Starting phenix.real_space_refine on Wed Mar 4 17:25:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7adp_11733/03_2026/7adp_11733.cif Found real_map, /net/cci-nas-00/data/ceres_data/7adp_11733/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7adp_11733/03_2026/7adp_11733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7adp_11733/03_2026/7adp_11733.map" model { file = "/net/cci-nas-00/data/ceres_data/7adp_11733/03_2026/7adp_11733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7adp_11733/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.24, per 1000 atoms: 0.22 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: 1.42 Conformation dependent library (CDL) restraints added in 618.4 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: 0.48 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: 2.89 Time building geometry restraints manager: 1.91 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: 8027 17.51 - 35.03: 920 35.03 - 52.54: 194 52.54 - 70.06: 25 70.06 - 87.57: 14 Dihedral angle restraints: 9180 sinusoidal: 3709 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 9177 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: 1.750 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.370 Find NCS groups from input model: 0.080 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 15.291 87.573 5627 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 covalent geometry : bond 0.00647 (15353) covalent geometry : angle 0.79148 (20809) SS BOND : bond 0.00339 ( 3) SS BOND : angle 0.90430 ( 6) hydrogen bonds : bond 0.13392 ( 620) hydrogen bonds : angle 6.58505 ( 1767) link_NAG-ASN : bond 0.08273 ( 3) link_NAG-ASN : angle 11.18092 ( 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 : 0.601 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: 0.1749 time to fit residues: 54.6391 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 : 0.590 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.099550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.073708 restraints weight = 43874.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.076267 restraints weight = 23252.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.077900 restraints weight = 16134.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.078907 restraints weight = 12951.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.079539 restraints weight = 11335.774| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2182 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= 0.150 Angle : 0.721 10.851 20824 Z= 0.365 Chirality : 0.047 0.232 2365 Planarity : 0.004 0.052 2625 Dihedral : 5.688 49.073 2096 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 1.05 % Allowed : 12.18 % Favored : 86.77 % 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: 0.21 (0.21), residues: 633 sheet: -2.02 (0.23), residues: 394 loop : -3.74 (0.16), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 20 TYR 0.015 0.002 TYR D 47 PHE 0.017 0.001 PHE A 530 TRP 0.040 0.002 TRP A 219 HIS 0.008 0.001 HIS A 580 Details of bonding type rmsd covalent geometry : bond 0.00333 (15353) covalent geometry : angle 0.70936 (20809) SS BOND : bond 0.00465 ( 3) SS BOND : angle 3.71368 ( 6) hydrogen bonds : bond 0.04272 ( 620) hydrogen bonds : angle 5.11838 ( 1767) link_NAG-ASN : bond 0.00708 ( 3) link_NAG-ASN : angle 5.52297 ( 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: 17 poor density : 173 time to evaluate : 0.564 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: 0.8429 (t) cc_final: 0.7962 (m) REVERT: B 51 ASP cc_start: 0.8497 (t0) cc_final: 0.7948 (t0) REVERT: B 197 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7807 (mp0) REVERT: B 223 ASN cc_start: 0.7376 (OUTLIER) cc_final: 0.6495 (t0) REVERT: C 29 MET cc_start: 0.8255 (tpp) cc_final: 0.8051 (mpp) REVERT: C 235 ASP cc_start: 0.8201 (p0) cc_final: 0.7688 (m-30) REVERT: C 236 ASP cc_start: 0.7842 (p0) cc_final: 0.7138 (p0) REVERT: E 91 TYR cc_start: 0.8704 (m-10) cc_final: 0.8237 (m-80) REVERT: F 16 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8513 (tm-30) REVERT: F 46 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8085 (pp) REVERT: F 106 MET cc_start: 0.8228 (mmm) cc_final: 0.7921 (mmp) REVERT: H 178 ARG cc_start: 0.8405 (mmm-85) cc_final: 0.8035 (tpp80) REVERT: H 195 ASN cc_start: 0.7830 (m-40) cc_final: 0.7239 (t0) REVERT: I 178 LEU cc_start: 0.4451 (OUTLIER) cc_final: 0.4076 (pp) outliers start: 17 outliers final: 8 residues processed: 187 average time/residue: 0.1518 time to fit residues: 40.2123 Evaluate side-chains 152 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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: 0.9990 chunk 52 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN C 71 GLN E 87 HIS H 147 HIS ** H 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.096496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.070140 restraints weight = 44361.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.073665 restraints weight = 25147.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.074162 restraints weight = 15310.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.074468 restraints weight = 14239.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.074497 restraints weight = 13207.732| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15359 Z= 0.187 Angle : 0.702 11.814 20824 Z= 0.358 Chirality : 0.046 0.214 2365 Planarity : 0.004 0.052 2625 Dihedral : 5.554 47.777 2096 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.03 % Allowed : 15.82 % Favored : 82.15 % 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: -2.33 (0.18), residues: 1830 helix: 0.67 (0.21), residues: 634 sheet: -1.52 (0.25), residues: 395 loop : -3.52 (0.17), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 76 TYR 0.018 0.002 TYR H 21 PHE 0.016 0.001 PHE A 530 TRP 0.020 0.001 TRP A 219 HIS 0.007 0.001 HIS H 62 Details of bonding type rmsd covalent geometry : bond 0.00434 (15353) covalent geometry : angle 0.69423 (20809) SS BOND : bond 0.00180 ( 3) SS BOND : angle 2.77783 ( 6) hydrogen bonds : bond 0.04385 ( 620) hydrogen bonds : angle 4.93286 ( 1767) link_NAG-ASN : bond 0.00356 ( 3) link_NAG-ASN : angle 4.64853 ( 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 187 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 917 SER cc_start: 0.8560 (t) cc_final: 0.8117 (m) REVERT: B 51 ASP cc_start: 0.8610 (t0) cc_final: 0.8032 (t0) REVERT: B 197 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8041 (mp0) REVERT: B 223 ASN cc_start: 0.7219 (OUTLIER) cc_final: 0.6672 (t0) REVERT: E 91 TYR cc_start: 0.8674 (m-10) cc_final: 0.8194 (m-80) REVERT: F 16 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8445 (tm-30) REVERT: F 106 MET cc_start: 0.8393 (mmm) cc_final: 0.7958 (mmp) REVERT: H 178 ARG cc_start: 0.8665 (mmm-85) cc_final: 0.8102 (tpp80) REVERT: H 181 GLU cc_start: 0.8923 (pm20) cc_final: 0.8661 (pm20) REVERT: H 195 ASN cc_start: 0.7903 (m-40) cc_final: 0.7299 (t0) REVERT: I 178 LEU cc_start: 0.4465 (OUTLIER) cc_final: 0.4042 (pp) outliers start: 33 outliers final: 22 residues processed: 181 average time/residue: 0.1407 time to fit residues: 36.3770 Evaluate side-chains 159 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 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 H residue 24 CYS Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain I residue 135 CYS Chi-restraints excluded: chain I residue 168 CYS Chi-restraints excluded: chain I residue 176 VAL 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: 0.4980 chunk 149 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 chunk 134 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** H 94 GLN ** 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 = 0.3688 r_free = 0.3688 target = 0.095892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.069279 restraints weight = 43997.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.072682 restraints weight = 25490.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.073307 restraints weight = 15608.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.073749 restraints weight = 13840.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.073805 restraints weight = 13054.996| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15359 Z= 0.173 Angle : 0.668 12.794 20824 Z= 0.340 Chirality : 0.045 0.198 2365 Planarity : 0.004 0.048 2625 Dihedral : 5.432 48.319 2096 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 2.65 % Allowed : 17.60 % Favored : 79.75 % 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: -1.97 (0.19), residues: 1830 helix: 0.89 (0.21), residues: 634 sheet: -1.24 (0.25), residues: 400 loop : -3.30 (0.18), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 169 TYR 0.018 0.002 TYR F 77 PHE 0.015 0.001 PHE A 530 TRP 0.015 0.001 TRP A 219 HIS 0.005 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00403 (15353) covalent geometry : angle 0.66285 (20809) SS BOND : bond 0.00128 ( 3) SS BOND : angle 2.23823 ( 6) hydrogen bonds : bond 0.04179 ( 620) hydrogen bonds : angle 4.78699 ( 1767) link_NAG-ASN : bond 0.00467 ( 3) link_NAG-ASN : angle 3.84091 ( 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 191 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 0.528 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 306 HIS cc_start: 0.7876 (t-90) cc_final: 0.7320 (t-90) REVERT: A 863 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8641 (mt) REVERT: A 917 SER cc_start: 0.8579 (t) cc_final: 0.8142 (m) REVERT: B 51 ASP cc_start: 0.8646 (t0) cc_final: 0.8060 (t0) REVERT: B 197 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8054 (mp0) REVERT: B 223 ASN cc_start: 0.7266 (OUTLIER) cc_final: 0.6674 (t0) REVERT: B 238 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7467 (t-90) REVERT: E 91 TYR cc_start: 0.8695 (m-10) cc_final: 0.8205 (m-80) REVERT: F 106 MET cc_start: 0.8405 (mmm) cc_final: 0.7985 (mmp) REVERT: H 83 LYS cc_start: 0.8752 (mmtp) cc_final: 0.8542 (mtpt) REVERT: H 152 ARG cc_start: 0.8526 (mmm160) cc_final: 0.8261 (mmm160) REVERT: H 195 ASN cc_start: 0.7923 (m-40) cc_final: 0.7357 (t0) REVERT: I 93 GLU cc_start: 0.8589 (pm20) cc_final: 0.8286 (pm20) REVERT: I 178 LEU cc_start: 0.4702 (OUTLIER) cc_final: 0.4249 (pp) outliers start: 43 outliers final: 27 residues processed: 183 average time/residue: 0.1284 time to fit residues: 34.0488 Evaluate side-chains 168 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 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 B residue 24 GLU Chi-restraints excluded: chain B residue 79 LEU 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 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 171 SER 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: 0.9990 chunk 134 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 135 optimal weight: 0.0370 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 B 238 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 = 0.3684 r_free = 0.3684 target = 0.095204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.069008 restraints weight = 44560.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.072601 restraints weight = 24873.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.073344 restraints weight = 14973.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.073611 restraints weight = 13204.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.073703 restraints weight = 12868.261| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15359 Z= 0.195 Angle : 0.685 13.655 20824 Z= 0.349 Chirality : 0.045 0.185 2365 Planarity : 0.004 0.047 2625 Dihedral : 5.334 48.545 2095 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 3.14 % Allowed : 19.20 % Favored : 77.66 % 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: -1.74 (0.19), residues: 1830 helix: 1.02 (0.21), residues: 635 sheet: -0.99 (0.26), residues: 393 loop : -3.17 (0.18), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 20 TYR 0.017 0.002 TYR A 898 PHE 0.014 0.001 PHE A 128 TRP 0.013 0.001 TRP A 219 HIS 0.005 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00456 (15353) covalent geometry : angle 0.67998 (20809) SS BOND : bond 0.00291 ( 3) SS BOND : angle 1.91814 ( 6) hydrogen bonds : bond 0.04283 ( 620) hydrogen bonds : angle 4.80093 ( 1767) link_NAG-ASN : bond 0.00496 ( 3) link_NAG-ASN : angle 3.69354 ( 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 196 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 HIS cc_start: 0.7901 (t-90) cc_final: 0.7309 (t-90) REVERT: A 447 GLU cc_start: 0.8407 (mm-30) cc_final: 0.7779 (mm-30) REVERT: B 51 ASP cc_start: 0.8617 (t0) cc_final: 0.8023 (t0) REVERT: B 60 MET cc_start: 0.8550 (tmm) cc_final: 0.8343 (ttt) REVERT: B 197 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8034 (mp0) REVERT: B 223 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.6792 (t0) REVERT: E 91 TYR cc_start: 0.8733 (m-10) cc_final: 0.8246 (m-80) REVERT: F 16 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8634 (tm-30) REVERT: F 100 TRP cc_start: 0.7945 (OUTLIER) cc_final: 0.7700 (t60) REVERT: F 106 MET cc_start: 0.8434 (mmm) cc_final: 0.7913 (mmp) REVERT: H 83 LYS cc_start: 0.8796 (mmtp) cc_final: 0.8563 (mtpt) REVERT: H 87 TYR cc_start: 0.6439 (m-80) cc_final: 0.6084 (m-10) REVERT: H 195 ASN cc_start: 0.7838 (m-40) cc_final: 0.7338 (t0) REVERT: I 178 LEU cc_start: 0.4761 (OUTLIER) cc_final: 0.4314 (pp) outliers start: 51 outliers final: 29 residues processed: 187 average time/residue: 0.1367 time to fit residues: 36.7967 Evaluate side-chains 171 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 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 852 THR 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 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 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 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: 10.0000 chunk 120 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 175 optimal weight: 0.0770 chunk 79 optimal weight: 0.0050 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 223 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** 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 = 0.3723 r_free = 0.3723 target = 0.097478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.071334 restraints weight = 44156.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.074816 restraints weight = 24247.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.075481 restraints weight = 14549.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.075715 restraints weight = 13254.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.075809 restraints weight = 13102.291| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15359 Z= 0.119 Angle : 0.641 16.465 20824 Z= 0.320 Chirality : 0.043 0.185 2365 Planarity : 0.004 0.043 2625 Dihedral : 5.060 50.268 2095 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.52 % Allowed : 21.11 % Favored : 76.37 % 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: -1.40 (0.20), residues: 1830 helix: 1.24 (0.21), residues: 633 sheet: -0.75 (0.27), residues: 411 loop : -2.97 (0.19), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 20 TYR 0.013 0.001 TYR H 21 PHE 0.012 0.001 PHE A 128 TRP 0.013 0.001 TRP A 219 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00268 (15353) covalent geometry : angle 0.63807 (20809) SS BOND : bond 0.00221 ( 3) SS BOND : angle 1.24985 ( 6) hydrogen bonds : bond 0.03602 ( 620) hydrogen bonds : angle 4.56651 ( 1767) link_NAG-ASN : bond 0.00540 ( 3) link_NAG-ASN : angle 3.06925 ( 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 200 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 HIS cc_start: 0.7988 (t-90) cc_final: 0.7350 (t-90) REVERT: A 447 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7738 (mm-30) REVERT: A 917 SER cc_start: 0.8560 (t) cc_final: 0.8171 (m) REVERT: B 51 ASP cc_start: 0.8628 (t0) cc_final: 0.8050 (t0) REVERT: B 150 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8373 (mp10) REVERT: B 197 GLU cc_start: 0.8543 (mt-10) cc_final: 0.7984 (mp0) REVERT: B 223 ASN cc_start: 0.7267 (OUTLIER) cc_final: 0.6189 (t0) REVERT: C 235 ASP cc_start: 0.8496 (m-30) cc_final: 0.8207 (p0) REVERT: E 91 TYR cc_start: 0.8687 (m-10) cc_final: 0.8233 (m-80) REVERT: F 16 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8600 (tm-30) REVERT: F 46 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8304 (pp) REVERT: F 106 MET cc_start: 0.8565 (mmm) cc_final: 0.8158 (mmp) REVERT: H 56 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8003 (m-30) REVERT: H 83 LYS cc_start: 0.8809 (mmtp) cc_final: 0.8603 (mtpt) REVERT: H 152 ARG cc_start: 0.8569 (mmm160) cc_final: 0.8360 (mmm160) REVERT: H 195 ASN cc_start: 0.7805 (m-40) cc_final: 0.7240 (t0) REVERT: I 178 LEU cc_start: 0.4573 (OUTLIER) cc_final: 0.4180 (pp) outliers start: 41 outliers final: 23 residues processed: 195 average time/residue: 0.1231 time to fit residues: 35.4862 Evaluate side-chains 175 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 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 955 VAL 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 C residue 152 LEU Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain E residue 51 LEU 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 56 ASP 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: 5.9990 chunk 90 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 164 optimal weight: 0.7980 chunk 180 optimal weight: 0.0370 chunk 110 optimal weight: 7.9990 chunk 179 optimal weight: 0.0770 chunk 70 optimal weight: 6.9990 overall best weight: 2.3820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 720 HIS B 223 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.094782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.068448 restraints weight = 44141.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.071992 restraints weight = 24817.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.072540 restraints weight = 14821.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.072666 restraints weight = 13650.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.072733 restraints weight = 13587.775| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3957 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= 0.207 Angle : 0.701 14.553 20824 Z= 0.353 Chirality : 0.046 0.169 2365 Planarity : 0.004 0.096 2625 Dihedral : 5.215 48.476 2095 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 2.89 % Allowed : 21.85 % Favored : 75.26 % 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: -1.44 (0.20), residues: 1830 helix: 1.15 (0.21), residues: 635 sheet: -0.71 (0.27), residues: 409 loop : -2.99 (0.19), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 20 TYR 0.018 0.002 TYR F 77 PHE 0.016 0.001 PHE A 128 TRP 0.013 0.001 TRP C 232 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00487 (15353) covalent geometry : angle 0.69770 (20809) SS BOND : bond 0.00391 ( 3) SS BOND : angle 1.44975 ( 6) hydrogen bonds : bond 0.04236 ( 620) hydrogen bonds : angle 4.71723 ( 1767) link_NAG-ASN : bond 0.00508 ( 3) link_NAG-ASN : angle 3.31988 ( 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 193 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 HIS cc_start: 0.8027 (t-90) cc_final: 0.7350 (t-90) REVERT: A 535 MET cc_start: 0.8252 (tmm) cc_final: 0.7955 (ttt) REVERT: A 550 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8332 (p) REVERT: B 24 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8748 (tm-30) REVERT: B 51 ASP cc_start: 0.8624 (t0) cc_final: 0.8028 (t0) REVERT: B 197 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8044 (mp0) REVERT: B 223 ASN cc_start: 0.7002 (OUTLIER) cc_final: 0.6279 (t0) REVERT: C 59 ARG cc_start: 0.9253 (ttp80) cc_final: 0.8961 (ttp80) REVERT: E 91 TYR cc_start: 0.8700 (m-10) cc_final: 0.8299 (m-80) REVERT: F 16 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8706 (tm-30) REVERT: F 106 MET cc_start: 0.8489 (mmm) cc_final: 0.7934 (mmp) REVERT: H 195 ASN cc_start: 0.7897 (m-40) cc_final: 0.7408 (t0) REVERT: I 92 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7344 (tm-30) REVERT: I 178 LEU cc_start: 0.4730 (OUTLIER) cc_final: 0.4241 (pp) outliers start: 47 outliers final: 32 residues processed: 185 average time/residue: 0.1156 time to fit residues: 31.9483 Evaluate side-chains 177 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 529 GLU 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 851 ILE Chi-restraints excluded: chain A residue 852 THR 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 152 LEU 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 147 HIS Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 193 ILE 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: 0.0070 chunk 99 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3692 r_free = 0.3692 target = 0.095735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.069517 restraints weight = 44023.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.072853 restraints weight = 24575.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.073423 restraints weight = 14991.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.073804 restraints weight = 13966.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.073839 restraints weight = 13048.522| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4083 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= 0.156 Angle : 0.673 14.797 20824 Z= 0.337 Chirality : 0.044 0.175 2365 Planarity : 0.004 0.049 2625 Dihedral : 5.122 49.507 2095 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 2.83 % Allowed : 23.02 % Favored : 74.15 % 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: -1.32 (0.20), residues: 1830 helix: 1.23 (0.21), residues: 634 sheet: -0.62 (0.27), residues: 409 loop : -2.91 (0.19), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 20 TYR 0.014 0.001 TYR A 898 PHE 0.015 0.001 PHE A 128 TRP 0.012 0.001 TRP A 219 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00365 (15353) covalent geometry : angle 0.66955 (20809) SS BOND : bond 0.00298 ( 3) SS BOND : angle 1.27133 ( 6) hydrogen bonds : bond 0.03945 ( 620) hydrogen bonds : angle 4.63970 ( 1767) link_NAG-ASN : bond 0.00518 ( 3) link_NAG-ASN : angle 3.14974 ( 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: 46 poor density : 149 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 917 SER cc_start: 0.8678 (t) cc_final: 0.8246 (m) REVERT: B 24 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8737 (tm-30) REVERT: B 51 ASP cc_start: 0.8602 (t0) cc_final: 0.8006 (t0) REVERT: B 150 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8481 (pm20) REVERT: B 182 MET cc_start: 0.8320 (ttp) cc_final: 0.7893 (ttp) REVERT: B 223 ASN cc_start: 0.7273 (OUTLIER) cc_final: 0.6328 (t0) REVERT: C 59 ARG cc_start: 0.9226 (ttp80) cc_final: 0.8489 (ttp80) REVERT: C 236 ASP cc_start: 0.8049 (p0) cc_final: 0.7478 (t0) REVERT: D 43 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.6413 (t80) REVERT: E 91 TYR cc_start: 0.8679 (m-10) cc_final: 0.8274 (m-80) REVERT: F 16 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8664 (tm-30) REVERT: F 106 MET cc_start: 0.8497 (mmm) cc_final: 0.8026 (mmp) REVERT: H 166 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.6170 (tp30) REVERT: H 195 ASN cc_start: 0.7896 (m-40) cc_final: 0.7392 (t0) REVERT: I 178 LEU cc_start: 0.4704 (OUTLIER) cc_final: 0.4199 (pp) outliers start: 46 outliers final: 31 residues processed: 187 average time/residue: 0.1334 time to fit residues: 36.5452 Evaluate side-chains 175 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 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 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 C residue 152 LEU Chi-restraints excluded: chain C residue 229 ASP 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 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 166 GLU Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 193 ILE 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: 0.7980 chunk 124 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 157 optimal weight: 0.0030 chunk 25 optimal weight: 9.9990 chunk 135 optimal weight: 0.6980 chunk 168 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** 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 = 0.3719 r_free = 0.3719 target = 0.097379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.071177 restraints weight = 43832.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.074541 restraints weight = 24286.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.075141 restraints weight = 14705.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.075527 restraints weight = 13804.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.075572 restraints weight = 12766.071| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15359 Z= 0.117 Angle : 0.660 15.101 20824 Z= 0.328 Chirality : 0.043 0.178 2365 Planarity : 0.004 0.045 2625 Dihedral : 4.924 50.701 2095 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 2.09 % Allowed : 23.26 % Favored : 74.65 % 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: -1.10 (0.20), residues: 1830 helix: 1.40 (0.21), residues: 635 sheet: -0.42 (0.27), residues: 410 loop : -2.83 (0.20), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 20 TYR 0.012 0.001 TYR H 21 PHE 0.011 0.001 PHE B 151 TRP 0.014 0.001 TRP A 119 HIS 0.004 0.001 HIS A 580 Details of bonding type rmsd covalent geometry : bond 0.00260 (15353) covalent geometry : angle 0.65751 (20809) SS BOND : bond 0.00182 ( 3) SS BOND : angle 0.95417 ( 6) hydrogen bonds : bond 0.03471 ( 620) hydrogen bonds : angle 4.45026 ( 1767) link_NAG-ASN : bond 0.00563 ( 3) link_NAG-ASN : angle 2.85722 ( 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 186 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.8170 (tmm) cc_final: 0.7820 (ttt) REVERT: A 549 GLU cc_start: 0.7142 (pm20) cc_final: 0.6625 (pp20) REVERT: A 716 SER cc_start: 0.8900 (m) cc_final: 0.8670 (p) REVERT: A 917 SER cc_start: 0.8555 (t) cc_final: 0.8110 (m) REVERT: B 24 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8728 (tm-30) REVERT: B 51 ASP cc_start: 0.8614 (t0) cc_final: 0.8020 (t0) REVERT: B 150 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8543 (pm20) REVERT: B 182 MET cc_start: 0.8225 (ttp) cc_final: 0.7805 (ttp) REVERT: B 197 GLU cc_start: 0.8516 (mt-10) cc_final: 0.7979 (mp0) REVERT: B 223 ASN cc_start: 0.7101 (OUTLIER) cc_final: 0.6382 (t0) REVERT: C 59 ARG cc_start: 0.9218 (ttp80) cc_final: 0.8367 (ttp80) REVERT: D 43 TYR cc_start: 0.6587 (OUTLIER) cc_final: 0.6268 (t80) REVERT: E 91 TYR cc_start: 0.8668 (m-10) cc_final: 0.8250 (m-80) REVERT: F 16 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8614 (tm-30) REVERT: F 106 MET cc_start: 0.8602 (mmm) cc_final: 0.8139 (mmp) REVERT: H 178 ARG cc_start: 0.8766 (mmm-85) cc_final: 0.8296 (tpp80) REVERT: H 195 ASN cc_start: 0.7986 (m-40) cc_final: 0.7431 (t0) REVERT: I 178 LEU cc_start: 0.4576 (OUTLIER) cc_final: 0.4177 (pp) outliers start: 34 outliers final: 19 residues processed: 181 average time/residue: 0.1223 time to fit residues: 33.1335 Evaluate side-chains 167 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 603 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 851 ILE 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 C residue 229 ASP 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 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 74 TRP Chi-restraints excluded: chain H residue 31 VAL 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: 1.9990 chunk 90 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 46 optimal weight: 0.0000 chunk 7 optimal weight: 4.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 783 HIS 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.095571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.069295 restraints weight = 43983.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.072743 restraints weight = 24396.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.073306 restraints weight = 14724.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.073582 restraints weight = 13716.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.073655 restraints weight = 12982.886| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15359 Z= 0.170 Angle : 0.690 15.096 20824 Z= 0.346 Chirality : 0.045 0.165 2365 Planarity : 0.004 0.042 2625 Dihedral : 5.035 49.415 2095 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 1.91 % Allowed : 23.69 % Favored : 74.40 % 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: -1.12 (0.20), residues: 1830 helix: 1.34 (0.21), residues: 637 sheet: -0.48 (0.27), residues: 410 loop : -2.79 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 20 TYR 0.015 0.001 TYR A 898 PHE 0.015 0.001 PHE A 128 TRP 0.011 0.001 TRP A 163 HIS 0.006 0.001 HIS H 147 Details of bonding type rmsd covalent geometry : bond 0.00398 (15353) covalent geometry : angle 0.68734 (20809) SS BOND : bond 0.00332 ( 3) SS BOND : angle 1.28165 ( 6) hydrogen bonds : bond 0.03934 ( 620) hydrogen bonds : angle 4.55750 ( 1767) link_NAG-ASN : bond 0.00510 ( 3) link_NAG-ASN : angle 2.98197 ( 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 177 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8456 (p) REVERT: A 535 MET cc_start: 0.8366 (tmm) cc_final: 0.8003 (ttt) REVERT: A 549 GLU cc_start: 0.7227 (pm20) cc_final: 0.6738 (pp20) REVERT: A 917 SER cc_start: 0.8681 (t) cc_final: 0.8325 (m) REVERT: B 24 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8762 (tm-30) REVERT: B 51 ASP cc_start: 0.8601 (t0) cc_final: 0.7993 (t0) REVERT: B 95 MET cc_start: 0.7743 (mmt) cc_final: 0.7483 (mmt) REVERT: B 150 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8561 (pm20) REVERT: B 182 MET cc_start: 0.8295 (ttp) cc_final: 0.7921 (ttp) REVERT: B 197 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8028 (mp0) REVERT: B 223 ASN cc_start: 0.7518 (OUTLIER) cc_final: 0.6343 (t0) REVERT: B 234 MET cc_start: 0.8727 (tpt) cc_final: 0.8415 (tpt) REVERT: C 59 ARG cc_start: 0.9230 (ttp80) cc_final: 0.8775 (ttp80) REVERT: C 242 MET cc_start: 0.7758 (mmm) cc_final: 0.7332 (mmm) REVERT: D 43 TYR cc_start: 0.6646 (OUTLIER) cc_final: 0.6365 (t80) REVERT: E 91 TYR cc_start: 0.8696 (m-10) cc_final: 0.8330 (m-80) REVERT: F 16 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8701 (tm-30) REVERT: F 46 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8436 (pp) REVERT: F 106 MET cc_start: 0.8503 (mmm) cc_final: 0.8020 (mmp) REVERT: H 9 GLN cc_start: 0.6952 (pt0) cc_final: 0.6741 (tt0) REVERT: H 178 ARG cc_start: 0.8765 (mmm-85) cc_final: 0.8316 (tpp80) REVERT: H 181 GLU cc_start: 0.9043 (pm20) cc_final: 0.8817 (pm20) REVERT: H 195 ASN cc_start: 0.8069 (m-40) cc_final: 0.7539 (t0) REVERT: I 178 LEU cc_start: 0.4491 (OUTLIER) cc_final: 0.3962 (pp) outliers start: 31 outliers final: 21 residues processed: 172 average time/residue: 0.1360 time to fit residues: 34.3351 Evaluate side-chains 171 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 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 26 GLN Chi-restraints excluded: chain E residue 51 LEU 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 149 ASN 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: 0.7980 chunk 133 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 185 optimal weight: 0.1980 chunk 75 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.096893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.070671 restraints weight = 43867.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.074187 restraints weight = 24228.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.074749 restraints weight = 14532.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.075075 restraints weight = 13511.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.075161 restraints weight = 12713.303| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15359 Z= 0.127 Angle : 0.673 16.073 20824 Z= 0.334 Chirality : 0.044 0.182 2365 Planarity : 0.004 0.045 2625 Dihedral : 4.917 50.438 2095 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 1.78 % Allowed : 24.18 % Favored : 74.03 % 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: -0.97 (0.20), residues: 1830 helix: 1.48 (0.21), residues: 627 sheet: -0.28 (0.27), residues: 410 loop : -2.73 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 20 TYR 0.011 0.001 TYR H 21 PHE 0.012 0.001 PHE A 128 TRP 0.013 0.001 TRP A 219 HIS 0.003 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00294 (15353) covalent geometry : angle 0.67087 (20809) SS BOND : bond 0.00187 ( 3) SS BOND : angle 1.05402 ( 6) hydrogen bonds : bond 0.03608 ( 620) hydrogen bonds : angle 4.47319 ( 1767) link_NAG-ASN : bond 0.00534 ( 3) link_NAG-ASN : angle 2.83012 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2645.33 seconds wall clock time: 46 minutes 27.27 seconds (2787.27 seconds total)