Starting phenix.real_space_refine on Sat Aug 23 18:29:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zho_60110/08_2025/8zho_60110.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zho_60110/08_2025/8zho_60110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zho_60110/08_2025/8zho_60110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zho_60110/08_2025/8zho_60110.map" model { file = "/net/cci-nas-00/data/ceres_data/8zho_60110/08_2025/8zho_60110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zho_60110/08_2025/8zho_60110.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3069 atoms to isotropic. 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 43 5.16 5 C 7231 2.51 5 N 1900 2.21 5 O 2249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11423 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 4932 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 31, 'TRANS': 590} Chain breaks: 2 Chain: "D" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1589 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain breaks: 1 Chain: "H" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" 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: 2.68, per 1000 atoms: 0.23 Number of scatterers: 11423 At special positions: 0 Unit cell: (94.86, 119.04, 179.49, 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 43 16.00 O 2249 8.00 N 1900 7.00 C 7231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 151 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS L 145 " - pdb=" SG CYS L 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 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 C 701 " - " ASN C 343 " Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 573.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2758 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 35 sheets defined 5.5% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.875A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.076A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.996A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.634A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'E' and resid 81 through 85 removed outlier: 4.168A pdb=" N GLU E 85 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 removed outlier: 3.515A pdb=" N GLU E 129 " --> pdb=" O SER E 126 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN E 131 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN E 133 " --> pdb=" O LEU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 191 removed outlier: 4.018A pdb=" N LYS E 191 " --> pdb=" O PRO E 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.581A pdb=" N ASP L 85 " --> pdb=" O LYS L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 138 Processing helix chain 'L' and resid 192 through 199 removed outlier: 3.569A pdb=" N LYS L 197 " --> pdb=" O PRO L 193 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS L 199 " --> pdb=" O GLN L 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.862A pdb=" N THR H 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 138 removed outlier: 3.729A pdb=" N THR H 138 " --> pdb=" O SER H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing sheet with id=AA1, first strand: chain 'C' and resid 48 through 54 removed outlier: 4.120A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 63 through 67 removed outlier: 3.546A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.882A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 152 through 160 removed outlier: 5.472A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.744A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.840A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.701A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.549A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.991A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 466 through 467 removed outlier: 3.862A pdb=" N ARG C 466 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY D 104 " --> pdb=" O ARG C 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.452A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.646A pdb=" N ALA D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.607A pdb=" N TRP D 36 " --> pdb=" O GLY D 49 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE D 57 " --> pdb=" O ILE D 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.168A pdb=" N LEU D 113 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 131 through 135 removed outlier: 5.802A pdb=" N LYS D 154 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU D 189 " --> pdb=" O LYS D 154 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR D 156 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR D 187 " --> pdb=" O TYR D 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 131 through 135 Processing sheet with id=AB9, first strand: chain 'D' and resid 163 through 165 removed outlier: 4.543A pdb=" N TYR D 205 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS D 207 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS D 220 " --> pdb=" O CYS D 207 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL D 209 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL D 218 " --> pdb=" O VAL D 209 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 9 through 10 removed outlier: 6.514A pdb=" N TRP E 37 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 9 through 10 Processing sheet with id=AC3, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AC4, first strand: chain 'E' and resid 119 through 123 removed outlier: 4.113A pdb=" N PHE E 123 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL E 138 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP E 143 " --> pdb=" O TYR E 177 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N TYR E 177 " --> pdb=" O ASP E 143 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 159 through 160 removed outlier: 4.588A pdb=" N TRP E 153 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS E 154 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR E 196 " --> pdb=" O VAL E 211 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL E 211 " --> pdb=" O TYR E 196 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N CYS E 198 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS E 209 " --> pdb=" O CYS E 198 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL E 200 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL E 207 " --> pdb=" O VAL E 200 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AC7, first strand: chain 'L' and resid 9 through 11 removed outlier: 7.493A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 125 through 129 removed outlier: 5.459A pdb=" N TYR L 183 " --> pdb=" O ASP L 149 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 125 through 129 removed outlier: 5.459A pdb=" N TYR L 183 " --> pdb=" O ASP L 149 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 165 through 166 removed outlier: 4.162A pdb=" N TRP L 159 " --> pdb=" O VAL L 166 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.843A pdb=" N VAL H 12 " --> pdb=" O THR H 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'H' and resid 59 through 61 removed outlier: 5.093A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR H 109 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 59 through 61 removed outlier: 5.093A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.964A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP H 151 " --> pdb=" O TYR H 183 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.964A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP H 151 " --> pdb=" O TYR H 183 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 158 through 161 removed outlier: 4.221A pdb=" N TYR H 201 " --> pdb=" O VAL H 218 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 987 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: 2.14 Time building geometry restraints manager: 1.09 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: 3635 1.34 - 1.46: 2830 1.46 - 1.58: 5195 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 11708 Sorted by residual: bond pdb=" N VAL C 382 " pdb=" CA VAL C 382 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 7.99e+00 bond pdb=" N LYS C 378 " pdb=" CA LYS C 378 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.21e-02 6.83e+03 7.21e+00 bond pdb=" N CYS C 379 " pdb=" CA CYS C 379 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.27e-02 6.20e+03 6.90e+00 bond pdb=" N THR C 376 " pdb=" CA THR C 376 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 6.14e+00 bond pdb=" N TYR C 380 " pdb=" CA TYR C 380 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.17e-02 7.31e+03 6.04e+00 ... (remaining 11703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 15798 2.35 - 4.70: 148 4.70 - 7.05: 9 7.05 - 9.40: 4 9.40 - 11.75: 1 Bond angle restraints: 15960 Sorted by residual: angle pdb=" CB MET C 153 " pdb=" CG MET C 153 " pdb=" SD MET C 153 " ideal model delta sigma weight residual 112.70 124.45 -11.75 3.00e+00 1.11e-01 1.53e+01 angle pdb=" N LYS C 386 " pdb=" CA LYS C 386 " pdb=" C LYS C 386 " ideal model delta sigma weight residual 114.64 108.81 5.83 1.52e+00 4.33e-01 1.47e+01 angle pdb=" C ASN L 1 " pdb=" CA ASN L 1 " pdb=" CB ASN L 1 " ideal model delta sigma weight residual 110.10 116.65 -6.55 1.90e+00 2.77e-01 1.19e+01 angle pdb=" CA GLU L 194 " pdb=" CB GLU L 194 " pdb=" CG GLU L 194 " ideal model delta sigma weight residual 114.10 120.99 -6.89 2.00e+00 2.50e-01 1.19e+01 angle pdb=" N ASP L 162 " pdb=" CA ASP L 162 " pdb=" C ASP L 162 " ideal model delta sigma weight residual 111.36 107.92 3.44 1.09e+00 8.42e-01 9.97e+00 ... (remaining 15955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6175 17.91 - 35.82: 598 35.82 - 53.74: 156 53.74 - 71.65: 21 71.65 - 89.56: 14 Dihedral angle restraints: 6964 sinusoidal: 2642 harmonic: 4322 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 -177.44 -89.56 1 1.00e+01 1.00e-02 9.53e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -143.29 57.29 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 97 " pdb=" CB CYS H 97 " ideal model delta sinusoidal sigma weight residual 93.00 54.59 38.41 1 1.00e+01 1.00e-02 2.08e+01 ... (remaining 6961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1162 0.034 - 0.068: 397 0.068 - 0.103: 143 0.103 - 0.137: 92 0.137 - 0.171: 3 Chirality restraints: 1797 Sorted by residual: chirality pdb=" CG LEU C 118 " pdb=" CB LEU C 118 " pdb=" CD1 LEU C 118 " pdb=" CD2 LEU C 118 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" CA LEU C 387 " pdb=" N LEU C 387 " pdb=" C LEU C 387 " pdb=" CB LEU C 387 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" CA VAL C 382 " pdb=" N VAL C 382 " pdb=" C VAL C 382 " pdb=" CB VAL C 382 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 1794 not shown) Planarity restraints: 2052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 155 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO H 156 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO H 156 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 156 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 59 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO L 60 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 208 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO H 209 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO H 209 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 209 " 0.022 5.00e-02 4.00e+02 ... (remaining 2049 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2789 2.80 - 3.32: 9237 3.32 - 3.85: 18795 3.85 - 4.37: 20341 4.37 - 4.90: 36500 Nonbonded interactions: 87662 Sorted by model distance: nonbonded pdb=" OG SER D 17 " pdb=" OE2 GLU D 82 " model vdw 2.273 3.040 nonbonded pdb=" ND2 ASN L 53 " pdb=" OE1 GLN L 54 " model vdw 2.313 3.120 nonbonded pdb=" OG SER E 2 " pdb=" N VAL E 3 " model vdw 2.314 3.120 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASN C 360 " pdb=" OG1 THR C 523 " model vdw 2.329 3.040 ... (remaining 87657 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=0.00 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.910 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 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 : 0.003 0.039 11726 Z= 0.150 Angle : 0.541 11.750 15997 Z= 0.294 Chirality : 0.045 0.171 1797 Planarity : 0.004 0.041 2051 Dihedral : 15.241 87.837 4155 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.62 % Allowed : 19.66 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -0.09 (0.22), residues: 1482 helix: -3.05 (0.44), residues: 57 sheet: 1.44 (0.23), residues: 528 loop : -0.83 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 87 TYR 0.014 0.001 TYR C 369 PHE 0.011 0.001 PHE C 135 TRP 0.011 0.001 TRP L 196 HIS 0.002 0.000 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00257 (11708) covalent geometry : angle 0.54081 (15960) SS BOND : bond 0.00103 ( 17) SS BOND : angle 0.43315 ( 34) hydrogen bonds : bond 0.27084 ( 343) hydrogen bonds : angle 9.92582 ( 987) link_NAG-ASN : bond 0.00211 ( 1) link_NAG-ASN : angle 0.89967 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 62 VAL cc_start: 0.4868 (m) cc_final: 0.4512 (t) REVERT: C 285 ILE cc_start: 0.6882 (mt) cc_final: 0.6303 (pt) REVERT: C 390 LEU cc_start: 0.5893 (mt) cc_final: 0.5692 (mt) REVERT: C 549 THR cc_start: 0.5794 (p) cc_final: 0.5555 (p) REVERT: D 43 GLN cc_start: 0.7595 (mp10) cc_final: 0.7272 (mp10) REVERT: E 153 TRP cc_start: 0.5107 (m100) cc_final: 0.4284 (m100) REVERT: L 61 ASP cc_start: 0.7692 (t70) cc_final: 0.7002 (m-30) REVERT: L 86 GLU cc_start: 0.7288 (tt0) cc_final: 0.6979 (mt-10) REVERT: L 109 VAL cc_start: 0.7148 (t) cc_final: 0.6635 (t) REVERT: H 154 PRO cc_start: 0.7443 (Cg_endo) cc_final: 0.7082 (Cg_exo) REVERT: H 208 LYS cc_start: 0.7753 (mttt) cc_final: 0.7331 (ptpp) outliers start: 8 outliers final: 6 residues processed: 117 average time/residue: 0.0948 time to fit residues: 16.4309 Evaluate side-chains 64 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain H residue 211 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 40.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 30.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 HIS L 38 GLN ** H 207 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 = 0.4769 r_free = 0.4769 target = 0.210490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.186752 restraints weight = 18763.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.183449 restraints weight = 31053.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.182111 restraints weight = 33059.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.181464 restraints weight = 33567.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.180434 restraints weight = 33417.492| |-----------------------------------------------------------------------------| r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 11726 Z= 0.332 Angle : 0.705 10.121 15997 Z= 0.381 Chirality : 0.050 0.300 1797 Planarity : 0.005 0.052 2051 Dihedral : 5.170 53.616 1640 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.82 % Allowed : 19.97 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -0.20 (0.22), residues: 1482 helix: -2.84 (0.52), residues: 58 sheet: 1.24 (0.24), residues: 522 loop : -0.82 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 104 TYR 0.039 0.002 TYR C 369 PHE 0.028 0.002 PHE H 80 TRP 0.016 0.002 TRP H 102 HIS 0.009 0.001 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00772 (11708) covalent geometry : angle 0.70232 (15960) SS BOND : bond 0.00482 ( 17) SS BOND : angle 1.48784 ( 34) hydrogen bonds : bond 0.04171 ( 343) hydrogen bonds : angle 6.54840 ( 987) link_NAG-ASN : bond 0.00090 ( 1) link_NAG-ASN : angle 1.59177 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 70 time to evaluate : 0.337 Fit side-chains REVERT: C 153 MET cc_start: 0.1886 (tpp) cc_final: 0.1597 (tpt) REVERT: L 78 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7575 (mt) REVERT: L 86 GLU cc_start: 0.7343 (tt0) cc_final: 0.7128 (tt0) REVERT: L 109 VAL cc_start: 0.7209 (t) cc_final: 0.6853 (t) REVERT: H 20 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8049 (mp) REVERT: H 114 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7718 (t) outliers start: 49 outliers final: 30 residues processed: 115 average time/residue: 0.0689 time to fit residues: 12.8545 Evaluate side-chains 81 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 48 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 52 CYS Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 202 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 117 optimal weight: 10.0000 chunk 125 optimal weight: 50.0000 chunk 128 optimal weight: 0.9980 chunk 10 optimal weight: 0.0470 chunk 87 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 40.0000 chunk 110 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 563 GLN H 204 ASN ** H 207 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 = 0.4803 r_free = 0.4803 target = 0.214454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.192333 restraints weight = 19046.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.188778 restraints weight = 30024.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.188330 restraints weight = 32003.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.186679 restraints weight = 25953.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.185041 restraints weight = 32073.810| |-----------------------------------------------------------------------------| r_work (final): 0.4529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11726 Z= 0.119 Angle : 0.523 9.487 15997 Z= 0.274 Chirality : 0.045 0.159 1797 Planarity : 0.004 0.064 2051 Dihedral : 4.133 47.840 1631 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.35 % Allowed : 21.14 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -0.11 (0.22), residues: 1482 helix: -2.55 (0.57), residues: 64 sheet: 1.21 (0.23), residues: 527 loop : -0.71 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 63 TYR 0.017 0.001 TYR C 369 PHE 0.010 0.001 PHE H 80 TRP 0.013 0.001 TRP H 110 HIS 0.009 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00268 (11708) covalent geometry : angle 0.52104 (15960) SS BOND : bond 0.00303 ( 17) SS BOND : angle 0.92836 ( 34) hydrogen bonds : bond 0.03223 ( 343) hydrogen bonds : angle 5.84159 ( 987) link_NAG-ASN : bond 0.00135 ( 1) link_NAG-ASN : angle 1.40656 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 52 time to evaluate : 0.443 Fit side-chains REVERT: D 90 ASP cc_start: 0.7454 (t0) cc_final: 0.7158 (t0) REVERT: D 203 GLN cc_start: -0.0260 (OUTLIER) cc_final: -0.0553 (pt0) REVERT: L 86 GLU cc_start: 0.7177 (tt0) cc_final: 0.6968 (tt0) REVERT: L 109 VAL cc_start: 0.7041 (t) cc_final: 0.6661 (t) outliers start: 43 outliers final: 26 residues processed: 90 average time/residue: 0.0717 time to fit residues: 10.7661 Evaluate side-chains 68 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 41 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 202 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 10 optimal weight: 40.0000 chunk 4 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 50.0000 chunk 129 optimal weight: 1.9990 chunk 121 optimal weight: 30.0000 chunk 87 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 82 optimal weight: 50.0000 chunk 32 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 HIS H 204 ASN ** H 207 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 = 0.4774 r_free = 0.4774 target = 0.203889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.192457 restraints weight = 18067.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.189818 restraints weight = 33223.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.186749 restraints weight = 29516.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.184647 restraints weight = 42421.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.183882 restraints weight = 42513.086| |-----------------------------------------------------------------------------| r_work (final): 0.4556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11726 Z= 0.182 Angle : 0.543 8.726 15997 Z= 0.286 Chirality : 0.046 0.291 1797 Planarity : 0.004 0.051 2051 Dihedral : 4.114 31.063 1630 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.29 % Allowed : 19.89 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -0.15 (0.22), residues: 1482 helix: -2.10 (0.63), residues: 58 sheet: 1.02 (0.23), residues: 545 loop : -0.70 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 63 TYR 0.020 0.001 TYR C 369 PHE 0.021 0.002 PHE E 123 TRP 0.013 0.001 TRP C 436 HIS 0.008 0.001 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00426 (11708) covalent geometry : angle 0.54124 (15960) SS BOND : bond 0.00387 ( 17) SS BOND : angle 1.07739 ( 34) hydrogen bonds : bond 0.02963 ( 343) hydrogen bonds : angle 5.66041 ( 987) link_NAG-ASN : bond 0.00013 ( 1) link_NAG-ASN : angle 1.76363 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 49 time to evaluate : 0.344 Fit side-chains REVERT: D 102 TYR cc_start: 0.8286 (p90) cc_final: 0.8078 (p90) REVERT: D 203 GLN cc_start: -0.0067 (OUTLIER) cc_final: -0.0481 (pt0) REVERT: E 141 ILE cc_start: 0.2635 (tp) cc_final: 0.2127 (mp) REVERT: L 78 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7368 (mt) REVERT: L 86 GLU cc_start: 0.7020 (tt0) cc_final: 0.6807 (tt0) outliers start: 55 outliers final: 42 residues processed: 100 average time/residue: 0.0706 time to fit residues: 11.2921 Evaluate side-chains 89 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 45 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain H residue 52 CYS Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 202 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 33 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 9 optimal weight: 40.0000 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 140 optimal weight: 40.0000 chunk 80 optimal weight: 7.9990 chunk 58 optimal weight: 30.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 HIS ** H 207 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 = 0.4771 r_free = 0.4771 target = 0.203576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.187965 restraints weight = 17993.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.185136 restraints weight = 33388.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.184391 restraints weight = 37858.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.182368 restraints weight = 38054.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.181992 restraints weight = 39286.134| |-----------------------------------------------------------------------------| r_work (final): 0.4542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11726 Z= 0.173 Angle : 0.538 8.789 15997 Z= 0.283 Chirality : 0.045 0.196 1797 Planarity : 0.004 0.065 2051 Dihedral : 4.101 20.232 1630 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.45 % Allowed : 19.81 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -0.19 (0.22), residues: 1482 helix: -1.88 (0.66), residues: 58 sheet: 0.84 (0.22), residues: 562 loop : -0.66 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 104 TYR 0.019 0.001 TYR C 369 PHE 0.014 0.001 PHE H 80 TRP 0.012 0.001 TRP C 436 HIS 0.010 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00407 (11708) covalent geometry : angle 0.53573 (15960) SS BOND : bond 0.00594 ( 17) SS BOND : angle 1.08721 ( 34) hydrogen bonds : bond 0.02832 ( 343) hydrogen bonds : angle 5.52676 ( 987) link_NAG-ASN : bond 0.00025 ( 1) link_NAG-ASN : angle 1.71514 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 52 time to evaluate : 0.414 Fit side-chains REVERT: C 424 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7708 (tptt) REVERT: D 102 TYR cc_start: 0.8214 (p90) cc_final: 0.7995 (p90) REVERT: E 29 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8241 (mt) REVERT: L 62 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6738 (ptt90) REVERT: L 78 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7308 (mt) outliers start: 57 outliers final: 39 residues processed: 102 average time/residue: 0.0647 time to fit residues: 10.9036 Evaluate side-chains 88 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 45 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain H residue 52 CYS Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 120 optimal weight: 50.0000 chunk 60 optimal weight: 30.0000 chunk 94 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 118 optimal weight: 50.0000 chunk 111 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 82 optimal weight: 40.0000 chunk 20 optimal weight: 30.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 HIS H 204 ASN ** H 207 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 = 0.4770 r_free = 0.4770 target = 0.203383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.192053 restraints weight = 17991.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.189396 restraints weight = 32276.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.187544 restraints weight = 38322.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.179507 restraints weight = 39371.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.176025 restraints weight = 38099.886| |-----------------------------------------------------------------------------| r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11726 Z= 0.164 Angle : 0.543 8.466 15997 Z= 0.282 Chirality : 0.045 0.261 1797 Planarity : 0.004 0.048 2051 Dihedral : 4.067 21.499 1628 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.98 % Allowed : 20.12 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -0.15 (0.22), residues: 1482 helix: -1.74 (0.68), residues: 58 sheet: 0.89 (0.22), residues: 558 loop : -0.64 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 104 TYR 0.017 0.001 TYR C 369 PHE 0.014 0.001 PHE H 80 TRP 0.013 0.001 TRP H 38 HIS 0.011 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00387 (11708) covalent geometry : angle 0.54082 (15960) SS BOND : bond 0.00474 ( 17) SS BOND : angle 1.08485 ( 34) hydrogen bonds : bond 0.02714 ( 343) hydrogen bonds : angle 5.45856 ( 987) link_NAG-ASN : bond 0.00043 ( 1) link_NAG-ASN : angle 1.71495 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 48 time to evaluate : 0.460 Fit side-chains REVERT: D 102 TYR cc_start: 0.8176 (p90) cc_final: 0.7903 (p90) REVERT: E 29 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8296 (mt) REVERT: E 141 ILE cc_start: 0.2778 (tp) cc_final: 0.2291 (mp) REVERT: L 8 HIS cc_start: 0.5393 (OUTLIER) cc_final: 0.5117 (t-90) REVERT: L 62 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6827 (ptt90) REVERT: L 78 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7265 (mm) REVERT: H 155 GLU cc_start: 0.4396 (OUTLIER) cc_final: 0.4115 (pp20) outliers start: 51 outliers final: 39 residues processed: 93 average time/residue: 0.0903 time to fit residues: 13.4567 Evaluate side-chains 88 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 44 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain L residue 8 HIS Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain H residue 52 CYS Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 155 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 47 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 100 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 88 optimal weight: 0.0470 chunk 90 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 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 = 0.4787 r_free = 0.4787 target = 0.205207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.193996 restraints weight = 18037.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.190893 restraints weight = 32072.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.188874 restraints weight = 38376.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.188113 restraints weight = 37318.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.186681 restraints weight = 39292.325| |-----------------------------------------------------------------------------| r_work (final): 0.4594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 11726 Z= 0.105 Angle : 0.513 7.919 15997 Z= 0.265 Chirality : 0.044 0.201 1797 Planarity : 0.004 0.072 2051 Dihedral : 3.930 20.218 1628 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.35 % Allowed : 20.59 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -0.09 (0.22), residues: 1482 helix: -1.51 (0.70), residues: 58 sheet: 0.91 (0.22), residues: 559 loop : -0.62 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 466 TYR 0.015 0.001 TYR H 183 PHE 0.010 0.001 PHE D 29 TRP 0.011 0.001 TRP H 110 HIS 0.017 0.002 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00244 (11708) covalent geometry : angle 0.51104 (15960) SS BOND : bond 0.00462 ( 17) SS BOND : angle 1.10514 ( 34) hydrogen bonds : bond 0.02544 ( 343) hydrogen bonds : angle 5.27270 ( 987) link_NAG-ASN : bond 0.00160 ( 1) link_NAG-ASN : angle 1.53975 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 47 time to evaluate : 0.464 Fit side-chains REVERT: C 465 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: D 102 TYR cc_start: 0.8152 (p90) cc_final: 0.7952 (p90) REVERT: E 141 ILE cc_start: 0.2613 (tp) cc_final: 0.2141 (mp) REVERT: L 62 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6723 (ptt90) REVERT: L 78 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7213 (mt) REVERT: H 104 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8410 (mtt90) outliers start: 43 outliers final: 32 residues processed: 86 average time/residue: 0.0916 time to fit residues: 12.6232 Evaluate side-chains 77 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 41 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 104 ARG Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 47 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 97 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 140 optimal weight: 40.0000 chunk 41 optimal weight: 0.0070 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN L 8 HIS ** H 207 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 = 0.4764 r_free = 0.4764 target = 0.202941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.191247 restraints weight = 17848.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.188532 restraints weight = 32421.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.186772 restraints weight = 32696.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.185597 restraints weight = 36812.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.183858 restraints weight = 35550.806| |-----------------------------------------------------------------------------| r_work (final): 0.4560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11726 Z= 0.177 Angle : 0.559 9.539 15997 Z= 0.288 Chirality : 0.045 0.191 1797 Planarity : 0.004 0.050 2051 Dihedral : 4.090 19.368 1628 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.45 % Allowed : 20.20 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -0.15 (0.22), residues: 1482 helix: -1.53 (0.70), residues: 58 sheet: 0.80 (0.22), residues: 558 loop : -0.59 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 87 TYR 0.020 0.001 TYR C 369 PHE 0.018 0.001 PHE H 173 TRP 0.013 0.001 TRP H 38 HIS 0.011 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00418 (11708) covalent geometry : angle 0.55604 (15960) SS BOND : bond 0.00545 ( 17) SS BOND : angle 1.20865 ( 34) hydrogen bonds : bond 0.02735 ( 343) hydrogen bonds : angle 5.40764 ( 987) link_NAG-ASN : bond 0.00041 ( 1) link_NAG-ASN : angle 1.80527 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 45 time to evaluate : 0.446 Fit side-chains REVERT: C 465 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7676 (tt0) REVERT: D 48 MET cc_start: 0.8130 (ptt) cc_final: 0.7918 (ptt) REVERT: D 102 TYR cc_start: 0.8148 (p90) cc_final: 0.7939 (p90) REVERT: E 29 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8224 (mt) REVERT: E 141 ILE cc_start: 0.2839 (tp) cc_final: 0.2313 (mp) REVERT: L 8 HIS cc_start: 0.5265 (OUTLIER) cc_final: 0.4904 (t-90) REVERT: L 62 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6751 (ptt90) REVERT: L 78 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7251 (mm) REVERT: H 104 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8500 (mtt90) outliers start: 57 outliers final: 39 residues processed: 95 average time/residue: 0.0908 time to fit residues: 13.7069 Evaluate side-chains 87 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 42 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain L residue 8 HIS Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 104 ARG Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 126 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 120 optimal weight: 50.0000 chunk 128 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 129 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 6 optimal weight: 40.0000 chunk 61 optimal weight: 30.0000 overall best weight: 3.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN L 35 GLN ** H 207 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 = 0.4731 r_free = 0.4731 target = 0.199635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.187761 restraints weight = 17757.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.184883 restraints weight = 32094.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.183079 restraints weight = 33423.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.182182 restraints weight = 40366.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.180610 restraints weight = 39169.442| |-----------------------------------------------------------------------------| r_work (final): 0.4524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 11726 Z= 0.322 Angle : 0.673 12.228 15997 Z= 0.354 Chirality : 0.050 0.235 1797 Planarity : 0.005 0.077 2051 Dihedral : 4.741 23.009 1628 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.06 % Allowed : 20.59 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -0.47 (0.22), residues: 1482 helix: -1.77 (0.69), residues: 58 sheet: 0.63 (0.22), residues: 561 loop : -0.85 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 68 TYR 0.029 0.002 TYR C 369 PHE 0.022 0.002 PHE L 2 TRP 0.019 0.002 TRP H 38 HIS 0.041 0.002 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00762 (11708) covalent geometry : angle 0.66929 (15960) SS BOND : bond 0.00632 ( 17) SS BOND : angle 1.52433 ( 34) hydrogen bonds : bond 0.03210 ( 343) hydrogen bonds : angle 5.81805 ( 987) link_NAG-ASN : bond 0.00196 ( 1) link_NAG-ASN : angle 2.10288 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 48 time to evaluate : 0.448 Fit side-chains REVERT: C 409 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: C 465 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: D 48 MET cc_start: 0.8091 (ptt) cc_final: 0.7797 (ptt) REVERT: E 83 GLU cc_start: 0.6635 (pp20) cc_final: 0.6335 (pp20) REVERT: E 141 ILE cc_start: 0.2963 (tp) cc_final: 0.2423 (mp) REVERT: L 62 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6833 (ptt90) REVERT: L 78 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7301 (mm) REVERT: H 104 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8606 (mtt90) outliers start: 52 outliers final: 41 residues processed: 94 average time/residue: 0.0836 time to fit residues: 12.7198 Evaluate side-chains 88 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 42 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain H residue 52 CYS Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 104 ARG Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 66 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 129 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 HIS ** H 207 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 = 0.4770 r_free = 0.4770 target = 0.211134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.188250 restraints weight = 18852.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.184305 restraints weight = 31004.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.182380 restraints weight = 30895.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.181572 restraints weight = 31841.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.181020 restraints weight = 32121.785| |-----------------------------------------------------------------------------| r_work (final): 0.4484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11726 Z= 0.119 Angle : 0.559 13.337 15997 Z= 0.283 Chirality : 0.045 0.184 1797 Planarity : 0.004 0.056 2051 Dihedral : 4.172 21.694 1628 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.20 % Allowed : 21.76 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -0.26 (0.22), residues: 1482 helix: -1.65 (0.70), residues: 58 sheet: 0.71 (0.22), residues: 566 loop : -0.66 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 87 TYR 0.017 0.001 TYR D 187 PHE 0.014 0.001 PHE H 173 TRP 0.019 0.001 TRP L 159 HIS 0.012 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00273 (11708) covalent geometry : angle 0.55664 (15960) SS BOND : bond 0.00498 ( 17) SS BOND : angle 1.14457 ( 34) hydrogen bonds : bond 0.02560 ( 343) hydrogen bonds : angle 5.34482 ( 987) link_NAG-ASN : bond 0.00109 ( 1) link_NAG-ASN : angle 1.58609 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 44 time to evaluate : 0.448 Fit side-chains REVERT: C 424 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7698 (tptt) REVERT: C 465 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: E 141 ILE cc_start: 0.3152 (tp) cc_final: 0.2598 (mp) REVERT: L 8 HIS cc_start: 0.5153 (OUTLIER) cc_final: 0.4716 (t-90) REVERT: L 78 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7399 (mm) REVERT: H 104 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8508 (mtt90) outliers start: 41 outliers final: 32 residues processed: 80 average time/residue: 0.0871 time to fit residues: 11.3179 Evaluate side-chains 77 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 40 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain L residue 8 HIS Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 104 ARG Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 126 optimal weight: 0.6980 chunk 21 optimal weight: 50.0000 chunk 88 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 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 = 0.4764 r_free = 0.4764 target = 0.202924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.189623 restraints weight = 17893.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.188067 restraints weight = 38017.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.186875 restraints weight = 36310.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.185421 restraints weight = 37177.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.184823 restraints weight = 41880.206| |-----------------------------------------------------------------------------| r_work (final): 0.4572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11726 Z= 0.145 Angle : 0.560 12.244 15997 Z= 0.284 Chirality : 0.045 0.181 1797 Planarity : 0.004 0.081 2051 Dihedral : 4.174 21.296 1628 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.20 % Allowed : 21.61 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -0.21 (0.22), residues: 1482 helix: -1.64 (0.71), residues: 58 sheet: 0.85 (0.23), residues: 550 loop : -0.69 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 87 TYR 0.019 0.001 TYR D 187 PHE 0.018 0.001 PHE D 157 TRP 0.012 0.001 TRP H 110 HIS 0.023 0.002 HIS L 8 Details of bonding type rmsd covalent geometry : bond 0.00342 (11708) covalent geometry : angle 0.55807 (15960) SS BOND : bond 0.00497 ( 17) SS BOND : angle 1.16369 ( 34) hydrogen bonds : bond 0.02575 ( 343) hydrogen bonds : angle 5.30328 ( 987) link_NAG-ASN : bond 0.00085 ( 1) link_NAG-ASN : angle 1.68807 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1701.35 seconds wall clock time: 30 minutes 27.61 seconds (1827.61 seconds total)