Starting phenix.real_space_refine on Fri Jul 3 16:58:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7adp_11733/07_2026/7adp_11733.cif Found real_map, /net/cci-nas-00/data/ceres_data/7adp_11733/07_2026/7adp_11733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7adp_11733/07_2026/7adp_11733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7adp_11733/07_2026/7adp_11733.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7adp_11733/07_2026/7adp_11733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7adp_11733/07_2026/7adp_11733.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7adp_11733/07_2026/7adp_11733.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7adp_11733/07_2026/7adp_11733.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 9643 2.51 5 N 2580 2.21 5 O 2743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15026 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 6983 Classifications: {'peptide': 881} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 41, 'TRANS': 839} Chain breaks: 7 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2249 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 4, 'TRANS': 268} Chain breaks: 1 Chain: "C" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1562 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 353 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 39} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 726 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain breaks: 1 Chain: "F" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "H" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1304 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1026 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.67, per 1000 atoms: 0.18 Number of scatterers: 15026 At special positions: 0 Unit cell: (157.536, 141.126, 173.946, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2743 8.00 N 2580 7.00 C 9643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS I 135 " - pdb=" SG CYS I 168 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 370 " " NAG A1002 " - " ASN A 818 " " NAG I 301 " - " ASN I 182 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 428.3 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3544 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 26 sheets defined 37.6% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 482 through 502 removed outlier: 3.599A pdb=" N LEU A 502 " --> pdb=" O TRP A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 666 Processing helix chain 'A' and resid 876 through 879 removed outlier: 3.657A pdb=" N ASP A 879 " --> pdb=" O ALA A 876 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 876 through 879' Processing helix chain 'A' and resid 962 through 992 removed outlier: 4.171A pdb=" N SER A 966 " --> pdb=" O TYR A 962 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 25 removed outlier: 3.813A pdb=" N TRP B 22 " --> pdb=" O LYS B 18 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG B 23 " --> pdb=" O MET B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 44 removed outlier: 4.674A pdb=" N GLU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 49 removed outlier: 3.581A pdb=" N GLY B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 59 Processing helix chain 'B' and resid 59 through 67 removed outlier: 4.550A pdb=" N ASP B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 83 removed outlier: 3.797A pdb=" N PHE B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU B 78 " --> pdb=" O PHE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 100 removed outlier: 3.665A pdb=" N LEU B 92 " --> pdb=" O ARG B 88 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 removed outlier: 3.709A pdb=" N ALA B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 135 removed outlier: 3.606A pdb=" N ARG B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 151 removed outlier: 3.644A pdb=" N ALA B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 168 removed outlier: 4.065A pdb=" N GLU B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 182 removed outlier: 3.512A pdb=" N CYS B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 201 removed outlier: 4.147A pdb=" N CYS B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 223 removed outlier: 3.728A pdb=" N LEU B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 240 Processing helix chain 'B' and resid 246 through 272 removed outlier: 3.555A pdb=" N GLY B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 292 removed outlier: 4.321A pdb=" N LEU B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 39 removed outlier: 3.866A pdb=" N ARG C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Proline residue: C 19 - end of helix Processing helix chain 'C' and resid 46 through 64 Processing helix chain 'C' and resid 69 through 82 removed outlier: 3.627A pdb=" N PHE C 73 " --> pdb=" O PRO C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 148 through 153 removed outlier: 3.617A pdb=" N LEU C 152 " --> pdb=" O PHE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 187 removed outlier: 3.965A pdb=" N PHE C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 227 removed outlier: 3.667A pdb=" N LEU C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'D' and resid 161 through 166 Processing helix chain 'E' and resid 5 through 34 Processing helix chain 'E' and resid 43 through 64 removed outlier: 3.676A pdb=" N GLY E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 76 removed outlier: 4.076A pdb=" N GLU E 75 " --> pdb=" O ASP E 71 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 71 through 76' Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'E' and resid 80 through 86 removed outlier: 3.576A pdb=" N LEU E 84 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN E 86 " --> pdb=" O ASP E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 95 through 100 removed outlier: 3.501A pdb=" N ARG E 98 " --> pdb=" O HIS E 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 44 removed outlier: 4.258A pdb=" N LEU F 44 " --> pdb=" O THR F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 71 Processing helix chain 'F' and resid 81 through 86 removed outlier: 3.662A pdb=" N PHE F 85 " --> pdb=" O ARG F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 109 removed outlier: 3.764A pdb=" N LEU F 93 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE F 94 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL F 109 " --> pdb=" O GLY F 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 21 removed outlier: 3.507A pdb=" N TYR H 21 " --> pdb=" O HIS H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 85 removed outlier: 4.225A pdb=" N LEU H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 120 Processing helix chain 'H' and resid 166 through 177 Processing helix chain 'H' and resid 178 through 183 removed outlier: 5.186A pdb=" N GLU H 181 " --> pdb=" O ARG H 178 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU H 183 " --> pdb=" O TYR H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 192 Processing helix chain 'H' and resid 199 through 206 removed outlier: 3.502A pdb=" N ASN H 203 " --> pdb=" O ASN H 199 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL H 206 " --> pdb=" O ILE H 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 104 removed outlier: 3.572A pdb=" N LEU I 104 " --> pdb=" O ASP I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 139 removed outlier: 4.267A pdb=" N GLU I 139 " --> pdb=" O CYS I 135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 44 removed outlier: 6.917A pdb=" N ALA A 57 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ALA A 43 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A 55 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A 64 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 109 removed outlier: 3.659A pdb=" N TRP A 119 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 154 Processing sheet with id=AA6, first strand: chain 'A' and resid 177 through 179 removed outlier: 4.166A pdb=" N MET A 177 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 189 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A 179 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 188 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 235 through 239 Processing sheet with id=AA8, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.562A pdb=" N HIS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR A 300 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN A 315 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU A 302 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 319 through 326 removed outlier: 7.160A pdb=" N THR A 319 " --> pdb=" O CYS A 338 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N CYS A 338 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU A 321 " --> pdb=" O MET A 336 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 325 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 377 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR A 389 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 12.117A pdb=" N LEU A 379 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 11.819A pdb=" N LEU A 387 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 406 through 409 removed outlier: 6.593A pdb=" N LEU A 430 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER A 444 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE A 432 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 457 removed outlier: 4.073A pdb=" N CYS A 454 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AB4, first strand: chain 'A' and resid 570 through 576 removed outlier: 3.682A pdb=" N MET A 573 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 575 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLN A 586 " --> pdb=" O GLN A 575 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 625 through 627 removed outlier: 4.109A pdb=" N GLN A 625 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 696 through 699 Processing sheet with id=AB7, first strand: chain 'A' and resid 706 through 712 removed outlier: 7.208A pdb=" N VAL A 744 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL A 710 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA A 742 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLY A 712 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N LEU A 740 " --> pdb=" O GLY A 712 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS A 771 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP A 763 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 769 " --> pdb=" O ASP A 763 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N THR I 191 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER A 772 " --> pdb=" O THR I 191 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.046A pdb=" N GLY A 813 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS A 783 " --> pdb=" O GLN A 794 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.046A pdb=" N GLY A 813 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 845 through 849 removed outlier: 4.112A pdb=" N ALA A 846 " --> pdb=" O GLY A 864 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 921 through 926 removed outlier: 4.148A pdb=" N GLY A 921 " --> pdb=" O TYR A 938 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 938 " --> pdb=" O GLY A 921 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS A 933 " --> pdb=" O VAL A 947 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 5 through 6 removed outlier: 7.012A pdb=" N LYS H 5 " --> pdb=" O PHE H 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'H' and resid 56 through 62 removed outlier: 4.000A pdb=" N LEU H 60 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASN H 27 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL H 26 " --> pdb=" O GLN H 94 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLN H 94 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY H 28 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR H 92 " --> pdb=" O GLY H 28 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU H 30 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA H 123 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 144 through 145 Processing sheet with id=AC6, first strand: chain 'I' and resid 52 through 54 Processing sheet with id=AC7, first strand: chain 'I' and resid 69 through 70 removed outlier: 3.640A pdb=" N ARG I 69 " --> pdb=" O HIS I 58 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 156 through 163 621 hydrogen bonds defined for protein. 1767 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: 2.00 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4841 1.34 - 1.46: 3411 1.46 - 1.58: 7001 1.58 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 15353 Sorted by residual: bond pdb=" CG LEU A 54 " pdb=" CD2 LEU A 54 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.55e+00 bond pdb=" CG1 ILE A 863 " pdb=" CD1 ILE A 863 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.35e+00 bond pdb=" C1 NAG A1001 " pdb=" O5 NAG A1001 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.99e+00 bond pdb=" C1 NAG A1002 " pdb=" O5 NAG A1002 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.96e+00 bond pdb=" CB THR A 425 " pdb=" CG2 THR A 425 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.23e+00 ... (remaining 15348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 19930 1.75 - 3.50: 746 3.50 - 5.25: 109 5.25 - 7.00: 19 7.00 - 8.74: 5 Bond angle restraints: 20809 Sorted by residual: angle pdb=" C ASP A 231 " pdb=" N GLU A 232 " pdb=" CA GLU A 232 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C ARG F 72 " pdb=" N ARG F 73 " pdb=" CA ARG F 73 " ideal model delta sigma weight residual 121.54 128.31 -6.77 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C HIS I 164 " pdb=" N PRO I 165 " pdb=" CA PRO I 165 " ideal model delta sigma weight residual 127.00 135.33 -8.33 2.40e+00 1.74e-01 1.20e+01 angle pdb=" CA TRP F 100 " pdb=" CB TRP F 100 " pdb=" CG TRP F 100 " ideal model delta sigma weight residual 113.60 119.90 -6.30 1.90e+00 2.77e-01 1.10e+01 angle pdb=" CA GLU F 16 " pdb=" CB GLU F 16 " pdb=" CG GLU F 16 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.86e+00 ... (remaining 20804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 7974 17.51 - 35.03: 916 35.03 - 52.54: 189 52.54 - 70.06: 24 70.06 - 87.57: 14 Dihedral angle restraints: 9117 sinusoidal: 3646 harmonic: 5471 Sorted by residual: dihedral pdb=" CA GLU A 232 " pdb=" C GLU A 232 " pdb=" N ALA A 233 " pdb=" CA ALA A 233 " ideal model delta harmonic sigma weight residual 180.00 139.17 40.83 0 5.00e+00 4.00e-02 6.67e+01 dihedral pdb=" CB CYS I 135 " pdb=" SG CYS I 135 " pdb=" SG CYS I 168 " pdb=" CB CYS I 168 " ideal model delta sinusoidal sigma weight residual 93.00 160.65 -67.65 1 1.00e+01 1.00e-02 5.95e+01 dihedral pdb=" CA PRO H 59 " pdb=" C PRO H 59 " pdb=" N LEU H 60 " pdb=" CA LEU H 60 " ideal model delta harmonic sigma weight residual -180.00 -141.89 -38.11 0 5.00e+00 4.00e-02 5.81e+01 ... (remaining 9114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1543 0.039 - 0.079: 575 0.079 - 0.118: 203 0.118 - 0.157: 39 0.157 - 0.196: 5 Chirality restraints: 2365 Sorted by residual: chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 370 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA GLU F 16 " pdb=" N GLU F 16 " pdb=" C GLU F 16 " pdb=" CB GLU F 16 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA ILE A 863 " pdb=" N ILE A 863 " pdb=" C ILE A 863 " pdb=" CB ILE A 863 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 2362 not shown) Planarity restraints: 2628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 370 " 0.257 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" CG ASN A 370 " -0.111 2.00e-02 2.50e+03 pdb=" OD1 ASN A 370 " -0.052 2.00e-02 2.50e+03 pdb=" ND2 ASN A 370 " -0.458 2.00e-02 2.50e+03 pdb=" C1 NAG A1001 " 0.364 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 818 " -0.158 2.00e-02 2.50e+03 1.70e-01 3.62e+02 pdb=" CG ASN A 818 " 0.064 2.00e-02 2.50e+03 pdb=" OD1 ASN A 818 " 0.037 2.00e-02 2.50e+03 pdb=" ND2 ASN A 818 " 0.266 2.00e-02 2.50e+03 pdb=" C1 NAG A1002 " -0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 182 " -0.137 2.00e-02 2.50e+03 1.52e-01 2.91e+02 pdb=" CG ASN I 182 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN I 182 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN I 182 " 0.249 2.00e-02 2.50e+03 pdb=" C1 NAG I 301 " -0.181 2.00e-02 2.50e+03 ... (remaining 2625 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 124 2.51 - 3.11: 11979 3.11 - 3.71: 22328 3.71 - 4.30: 29451 4.30 - 4.90: 50394 Nonbonded interactions: 114276 Sorted by model distance: nonbonded pdb=" O GLN A 533 " pdb=" OG SER A 550 " model vdw 1.915 3.040 nonbonded pdb=" O HIS A 751 " pdb=" OG1 THR A 755 " model vdw 1.993 3.040 nonbonded pdb=" OG SER I 136 " pdb=" O GLY I 166 " model vdw 2.080 3.040 nonbonded pdb=" OG1 THR A 857 " pdb=" OG SER A 950 " model vdw 2.088 3.040 nonbonded pdb=" OD1 ASP A 239 " pdb=" OG SER A 241 " model vdw 2.096 3.040 ... (remaining 114271 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.040 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 15359 Z= 0.274 Angle : 0.825 17.521 20824 Z= 0.434 Chirality : 0.046 0.196 2365 Planarity : 0.005 0.070 2625 Dihedral : 15.280 87.573 5564 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.12 % Allowed : 4.18 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.91 (0.15), residues: 1830 helix: -1.93 (0.17), residues: 617 sheet: -3.06 (0.21), residues: 385 loop : -4.46 (0.14), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 73 TYR 0.023 0.002 TYR F 110 PHE 0.021 0.002 PHE A 292 TRP 0.016 0.002 TRP F 100 HIS 0.009 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.27 (15353) covalent geometry : angle 0.79148 / 0.43 (20809) SS BOND : bond 0.00339 / 0.17 ( 3) SS BOND : angle 0.90430 / 0.47 ( 6) hydrogen bonds : bond 0.13392 / 8.90 ( 620) hydrogen bonds : angle 6.58505 / 4.41 ( 1767) link_NAG-ASN : bond 0.08273 / 4.17 ( 3) link_NAG-ASN : angle 11.18092 / 6.14 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 227 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 ASP cc_start: 0.7982 (m-30) cc_final: 0.7766 (p0) REVERT: B 51 ASP cc_start: 0.8644 (t0) cc_final: 0.8165 (t0) REVERT: B 197 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7956 (mt-10) REVERT: C 31 ARG cc_start: 0.8350 (ttt-90) cc_final: 0.7960 (ptt-90) REVERT: C 39 GLN cc_start: 0.8391 (mt0) cc_final: 0.8119 (tm-30) REVERT: E 71 ASP cc_start: 0.7941 (m-30) cc_final: 0.7590 (m-30) REVERT: E 91 TYR cc_start: 0.8370 (m-10) cc_final: 0.7790 (m-80) REVERT: H 98 ARG cc_start: 0.7382 (mtp180) cc_final: 0.7169 (mtm180) outliers start: 2 outliers final: 1 residues processed: 229 average time/residue: 0.1395 time to fit residues: 43.8796 Evaluate side-chains 141 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 174 HIS A 521 ASN B 222 ASN B 223 ASN C 154 GLN C 175 ASN I 171 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.099544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.073728 restraints weight = 43870.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.076248 restraints weight = 23212.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.077882 restraints weight = 16152.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.078915 restraints weight = 12987.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.079555 restraints weight = 11343.853| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15359 Z= 0.159 Angle : 0.723 10.907 20824 Z= 0.366 Chirality : 0.047 0.231 2365 Planarity : 0.004 0.052 2625 Dihedral : 5.504 37.313 2033 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 0.98 % Allowed : 12.12 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.18), residues: 1830 helix: 0.20 (0.21), residues: 633 sheet: -1.98 (0.23), residues: 392 loop : -3.74 (0.16), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 20 TYR 0.012 0.002 TYR H 21 PHE 0.017 0.001 PHE A 530 TRP 0.041 0.002 TRP A 219 HIS 0.007 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (15353) covalent geometry : angle 0.71110 / 0.36 (20809) SS BOND : bond 0.00574 / 0.29 ( 3) SS BOND : angle 4.24647 / 2.96 ( 6) hydrogen bonds : bond 0.04273 / 2.85 ( 620) hydrogen bonds : angle 5.11235 / 3.48 ( 1767) link_NAG-ASN : bond 0.00308 / 0.15 ( 3) link_NAG-ASN : angle 5.42187 / 3.00 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 917 SER cc_start: 0.8435 (t) cc_final: 0.7968 (m) REVERT: B 51 ASP cc_start: 0.8495 (t0) cc_final: 0.7946 (t0) REVERT: B 197 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7881 (mp0) REVERT: B 223 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.6479 (t0) REVERT: C 235 ASP cc_start: 0.8199 (p0) cc_final: 0.7687 (m-30) REVERT: C 236 ASP cc_start: 0.7839 (p0) cc_final: 0.7145 (p0) REVERT: E 71 ASP cc_start: 0.7802 (m-30) cc_final: 0.7465 (m-30) REVERT: E 91 TYR cc_start: 0.8706 (m-10) cc_final: 0.8286 (m-80) REVERT: F 16 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8521 (tm-30) REVERT: F 46 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8094 (pp) REVERT: F 106 MET cc_start: 0.8231 (mmm) cc_final: 0.7920 (mmp) REVERT: H 9 GLN cc_start: 0.6539 (pt0) cc_final: 0.6336 (pt0) REVERT: H 178 ARG cc_start: 0.8399 (mmm-85) cc_final: 0.8026 (tpp80) REVERT: H 195 ASN cc_start: 0.7840 (m-40) cc_final: 0.7237 (t0) REVERT: H 203 ASN cc_start: 0.8577 (t0) cc_final: 0.8368 (t0) REVERT: I 178 LEU cc_start: 0.4452 (OUTLIER) cc_final: 0.4077 (pp) outliers start: 16 outliers final: 8 residues processed: 187 average time/residue: 0.1214 time to fit residues: 32.3785 Evaluate side-chains 153 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain I residue 168 CYS Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 118 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 156 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN C 71 GLN H 147 HIS ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.098199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.072049 restraints weight = 44210.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.075621 restraints weight = 24781.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.076199 restraints weight = 14966.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.076514 restraints weight = 13767.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.076543 restraints weight = 12833.630| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15359 Z= 0.146 Angle : 0.672 12.975 20824 Z= 0.341 Chirality : 0.045 0.218 2365 Planarity : 0.004 0.049 2625 Dihedral : 5.268 40.259 2033 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 1.91 % Allowed : 15.20 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.19), residues: 1830 helix: 0.80 (0.21), residues: 633 sheet: -1.41 (0.25), residues: 393 loop : -3.44 (0.17), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 76 TYR 0.018 0.001 TYR H 21 PHE 0.014 0.001 PHE A 530 TRP 0.020 0.001 TRP A 219 HIS 0.006 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (15353) covalent geometry : angle 0.66429 / 0.34 (20809) SS BOND : bond 0.00214 / 0.11 ( 3) SS BOND : angle 2.63887 / 1.83 ( 6) hydrogen bonds : bond 0.04058 / 2.72 ( 620) hydrogen bonds : angle 4.83565 / 3.29 ( 1767) link_NAG-ASN : bond 0.00427 / 0.22 ( 3) link_NAG-ASN : angle 4.40363 / 2.37 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 917 SER cc_start: 0.8482 (t) cc_final: 0.8067 (m) REVERT: B 51 ASP cc_start: 0.8610 (t0) cc_final: 0.8026 (t0) REVERT: B 197 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8007 (mp0) REVERT: B 223 ASN cc_start: 0.6964 (OUTLIER) cc_final: 0.6444 (t0) REVERT: C 235 ASP cc_start: 0.8276 (p0) cc_final: 0.7760 (m-30) REVERT: C 236 ASP cc_start: 0.8111 (p0) cc_final: 0.7902 (t0) REVERT: E 91 TYR cc_start: 0.8654 (m-10) cc_final: 0.8175 (m-80) REVERT: F 16 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8431 (tm-30) REVERT: F 106 MET cc_start: 0.8358 (mmm) cc_final: 0.7934 (mmp) REVERT: H 178 ARG cc_start: 0.8638 (mmm-85) cc_final: 0.8182 (tpp80) REVERT: H 195 ASN cc_start: 0.7829 (m-40) cc_final: 0.7235 (t0) REVERT: I 178 LEU cc_start: 0.4272 (OUTLIER) cc_final: 0.3913 (pp) outliers start: 31 outliers final: 20 residues processed: 183 average time/residue: 0.1048 time to fit residues: 28.0806 Evaluate side-chains 159 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 168 CYS Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 84 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 134 optimal weight: 0.0030 chunk 17 optimal weight: 2.9990 overall best weight: 2.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN E 87 HIS ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.095874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.069712 restraints weight = 44223.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.073319 restraints weight = 24724.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.073846 restraints weight = 14891.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.074183 restraints weight = 13302.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.074261 restraints weight = 12798.378| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15359 Z= 0.197 Angle : 0.687 11.678 20824 Z= 0.351 Chirality : 0.046 0.186 2365 Planarity : 0.004 0.048 2625 Dihedral : 5.282 44.544 2033 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 3.38 % Allowed : 17.35 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.19), residues: 1830 helix: 0.89 (0.21), residues: 634 sheet: -1.17 (0.26), residues: 398 loop : -3.25 (0.18), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 169 TYR 0.020 0.002 TYR F 77 PHE 0.019 0.001 PHE A 128 TRP 0.014 0.001 TRP A 219 HIS 0.005 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (15353) covalent geometry : angle 0.68253 / 0.35 (20809) SS BOND : bond 0.00145 / 0.07 ( 3) SS BOND : angle 1.89843 / 1.11 ( 6) hydrogen bonds : bond 0.04361 / 2.94 ( 620) hydrogen bonds : angle 4.78751 / 3.25 ( 1767) link_NAG-ASN : bond 0.00519 / 0.27 ( 3) link_NAG-ASN : angle 3.60927 / 1.99 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 149 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 HIS cc_start: 0.7884 (t-90) cc_final: 0.7327 (t-90) REVERT: A 863 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8601 (mt) REVERT: A 917 SER cc_start: 0.8667 (t) cc_final: 0.8231 (m) REVERT: B 51 ASP cc_start: 0.8633 (t0) cc_final: 0.8049 (t0) REVERT: B 197 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8032 (mp0) REVERT: B 222 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7475 (t0) REVERT: B 223 ASN cc_start: 0.7158 (OUTLIER) cc_final: 0.6898 (t0) REVERT: B 238 HIS cc_start: 0.7923 (OUTLIER) cc_final: 0.7457 (t-90) REVERT: E 91 TYR cc_start: 0.8707 (m-10) cc_final: 0.8213 (m-80) REVERT: F 16 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8506 (tm-30) REVERT: F 20 ARG cc_start: 0.7702 (mtm110) cc_final: 0.7184 (mtm110) REVERT: F 100 TRP cc_start: 0.7961 (OUTLIER) cc_final: 0.7697 (t60) REVERT: F 106 MET cc_start: 0.8405 (mmm) cc_final: 0.7979 (mmp) REVERT: H 195 ASN cc_start: 0.7946 (m-40) cc_final: 0.7352 (t0) REVERT: I 93 GLU cc_start: 0.8597 (pm20) cc_final: 0.8320 (pm20) REVERT: I 178 LEU cc_start: 0.4784 (OUTLIER) cc_final: 0.4282 (pp) outliers start: 55 outliers final: 28 residues processed: 193 average time/residue: 0.1374 time to fit residues: 38.7960 Evaluate side-chains 171 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 100 TRP Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 168 CYS Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 87 optimal weight: 0.1980 chunk 134 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 GLN A 580 HIS A 737 ASN B 223 ASN B 238 HIS ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 141 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.094108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.067867 restraints weight = 44454.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.071342 restraints weight = 24992.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.071909 restraints weight = 15046.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.072191 restraints weight = 14005.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.072280 restraints weight = 13244.817| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15359 Z= 0.239 Angle : 0.729 12.384 20824 Z= 0.370 Chirality : 0.047 0.180 2365 Planarity : 0.004 0.048 2625 Dihedral : 5.328 28.943 2032 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 3.32 % Allowed : 19.75 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.19), residues: 1830 helix: 0.95 (0.21), residues: 633 sheet: -1.08 (0.26), residues: 395 loop : -3.17 (0.18), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 20 TYR 0.020 0.002 TYR A 898 PHE 0.022 0.002 PHE A 128 TRP 0.020 0.002 TRP D 17 HIS 0.006 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (15353) covalent geometry : angle 0.72401 / 0.37 (20809) SS BOND : bond 0.00324 / 0.16 ( 3) SS BOND : angle 1.80641 / 0.94 ( 6) hydrogen bonds : bond 0.04583 / 3.10 ( 620) hydrogen bonds : angle 4.92487 / 3.35 ( 1767) link_NAG-ASN : bond 0.00502 / 0.26 ( 3) link_NAG-ASN : angle 3.75416 / 2.06 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 150 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 HIS cc_start: 0.8005 (t-90) cc_final: 0.7391 (t-90) REVERT: B 24 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8753 (tm-30) REVERT: B 51 ASP cc_start: 0.8629 (t0) cc_final: 0.8042 (t0) REVERT: B 60 MET cc_start: 0.8631 (tmm) cc_final: 0.8388 (ttt) REVERT: B 223 ASN cc_start: 0.7296 (OUTLIER) cc_final: 0.6365 (t0) REVERT: E 91 TYR cc_start: 0.8710 (m-10) cc_final: 0.8300 (m-80) REVERT: F 16 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8637 (tm-30) REVERT: F 20 ARG cc_start: 0.7701 (mtm110) cc_final: 0.7306 (mtm110) REVERT: F 106 MET cc_start: 0.8429 (mmm) cc_final: 0.7922 (mmp) REVERT: H 195 ASN cc_start: 0.7868 (m-40) cc_final: 0.7402 (t0) REVERT: I 178 LEU cc_start: 0.4908 (OUTLIER) cc_final: 0.4411 (pp) outliers start: 54 outliers final: 33 residues processed: 193 average time/residue: 0.1360 time to fit residues: 38.2665 Evaluate side-chains 175 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 144 ASP Chi-restraints excluded: chain I residue 168 CYS Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 159 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 185 optimal weight: 4.9990 chunk 38 optimal weight: 0.3980 chunk 152 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 HIS ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 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 = 0.3709 r_free = 0.3709 target = 0.096665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.070545 restraints weight = 43821.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.074080 restraints weight = 24446.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.074712 restraints weight = 14893.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.074937 restraints weight = 13545.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.074957 restraints weight = 12757.744| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15359 Z= 0.124 Angle : 0.659 16.690 20824 Z= 0.329 Chirality : 0.044 0.184 2365 Planarity : 0.004 0.043 2625 Dihedral : 4.962 27.230 2032 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 2.34 % Allowed : 21.78 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.20), residues: 1830 helix: 1.21 (0.21), residues: 636 sheet: -0.79 (0.27), residues: 409 loop : -2.96 (0.19), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 59 TYR 0.015 0.001 TYR F 77 PHE 0.016 0.001 PHE A 128 TRP 0.013 0.001 TRP A 790 HIS 0.005 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (15353) covalent geometry : angle 0.65597 / 0.33 (20809) SS BOND : bond 0.00184 / 0.09 ( 3) SS BOND : angle 1.32660 / 0.72 ( 6) hydrogen bonds : bond 0.03778 / 2.53 ( 620) hydrogen bonds : angle 4.66413 / 3.18 ( 1767) link_NAG-ASN : bond 0.00563 / 0.29 ( 3) link_NAG-ASN : angle 3.15305 / 1.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 HIS cc_start: 0.8034 (t-90) cc_final: 0.7383 (t-90) REVERT: A 447 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7757 (mm-30) REVERT: A 917 SER cc_start: 0.8690 (t) cc_final: 0.8239 (m) REVERT: B 51 ASP cc_start: 0.8674 (t0) cc_final: 0.8059 (t0) REVERT: B 60 MET cc_start: 0.8538 (tmm) cc_final: 0.8307 (ttt) REVERT: B 223 ASN cc_start: 0.7083 (OUTLIER) cc_final: 0.6322 (t0) REVERT: C 236 ASP cc_start: 0.8432 (p0) cc_final: 0.7866 (t0) REVERT: E 91 TYR cc_start: 0.8699 (m-10) cc_final: 0.8323 (m-80) REVERT: F 16 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8502 (tm-30) REVERT: F 20 ARG cc_start: 0.7692 (mtm110) cc_final: 0.7271 (mtm110) REVERT: F 106 MET cc_start: 0.8541 (mmm) cc_final: 0.8106 (mmp) REVERT: H 195 ASN cc_start: 0.7887 (m-40) cc_final: 0.7325 (t0) REVERT: I 178 LEU cc_start: 0.4613 (OUTLIER) cc_final: 0.4186 (pp) outliers start: 38 outliers final: 23 residues processed: 187 average time/residue: 0.1328 time to fit residues: 36.5450 Evaluate side-chains 166 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 184 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 179 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 HIS ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** 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 = 0.3668 r_free = 0.3668 target = 0.094263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.067989 restraints weight = 44113.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.071339 restraints weight = 24938.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.072002 restraints weight = 15107.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.072226 restraints weight = 14100.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.072298 restraints weight = 13184.089| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15359 Z= 0.220 Angle : 0.712 13.679 20824 Z= 0.360 Chirality : 0.046 0.169 2365 Planarity : 0.005 0.101 2625 Dihedral : 5.124 27.343 2032 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 3.20 % Allowed : 22.28 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.20), residues: 1830 helix: 1.09 (0.21), residues: 638 sheet: -0.86 (0.26), residues: 411 loop : -2.99 (0.19), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 59 TYR 0.018 0.002 TYR A 898 PHE 0.019 0.001 PHE A 128 TRP 0.010 0.001 TRP A 219 HIS 0.013 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (15353) covalent geometry : angle 0.70830 / 0.36 (20809) SS BOND : bond 0.00419 / 0.21 ( 3) SS BOND : angle 1.43629 / 0.75 ( 6) hydrogen bonds : bond 0.04365 / 2.94 ( 620) hydrogen bonds : angle 4.81931 / 3.28 ( 1767) link_NAG-ASN : bond 0.00520 / 0.27 ( 3) link_NAG-ASN : angle 3.35012 / 1.90 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 142 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 HIS cc_start: 0.8048 (t-90) cc_final: 0.7363 (t-90) REVERT: A 535 MET cc_start: 0.8276 (tmm) cc_final: 0.7991 (ttt) REVERT: A 550 SER cc_start: 0.8573 (OUTLIER) cc_final: 0.8368 (p) REVERT: B 24 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8754 (tm-30) REVERT: B 51 ASP cc_start: 0.8640 (t0) cc_final: 0.8044 (t0) REVERT: B 223 ASN cc_start: 0.7382 (OUTLIER) cc_final: 0.6532 (t0) REVERT: C 236 ASP cc_start: 0.8459 (p0) cc_final: 0.7906 (t0) REVERT: E 91 TYR cc_start: 0.8717 (m-10) cc_final: 0.8354 (m-80) REVERT: F 16 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8503 (tm-30) REVERT: F 20 ARG cc_start: 0.7784 (mtm110) cc_final: 0.7435 (mtm110) REVERT: F 106 MET cc_start: 0.8433 (mmm) cc_final: 0.7988 (mmp) REVERT: H 195 ASN cc_start: 0.7976 (m-40) cc_final: 0.7474 (t0) REVERT: I 178 LEU cc_start: 0.4781 (OUTLIER) cc_final: 0.4305 (pp) outliers start: 52 outliers final: 31 residues processed: 185 average time/residue: 0.1282 time to fit residues: 35.3736 Evaluate side-chains 174 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 GLN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 HIS ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.096068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.069930 restraints weight = 43942.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.073536 restraints weight = 24318.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.074324 restraints weight = 14525.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.074592 restraints weight = 12773.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.074680 restraints weight = 12406.593| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15359 Z= 0.137 Angle : 0.658 14.736 20824 Z= 0.331 Chirality : 0.044 0.175 2365 Planarity : 0.004 0.045 2625 Dihedral : 4.894 26.685 2032 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.65 % Allowed : 23.88 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.20), residues: 1830 helix: 1.32 (0.21), residues: 634 sheet: -0.65 (0.27), residues: 411 loop : -2.89 (0.20), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 59 TYR 0.014 0.001 TYR F 77 PHE 0.017 0.001 PHE A 128 TRP 0.018 0.001 TRP A 187 HIS 0.004 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (15353) covalent geometry : angle 0.65468 / 0.33 (20809) SS BOND : bond 0.00263 / 0.13 ( 3) SS BOND : angle 1.15101 / 0.60 ( 6) hydrogen bonds : bond 0.03783 / 2.53 ( 620) hydrogen bonds : angle 4.64385 / 3.17 ( 1767) link_NAG-ASN : bond 0.00550 / 0.29 ( 3) link_NAG-ASN : angle 3.01642 / 1.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 917 SER cc_start: 0.8647 (t) cc_final: 0.8204 (m) REVERT: B 24 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8738 (tm-30) REVERT: B 51 ASP cc_start: 0.8590 (t0) cc_final: 0.7986 (t0) REVERT: B 60 MET cc_start: 0.8489 (tmm) cc_final: 0.8263 (ttt) REVERT: B 150 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8472 (pm20) REVERT: B 182 MET cc_start: 0.8327 (ttp) cc_final: 0.7929 (ttp) REVERT: B 223 ASN cc_start: 0.7567 (OUTLIER) cc_final: 0.6426 (t0) REVERT: C 51 ASP cc_start: 0.8879 (m-30) cc_final: 0.8658 (p0) REVERT: C 236 ASP cc_start: 0.8372 (p0) cc_final: 0.7854 (t0) REVERT: C 242 MET cc_start: 0.7847 (mmm) cc_final: 0.7573 (mmm) REVERT: D 43 TYR cc_start: 0.6691 (OUTLIER) cc_final: 0.6404 (t80) REVERT: E 91 TYR cc_start: 0.8684 (m-10) cc_final: 0.8313 (m-80) REVERT: F 16 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8534 (tm-30) REVERT: F 20 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7490 (mtm110) REVERT: F 106 MET cc_start: 0.8540 (mmm) cc_final: 0.8059 (mmp) REVERT: H 195 ASN cc_start: 0.7971 (m-40) cc_final: 0.7477 (t0) REVERT: I 97 ARG cc_start: 0.6785 (ttp-110) cc_final: 0.6476 (ttp80) REVERT: I 178 LEU cc_start: 0.4742 (OUTLIER) cc_final: 0.4280 (pp) outliers start: 43 outliers final: 27 residues processed: 187 average time/residue: 0.1386 time to fit residues: 37.6177 Evaluate side-chains 168 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 107 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 157 optimal weight: 0.0050 chunk 25 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 HIS ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 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 = 0.3694 r_free = 0.3694 target = 0.095836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.069638 restraints weight = 43986.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.073017 restraints weight = 24509.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.073742 restraints weight = 14720.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.073994 restraints weight = 13670.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.074043 restraints weight = 12685.854| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15359 Z= 0.147 Angle : 0.675 13.689 20824 Z= 0.339 Chirality : 0.044 0.218 2365 Planarity : 0.004 0.055 2625 Dihedral : 4.842 26.229 2032 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 2.28 % Allowed : 23.88 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.20), residues: 1830 helix: 1.35 (0.21), residues: 634 sheet: -0.65 (0.26), residues: 410 loop : -2.83 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 59 TYR 0.013 0.001 TYR F 77 PHE 0.016 0.001 PHE A 128 TRP 0.016 0.001 TRP A 187 HIS 0.005 0.001 HIS A 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (15353) covalent geometry : angle 0.67244 / 0.34 (20809) SS BOND : bond 0.00299 / 0.15 ( 3) SS BOND : angle 1.14515 / 0.62 ( 6) hydrogen bonds : bond 0.03879 / 2.64 ( 620) hydrogen bonds : angle 4.64980 / 3.18 ( 1767) link_NAG-ASN : bond 0.00549 / 0.29 ( 3) link_NAG-ASN : angle 2.95569 / 1.74 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.8313 (tmm) cc_final: 0.7972 (ttt) REVERT: A 549 GLU cc_start: 0.7146 (pm20) cc_final: 0.6514 (pp20) REVERT: A 917 SER cc_start: 0.8650 (t) cc_final: 0.8214 (m) REVERT: B 24 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8753 (tm-30) REVERT: B 51 ASP cc_start: 0.8612 (t0) cc_final: 0.8003 (t0) REVERT: B 60 MET cc_start: 0.8542 (tmm) cc_final: 0.8309 (ttt) REVERT: B 150 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8512 (pm20) REVERT: B 182 MET cc_start: 0.8305 (ttp) cc_final: 0.7925 (ttp) REVERT: B 223 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.6715 (t0) REVERT: C 236 ASP cc_start: 0.8424 (p0) cc_final: 0.7844 (t0) REVERT: C 242 MET cc_start: 0.7929 (mmm) cc_final: 0.7664 (mmm) REVERT: D 43 TYR cc_start: 0.6698 (OUTLIER) cc_final: 0.6364 (t80) REVERT: E 91 TYR cc_start: 0.8687 (m-10) cc_final: 0.8308 (m-80) REVERT: F 16 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8545 (tm-30) REVERT: F 20 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7497 (mtm110) REVERT: F 106 MET cc_start: 0.8526 (mmm) cc_final: 0.8048 (mmp) REVERT: H 195 ASN cc_start: 0.8106 (m-40) cc_final: 0.7564 (t0) REVERT: I 178 LEU cc_start: 0.4660 (OUTLIER) cc_final: 0.4165 (pp) outliers start: 37 outliers final: 30 residues processed: 176 average time/residue: 0.1211 time to fit residues: 32.2867 Evaluate side-chains 175 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain A residue 580 HIS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 146 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 HIS ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 HIS ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 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 = 0.3689 r_free = 0.3689 target = 0.095570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.069327 restraints weight = 43920.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.072716 restraints weight = 24479.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.073258 restraints weight = 14720.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.073590 restraints weight = 13913.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.073626 restraints weight = 12902.670| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15359 Z= 0.159 Angle : 0.688 15.589 20824 Z= 0.346 Chirality : 0.045 0.210 2365 Planarity : 0.004 0.044 2625 Dihedral : 4.844 26.082 2032 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 2.28 % Allowed : 24.31 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.20), residues: 1830 helix: 1.35 (0.21), residues: 635 sheet: -0.50 (0.27), residues: 398 loop : -2.82 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 76 TYR 0.014 0.001 TYR A 898 PHE 0.016 0.001 PHE A 128 TRP 0.016 0.001 TRP A 187 HIS 0.006 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (15353) covalent geometry : angle 0.68482 / 0.35 (20809) SS BOND : bond 0.00302 / 0.15 ( 3) SS BOND : angle 1.22731 / 0.67 ( 6) hydrogen bonds : bond 0.03889 / 2.62 ( 620) hydrogen bonds : angle 4.66523 / 3.20 ( 1767) link_NAG-ASN : bond 0.00533 / 0.28 ( 3) link_NAG-ASN : angle 2.94813 / 1.74 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8470 (p) REVERT: A 535 MET cc_start: 0.8397 (tmm) cc_final: 0.8034 (ttt) REVERT: A 549 GLU cc_start: 0.7186 (pm20) cc_final: 0.6614 (pp20) REVERT: A 917 SER cc_start: 0.8667 (t) cc_final: 0.8236 (m) REVERT: B 24 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8776 (tm-30) REVERT: B 51 ASP cc_start: 0.8617 (t0) cc_final: 0.8008 (t0) REVERT: B 60 MET cc_start: 0.8571 (tmm) cc_final: 0.8312 (ttt) REVERT: B 95 MET cc_start: 0.7746 (mmt) cc_final: 0.7430 (mmt) REVERT: B 150 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8515 (pm20) REVERT: B 182 MET cc_start: 0.8284 (ttp) cc_final: 0.7907 (ttp) REVERT: C 51 ASP cc_start: 0.8925 (m-30) cc_final: 0.8714 (p0) REVERT: C 59 ARG cc_start: 0.9099 (ttp80) cc_final: 0.8344 (ttp80) REVERT: C 236 ASP cc_start: 0.8447 (p0) cc_final: 0.7885 (t0) REVERT: C 242 MET cc_start: 0.7935 (mmm) cc_final: 0.7650 (mmm) REVERT: D 43 TYR cc_start: 0.6606 (OUTLIER) cc_final: 0.6308 (t80) REVERT: E 91 TYR cc_start: 0.8689 (m-10) cc_final: 0.8322 (m-80) REVERT: F 16 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8553 (tm-30) REVERT: F 20 ARG cc_start: 0.7800 (mtm110) cc_final: 0.7511 (mtm110) REVERT: F 106 MET cc_start: 0.8474 (mmm) cc_final: 0.8003 (mmp) REVERT: H 178 ARG cc_start: 0.8753 (mmm-85) cc_final: 0.8398 (tpp80) REVERT: H 195 ASN cc_start: 0.8108 (m-40) cc_final: 0.7581 (t0) REVERT: I 178 LEU cc_start: 0.4719 (OUTLIER) cc_final: 0.4223 (pp) outliers start: 37 outliers final: 27 residues processed: 172 average time/residue: 0.1231 time to fit residues: 31.8042 Evaluate side-chains 173 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 338 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 32 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 119 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 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 = 0.3713 r_free = 0.3713 target = 0.096946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.070888 restraints weight = 43220.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.074364 restraints weight = 23757.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.074859 restraints weight = 14102.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.075295 restraints weight = 13377.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.075386 restraints weight = 12290.724| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15359 Z= 0.126 Angle : 0.661 16.093 20824 Z= 0.330 Chirality : 0.044 0.183 2365 Planarity : 0.004 0.045 2625 Dihedral : 4.672 24.602 2032 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 2.15 % Allowed : 24.31 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.20), residues: 1830 helix: 1.48 (0.21), residues: 634 sheet: -0.36 (0.27), residues: 410 loop : -2.77 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 76 TYR 0.011 0.001 TYR A 672 PHE 0.014 0.001 PHE A 128 TRP 0.017 0.001 TRP A 187 HIS 0.005 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15353) covalent geometry : angle 0.65832 / 0.33 (20809) SS BOND : bond 0.00209 / 0.10 ( 3) SS BOND : angle 1.01245 / 0.54 ( 6) hydrogen bonds : bond 0.03585 / 2.42 ( 620) hydrogen bonds : angle 4.53136 / 3.11 ( 1767) link_NAG-ASN : bond 0.00547 / 0.29 ( 3) link_NAG-ASN : angle 2.77507 / 1.67 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2604.11 seconds wall clock time: 45 minutes 53.42 seconds (2753.42 seconds total)