1.73 (0.19), residues: 740 sheet: -0.12 (0.41), residues: 138 loop : -0.36 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 247 HIS 0.006 0.001 HIS A 269 PHE 0.019 0.002 PHE D 177 TYR 0.051 0.002 TYR D 95 ARG 0.005 0.000 ARG E 68 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 615) hydrogen bonds : angle 4.47195 ( 1794) metal coordination : bond 0.01298 ( 8) metal coordination : angle 4.68042 ( 6) covalent geometry : bond 0.00352 (11308) covalent geometry : angle 0.59592 (15301) Misc. bond : bond 0.00086 ( 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 190 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 1.509 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 242 PHE cc_start: 0.9164 (m-80) cc_final: 0.8939 (m-80) REVERT: A 255 LEU cc_start: 0.9368 (tp) cc_final: 0.9011 (tp) REVERT: A 554 ILE cc_start: 0.9455 (mm) cc_final: 0.9204 (mm) REVERT: A 555 ASP cc_start: 0.9422 (t0) cc_final: 0.9152 (t0) REVERT: A 668 MET cc_start: 0.9125 (tpp) cc_final: 0.8288 (tpp) REVERT: A 689 MET cc_start: 0.8533 (ttm) cc_final: 0.8032 (ttp) REVERT: A 698 LYS cc_start: 0.9079 (mmtp) cc_final: 0.8776 (mtpt) REVERT: A 699 LYS cc_start: 0.8770 (mttp) cc_final: 0.8490 (tmtt) REVERT: B 143 MET cc_start: 0.9034 (ptp) cc_final: 0.8529 (pmm) REVERT: B 146 MET cc_start: 0.9201 (mmm) cc_final: 0.8643 (mmt) REVERT: B 308 MET cc_start: 0.7969 (tmm) cc_final: 0.7573 (tmm) REVERT: B 313 LEU cc_start: 0.9555 (mt) cc_final: 0.9353 (mt) REVERT: B 316 TYR cc_start: 0.9234 (t80) cc_final: 0.8534 (t80) REVERT: B 345 ASN cc_start: 0.8821 (t0) cc_final: 0.8470 (t0) REVERT: C 14 GLU cc_start: 0.9210 (pp20) cc_final: 0.8676 (pp20) REVERT: C 15 GLN cc_start: 0.8872 (pm20) cc_final: 0.8200 (pm20) REVERT: C 22 MET cc_start: 0.9042 (ttm) cc_final: 0.8578 (ttp) REVERT: C 121 MET cc_start: 0.9381 (mtp) cc_final: 0.9125 (mtp) REVERT: C 194 GLN cc_start: 0.9212 (tp-100) cc_final: 0.8961 (tp-100) REVERT: C 202 GLU cc_start: 0.8715 (mp0) cc_final: 0.8476 (mp0) REVERT: C 208 GLU cc_start: 0.9084 (tt0) cc_final: 0.8785 (tm-30) REVERT: C 223 ASP cc_start: 0.9420 (m-30) cc_final: 0.9060 (m-30) REVERT: D 26 MET cc_start: 0.9331 (mmm) cc_final: 0.8957 (mmm) REVERT: D 95 TYR cc_start: 0.9170 (m-80) cc_final: 0.8753 (m-10) REVERT: D 100 LEU cc_start: 0.9257 (tt) cc_final: 0.8583 (mt) REVERT: D 121 MET cc_start: 0.9674 (mtp) cc_final: 0.9029 (mmm) REVERT: D 147 LYS cc_start: 0.9653 (mttt) cc_final: 0.9156 (tppt) REVERT: D 150 GLN cc_start: 0.9321 (mt0) cc_final: 0.8889 (tp-100) REVERT: D 174 PHE cc_start: 0.9015 (t80) cc_final: 0.8798 (t80) REVERT: D 218 MET cc_start: 0.9339 (mtm) cc_final: 0.9043 (mtm) REVERT: D 219 GLN cc_start: 0.8992 (tp40) cc_final: 0.8369 (tp-100) REVERT: E 78 PHE cc_start: 0.3196 (m-80) cc_final: 0.2486 (m-80) REVERT: E 111 MET cc_start: 0.5647 (mmp) cc_final: 0.4613 (tpp) outliers start: 1 outliers final: 1 residues processed: 190 average time/residue: 0.3336 time to fit residues: 91.9537 Evaluate side-chains 152 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 26 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 80 optimal weight: 0.0040 chunk 51 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.079015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.046935 restraints weight = 220313.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.050279 restraints weight = 58519.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.052599 restraints weight = 29795.499| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11318 Z= 0.131 Angle : 0.581 9.977 15307 Z= 0.301 Chirality : 0.043 0.226 1697 Planarity : 0.003 0.039 1952 Dihedral : 6.469 57.416 1605 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.58 % Allowed : 1.83 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.23), residues: 1360 helix: 1.82 (0.19), residues: 737 sheet: 0.01 (0.43), residues: 127 loop : -0.43 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 604 HIS 0.004 0.001 HIS B 188 PHE 0.021 0.002 PHE D 177 TYR 0.028 0.002 TYR D 95 ARG 0.003 0.000 ARG A 626 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 615) hydrogen bonds : angle 4.43704 ( 1794) metal coordination : bond 0.00758 ( 8) metal coordination : angle 4.14516 ( 6) covalent geometry : bond 0.00278 (11308) covalent geometry : angle 0.57514 (15301) Misc. bond : bond 0.00054 ( 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 194 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 2.008 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: 0.8714 (mmp) cc_final: 0.8488 (mmp) REVERT: A 242 PHE cc_start: 0.9142 (m-80) cc_final: 0.8901 (m-80) REVERT: A 255 LEU cc_start: 0.9334 (tp) cc_final: 0.9061 (tp) REVERT: A 554 ILE cc_start: 0.9411 (mm) cc_final: 0.9144 (mm) REVERT: A 555 ASP cc_start: 0.9404 (t0) cc_final: 0.9146 (t0) REVERT: A 594 ASP cc_start: 0.8966 (m-30) cc_final: 0.8663 (m-30) REVERT: A 668 MET cc_start: 0.9090 (tpp) cc_final: 0.8308 (tpp) REVERT: A 698 LYS cc_start: 0.9117 (mmtp) cc_final: 0.8830 (mtpt) REVERT: A 699 LYS cc_start: 0.8786 (mttp) cc_final: 0.8551 (tmtt) REVERT: A 713 SER cc_start: 0.9526 (m) cc_final: 0.9316 (m) REVERT: B 94 MET cc_start: 0.8086 (tpp) cc_final: 0.7623 (mmm) REVERT: B 115 LEU cc_start: 0.9801 (mt) cc_final: 0.9560 (pp) REVERT: B 146 MET cc_start: 0.9224 (mmm) cc_final: 0.8388 (mmt) REVERT: B 239 HIS cc_start: 0.8202 (t70) cc_final: 0.7990 (t70) REVERT: B 316 TYR cc_start: 0.9199 (t80) cc_final: 0.8493 (t80) REVERT: C 14 GLU cc_start: 0.9148 (pp20) cc_final: 0.8914 (pp20) REVERT: C 22 MET cc_start: 0.8984 (ttm) cc_final: 0.8403 (ttp) REVERT: C 50 ASN cc_start: 0.9526 (m-40) cc_final: 0.9169 (t0) REVERT: C 121 MET cc_start: 0.9376 (mtp) cc_final: 0.9119 (mtp) REVERT: C 194 GLN cc_start: 0.9180 (tp-100) cc_final: 0.8883 (tp-100) REVERT: C 202 GLU cc_start: 0.8711 (mp0) cc_final: 0.8478 (mp0) REVERT: C 208 GLU cc_start: 0.9079 (tt0) cc_final: 0.8764 (tm-30) REVERT: C 217 ILE cc_start: 0.9817 (mm) cc_final: 0.9564 (mm) REVERT: D 26 MET cc_start: 0.9309 (mmm) cc_final: 0.9004 (mmm) REVERT: D 95 TYR cc_start: 0.9124 (m-80) cc_final: 0.8719 (m-10) REVERT: D 100 LEU cc_start: 0.9246 (tt) cc_final: 0.8542 (mt) REVERT: D 121 MET cc_start: 0.9661 (mtp) cc_final: 0.9036 (mmm) REVERT: D 147 LYS cc_start: 0.9664 (mttt) cc_final: 0.9159 (tppt) REVERT: D 150 GLN cc_start: 0.9285 (mt0) cc_final: 0.8883 (tp-100) REVERT: D 217 ILE cc_start: 0.9544 (mm) cc_final: 0.8942 (tp) REVERT: D 218 MET cc_start: 0.9337 (mtm) cc_final: 0.9049 (mtm) REVERT: D 219 GLN cc_start: 0.8991 (tp40) cc_final: 0.8585 (tm-30) REVERT: D 221 LEU cc_start: 0.9754 (mt) cc_final: 0.9532 (mt) REVERT: E 78 PHE cc_start: 0.3041 (m-80) cc_final: 0.2446 (m-80) REVERT: E 111 MET cc_start: 0.5776 (mmp) cc_final: 0.4678 (tpp) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3675 time to fit residues: 103.8872 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 : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 3 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 0.0770 chunk 56 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 129 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 overall best weight: 1.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.079441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.047269 restraints weight = 198264.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.050629 restraints weight = 57727.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.052911 restraints weight = 29884.816| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11318 Z= 0.132 Angle : 0.594 10.368 15307 Z= 0.308 Chirality : 0.043 0.210 1697 Planarity : 0.004 0.040 1952 Dihedral : 6.495 57.016 1605 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.58 % Allowed : 1.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.23), residues: 1360 helix: 1.77 (0.19), residues: 737 sheet: -0.10 (0.42), residues: 138 loop : -0.47 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.003 TRP A 604 HIS 0.004 0.001 HIS B 188 PHE 0.029 0.002 PHE B 53 TYR 0.027 0.002 TYR C 82 ARG 0.005 0.000 ARG A 626 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 615) hydrogen bonds : angle 4.46941 ( 1794) metal coordination : bond 0.00779 ( 8) metal coordination : angle 3.62299 ( 6) covalent geometry : bond 0.00282 (11308) covalent geometry : angle 0.58991 (15301) Misc. bond : bond 0.00287 ( 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 185 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 2.297 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: A 242 PHE cc_start: 0.9172 (m-80) cc_final: 0.8933 (m-80) REVERT: A 255 LEU cc_start: 0.9317 (tp) cc_final: 0.8915 (tp) REVERT: A 555 ASP cc_start: 0.9436 (t0) cc_final: 0.9164 (t0) REVERT: A 565 ASP cc_start: 0.8991 (t70) cc_final: 0.8682 (t70) REVERT: A 594 ASP cc_start: 0.8946 (m-30) cc_final: 0.8557 (m-30) REVERT: A 668 MET cc_start: 0.9089 (tpp) cc_final: 0.8284 (tpp) REVERT: A 698 LYS cc_start: 0.9085 (mmtp) cc_final: 0.8806 (mtpt) REVERT: A 699 LYS cc_start: 0.8826 (mttp) cc_final: 0.8559 (tmtt) REVERT: A 713 SER cc_start: 0.9531 (m) cc_final: 0.9329 (m) REVERT: B 115 LEU cc_start: 0.9808 (mt) cc_final: 0.9494 (pp) REVERT: B 146 MET cc_start: 0.9257 (mmm) cc_final: 0.8427 (mmt) REVERT: B 239 HIS cc_start: 0.8163 (t70) cc_final: 0.7953 (t70) REVERT: B 308 MET cc_start: 0.7693 (tmm) cc_final: 0.7442 (tmm) REVERT: B 316 TYR cc_start: 0.9219 (t80) cc_final: 0.8519 (t80) REVERT: B 345 ASN cc_start: 0.9129 (t0) cc_final: 0.8720 (p0) REVERT: C 22 MET cc_start: 0.8972 (ttm) cc_final: 0.8432 (ttp) REVERT: C 50 ASN cc_start: 0.9511 (m-40) cc_final: 0.9149 (t0) REVERT: C 121 MET cc_start: 0.9387 (mtp) cc_final: 0.9126 (mtp) REVERT: C 194 GLN cc_start: 0.9188 (tp-100) cc_final: 0.8890 (tp-100) REVERT: C 202 GLU cc_start: 0.8728 (mp0) cc_final: 0.8484 (mp0) REVERT: C 208 GLU cc_start: 0.9057 (tt0) cc_final: 0.8745 (tm-30) REVERT: C 216 LEU cc_start: 0.9489 (pp) cc_final: 0.9280 (pp) REVERT: C 223 ASP cc_start: 0.9369 (m-30) cc_final: 0.9011 (m-30) REVERT: D 14 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9186 (tm-30) REVERT: D 26 MET cc_start: 0.9303 (mmm) cc_final: 0.8976 (mmm) REVERT: D 95 TYR cc_start: 0.9135 (m-80) cc_final: 0.8731 (m-10) REVERT: D 100 LEU cc_start: 0.9251 (tt) cc_final: 0.8528 (mt) REVERT: D 121 MET cc_start: 0.9659 (mtp) cc_final: 0.9011 (mmm) REVERT: D 147 LYS cc_start: 0.9657 (mttt) cc_final: 0.9157 (tppt) REVERT: D 174 PHE cc_start: 0.9061 (t80) cc_final: 0.8772 (t80) REVERT: D 217 ILE cc_start: 0.9544 (mm) cc_final: 0.8961 (tp) REVERT: D 218 MET cc_start: 0.9343 (mtm) cc_final: 0.9054 (mtm) REVERT: D 219 GLN cc_start: 0.9014 (tp40) cc_final: 0.8593 (tm-30) REVERT: D 221 LEU cc_start: 0.9748 (mt) cc_final: 0.9543 (mt) REVERT: E 78 PHE cc_start: 0.2924 (m-80) cc_final: 0.2339 (m-80) REVERT: E 111 MET cc_start: 0.5858 (mmp) cc_final: 0.4651 (tpp) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.4115 time to fit residues: 111.5863 Evaluate side-chains 147 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 104 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.077867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.045939 restraints weight = 195971.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.049175 restraints weight = 58104.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.051383 restraints weight = 30363.090| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11318 Z= 0.194 Angle : 0.639 8.683 15307 Z= 0.335 Chirality : 0.044 0.202 1697 Planarity : 0.004 0.038 1952 Dihedral : 6.633 59.459 1605 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.58 % Allowed : 0.91 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.23), residues: 1360 helix: 1.66 (0.19), residues: 733 sheet: -0.01 (0.42), residues: 138 loop : -0.57 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 604 HIS 0.005 0.001 HIS A 235 PHE 0.021 0.002 PHE B 53 TYR 0.044 0.002 TYR E 157 ARG 0.006 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 615) hydrogen bonds : angle 4.56131 ( 1794) metal coordination : bond 0.01588 ( 8) metal coordination : angle 4.51232 ( 6) covalent geometry : bond 0.00405 (11308) covalent geometry : angle 0.63260 (15301) Misc. bond : bond 0.00041 ( 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 178 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 2.097 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 255 LEU cc_start: 0.9349 (tp) cc_final: 0.9115 (tp) REVERT: A 555 ASP cc_start: 0.9439 (t0) cc_final: 0.9171 (t0) REVERT: A 565 ASP cc_start: 0.9022 (t70) cc_final: 0.8667 (t70) REVERT: A 594 ASP cc_start: 0.8969 (m-30) cc_final: 0.8641 (m-30) REVERT: A 668 MET cc_start: 0.9112 (tpp) cc_final: 0.8310 (tpp) REVERT: A 698 LYS cc_start: 0.9093 (mmtp) cc_final: 0.8610 (mmmm) REVERT: A 699 LYS cc_start: 0.8882 (mttp) cc_final: 0.8637 (tmtt) REVERT: B 146 MET cc_start: 0.9266 (mmm) cc_final: 0.8468 (mmt) REVERT: B 308 MET cc_start: 0.7655 (tmm) cc_final: 0.7389 (tmm) REVERT: B 345 ASN cc_start: 0.9058 (t0) cc_final: 0.8644 (p0) REVERT: C 22 MET cc_start: 0.9026 (ttm) cc_final: 0.8499 (ttp) REVERT: C 50 ASN cc_start: 0.9549 (m-40) cc_final: 0.9194 (t0) REVERT: C 121 MET cc_start: 0.9398 (mtp) cc_final: 0.9098 (mtp) REVERT: C 194 GLN cc_start: 0.9178 (tp-100) cc_final: 0.8898 (tp-100) REVERT: C 202 GLU cc_start: 0.8668 (mp0) cc_final: 0.8409 (mp0) REVERT: C 208 GLU cc_start: 0.9093 (tt0) cc_final: 0.8786 (tm-30) REVERT: D 26 MET cc_start: 0.9316 (mmm) cc_final: 0.8988 (mmm) REVERT: D 95 TYR cc_start: 0.9142 (m-80) cc_final: 0.8731 (m-10) REVERT: D 100 LEU cc_start: 0.9295 (tt) cc_final: 0.8590 (mt) REVERT: D 121 MET cc_start: 0.9680 (mtp) cc_final: 0.9031 (mmm) REVERT: D 147 LYS cc_start: 0.9657 (mttt) cc_final: 0.8979 (tppt) REVERT: D 150 GLN cc_start: 0.9287 (mt0) cc_final: 0.8870 (pt0) REVERT: D 174 PHE cc_start: 0.9052 (t80) cc_final: 0.8819 (t80) REVERT: D 217 ILE cc_start: 0.9581 (mm) cc_final: 0.9005 (tp) REVERT: D 218 MET cc_start: 0.9364 (mtm) cc_final: 0.9057 (mtm) REVERT: D 219 GLN cc_start: 0.9029 (tp40) cc_final: 0.8377 (tp-100) REVERT: D 221 LEU cc_start: 0.9742 (mt) cc_final: 0.9498 (mt) REVERT: E 78 PHE cc_start: 0.2887 (m-80) cc_final: 0.2540 (m-80) REVERT: E 100 ILE cc_start: 0.5938 (mt) cc_final: 0.5124 (mt) REVERT: E 111 MET cc_start: 0.6061 (mmp) cc_final: 0.4807 (tpp) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2976 time to fit residues: 78.0755 Evaluate side-chains 139 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 3 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 42 optimal weight: 0.0870 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.079005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.047251 restraints weight = 164883.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.050451 restraints weight = 53372.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.052590 restraints weight = 28598.586| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11318 Z= 0.133 Angle : 0.609 8.718 15307 Z= 0.318 Chirality : 0.044 0.201 1697 Planarity : 0.004 0.048 1952 Dihedral : 6.494 56.717 1605 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.58 % Allowed : 0.33 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.23), residues: 1360 helix: 1.77 (0.19), residues: 733 sheet: 0.02 (0.44), residues: 131 loop : -0.59 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 604 HIS 0.005 0.001 HIS A 269 PHE 0.022 0.002 PHE B 53 TYR 0.042 0.002 TYR E 157 ARG 0.011 0.000 ARG E 41 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 615) hydrogen bonds : angle 4.47065 ( 1794) metal coordination : bond 0.00706 ( 8) metal coordination : angle 3.52577 ( 6) covalent geometry : bond 0.00279 (11308) covalent geometry : angle 0.60520 (15301) Misc. bond : bond 0.00106 ( 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 181 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.992 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 254 LEU cc_start: 0.9638 (tp) cc_final: 0.9428 (tt) REVERT: A 555 ASP cc_start: 0.9420 (t0) cc_final: 0.9166 (t0) REVERT: A 564 MET cc_start: 0.9167 (mmm) cc_final: 0.8963 (mmp) REVERT: A 565 ASP cc_start: 0.8986 (t70) cc_final: 0.8783 (t70) REVERT: A 594 ASP cc_start: 0.8934 (m-30) cc_final: 0.8615 (m-30) REVERT: A 640 TYR cc_start: 0.9524 (t80) cc_final: 0.9270 (t80) REVERT: A 668 MET cc_start: 0.9100 (tpp) cc_final: 0.8302 (tpp) REVERT: A 674 LEU cc_start: 0.9374 (tp) cc_final: 0.9131 (tp) REVERT: A 698 LYS cc_start: 0.9091 (mmtp) cc_final: 0.8650 (mtpt) REVERT: A 699 LYS cc_start: 0.8920 (mttp) cc_final: 0.8669 (tmtt) REVERT: B 115 LEU cc_start: 0.9803 (mt) cc_final: 0.9552 (pp) REVERT: B 146 MET cc_start: 0.9268 (mmm) cc_final: 0.8455 (mmt) REVERT: B 230 MET cc_start: 0.7967 (tpp) cc_final: 0.6855 (tmm) REVERT: B 308 MET cc_start: 0.7636 (tmm) cc_final: 0.7353 (tmm) REVERT: B 316 TYR cc_start: 0.9274 (t80) cc_final: 0.9020 (t80) REVERT: B 345 ASN cc_start: 0.9056 (t0) cc_final: 0.8642 (p0) REVERT: C 22 MET cc_start: 0.8945 (ttm) cc_final: 0.8416 (ttp) REVERT: C 50 ASN cc_start: 0.9515 (m-40) cc_final: 0.9148 (t0) REVERT: C 121 MET cc_start: 0.9381 (mtp) cc_final: 0.9114 (mtp) REVERT: C 194 GLN cc_start: 0.9190 (tp-100) cc_final: 0.8898 (tp-100) REVERT: C 202 GLU cc_start: 0.8759 (mp0) cc_final: 0.8517 (mp0) REVERT: C 208 GLU cc_start: 0.9088 (tt0) cc_final: 0.8756 (tm-30) REVERT: D 26 MET cc_start: 0.9269 (mmm) cc_final: 0.8890 (mmm) REVERT: D 95 TYR cc_start: 0.9139 (m-80) cc_final: 0.8745 (m-10) REVERT: D 100 LEU cc_start: 0.9249 (tt) cc_final: 0.8543 (mt) REVERT: D 121 MET cc_start: 0.9639 (mtp) cc_final: 0.8956 (mmm) REVERT: D 147 LYS cc_start: 0.9668 (mttt) cc_final: 0.9182 (tppt) REVERT: D 150 GLN cc_start: 0.9299 (mt0) cc_final: 0.8870 (tp-100) REVERT: D 174 PHE cc_start: 0.9025 (t80) cc_final: 0.8734 (t80) REVERT: D 217 ILE cc_start: 0.9558 (mm) cc_final: 0.8972 (tp) REVERT: D 218 MET cc_start: 0.9355 (mtm) cc_final: 0.9040 (mtm) REVERT: D 219 GLN cc_start: 0.9030 (tp40) cc_final: 0.8590 (tm-30) REVERT: D 221 LEU cc_start: 0.9741 (mt) cc_final: 0.9522 (mt) REVERT: E 78 PHE cc_start: 0.2866 (m-80) cc_final: 0.2488 (m-80) REVERT: E 100 ILE cc_start: 0.5913 (mt) cc_final: 0.5125 (mt) REVERT: E 111 MET cc_start: 0.6129 (mmp) cc_final: 0.4827 (tpp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2495 time to fit residues: 65.8218 Evaluate side-chains 148 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 69 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 0.0670 chunk 43 optimal weight: 3.9990 chunk 125 optimal weight: 40.0000 chunk 81 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 overall best weight: 4.3924 ------------------------------------------------------------------------------- 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 ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.076707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.044671 restraints weight = 225109.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.047838 restraints weight = 63231.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.049976 restraints weight = 32677.351| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11318 Z= 0.270 Angle : 0.721 11.959 15307 Z= 0.379 Chirality : 0.046 0.193 1697 Planarity : 0.005 0.043 1952 Dihedral : 6.741 59.639 1605 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.58 % Allowed : 0.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.23), residues: 1360 helix: 1.31 (0.19), residues: 736 sheet: -0.26 (0.43), residues: 127 loop : -0.69 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 604 HIS 0.007 0.002 HIS A 235 PHE 0.034 0.003 PHE A 268 TYR 0.039 0.003 TYR E 157 ARG 0.008 0.001 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 615) hydrogen bonds : angle 4.82565 ( 1794) metal coordination : bond 0.02261 ( 8) metal coordination : angle 5.36915 ( 6) covalent geometry : bond 0.00555 (11308) covalent geometry : angle 0.71368 (15301) Misc. bond : bond 0.00143 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5787.64 seconds wall clock time: 108 minutes 39.72 seconds (6519.72 seconds total)