Starting phenix.real_space_refine on Sun Jan 19 15:31:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zho_60110/01_2025/8zho_60110.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zho_60110/01_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_60110/01_2025/8zho_60110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zho_60110/01_2025/8zho_60110.map" model { file = "/net/cci-nas-00/data/ceres_data/8zho_60110/01_2025/8zho_60110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zho_60110/01_2025/8zho_60110.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.031 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 7.35, per 1000 atoms: 0.64 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: 2.61 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.63 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: 4.20 Time building geometry restraints manager: 3.09 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.720 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.750 ------------------------------------------------------------------------------- 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 11708 Z= 0.166 Angle : 0.541 11.750 15960 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (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 TRP 0.011 0.001 TRP L 196 HIS 0.002 0.000 HIS E 36 PHE 0.011 0.001 PHE C 135 TYR 0.014 0.001 TYR C 369 ARG 0.005 0.000 ARG D 87 *********************** 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 : 1.215 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: 0.7083 (Cg_exo) REVERT: H 208 LYS cc_start: 0.7753 (mttt) cc_final: 0.7332 (ptpp) outliers start: 8 outliers final: 6 residues processed: 117 average time/residue: 0.2401 time to fit residues: 41.0136 Evaluate side-chains 62 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 124 optimal weight: 30.0000 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 75 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS L 8 HIS L 38 GLN L 53 ASN L 54 GLN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.215245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.192642 restraints weight = 18995.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.189336 restraints weight = 30868.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.186995 restraints weight = 31787.348| |-----------------------------------------------------------------------------| r_work (final): 0.4549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 11708 Z= 0.293 Angle : 0.591 11.634 15960 Z= 0.312 Chirality : 0.046 0.187 1797 Planarity : 0.004 0.043 2051 Dihedral : 4.786 58.826 1640 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.12 % Allowed : 19.81 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.22), residues: 1482 helix: -2.69 (0.54), residues: 58 sheet: 1.34 (0.24), residues: 511 loop : -0.68 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 49 HIS 0.008 0.001 HIS L 8 PHE 0.024 0.002 PHE H 80 TYR 0.025 0.002 TYR C 369 ARG 0.005 0.001 ARG H 104 *********************** 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 105 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 65 time to evaluate : 1.567 Fit side-chains revert: symmetry clash REVERT: C 153 MET cc_start: 0.1994 (tpp) cc_final: 0.1727 (tpt) REVERT: L 61 ASP cc_start: 0.6534 (t70) cc_final: 0.6215 (t0) REVERT: L 109 VAL cc_start: 0.7030 (t) cc_final: 0.6676 (t) REVERT: H 114 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7550 (t) outliers start: 40 outliers final: 21 residues processed: 101 average time/residue: 0.1846 time to fit residues: 30.1006 Evaluate side-chains 68 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 1.468 ------------------------------------------------------------------------------- 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 386 LYS 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 D residue 11 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER 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 L residue 52 ASP Chi-restraints excluded: chain L residue 75 SER 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 48 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 12 optimal weight: 50.0000 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 544 ASN C 563 GLN ** L 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 HIS ** 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 = 0.4789 r_free = 0.4789 target = 0.213105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.189941 restraints weight = 18950.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.186209 restraints weight = 29570.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.184817 restraints weight = 32984.023| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11708 Z= 0.277 Angle : 0.557 9.097 15960 Z= 0.293 Chirality : 0.046 0.216 1797 Planarity : 0.004 0.064 2051 Dihedral : 4.551 51.437 1635 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.90 % Allowed : 20.51 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1482 helix: -2.23 (0.61), residues: 58 sheet: 1.35 (0.23), residues: 523 loop : -0.74 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 110 HIS 0.008 0.001 HIS C 49 PHE 0.018 0.001 PHE H 80 TYR 0.023 0.001 TYR C 369 ARG 0.005 0.001 ARG H 104 *********************** 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 104 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 54 time to evaluate : 1.190 Fit side-chains REVERT: D 90 ASP cc_start: 0.7546 (t0) cc_final: 0.7341 (t0) REVERT: E 141 ILE cc_start: 0.2553 (tp) cc_final: 0.2074 (mp) REVERT: L 78 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7335 (mt) REVERT: L 155 VAL cc_start: -0.2044 (OUTLIER) cc_final: -0.2443 (m) outliers start: 50 outliers final: 30 residues processed: 98 average time/residue: 0.1768 time to fit residues: 28.2525 Evaluate side-chains 72 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 40 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 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 483 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 18 VAL Chi-restraints excluded: chain D residue 51 ILE 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 218 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 ASN 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 54 TYR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 114 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 142 optimal weight: 10.0000 chunk 81 optimal weight: 0.2980 chunk 46 optimal weight: 0.3980 chunk 61 optimal weight: 20.0000 chunk 127 optimal weight: 0.3980 chunk 144 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4802 r_free = 0.4802 target = 0.214542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.192240 restraints weight = 18965.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.189201 restraints weight = 31072.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.187953 restraints weight = 29602.605| |-----------------------------------------------------------------------------| r_work (final): 0.4562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11708 Z= 0.168 Angle : 0.493 8.818 15960 Z= 0.256 Chirality : 0.044 0.170 1797 Planarity : 0.004 0.049 2051 Dihedral : 3.938 46.495 1631 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.74 % Allowed : 20.12 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.22), residues: 1482 helix: -1.99 (0.64), residues: 58 sheet: 1.25 (0.23), residues: 537 loop : -0.64 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 110 HIS 0.009 0.001 HIS C 49 PHE 0.010 0.001 PHE H 80 TYR 0.014 0.001 TYR C 369 ARG 0.003 0.000 ARG H 104 *********************** 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 101 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 53 time to evaluate : 1.325 Fit side-chains REVERT: E 29 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7975 (mt) REVERT: E 141 ILE cc_start: 0.2290 (tp) cc_final: 0.1883 (mp) REVERT: L 78 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.7262 (mt) outliers start: 48 outliers final: 33 residues processed: 96 average time/residue: 0.1603 time to fit residues: 26.5927 Evaluate side-chains 79 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 44 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 332 ILE Chi-restraints excluded: chain C residue 335 LEU 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 517 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 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 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 58 SER Chi-restraints excluded: chain E residue 84 ASP 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 78 ILE Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 52 CYS Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 92 THR 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 47 optimal weight: 3.9990 chunk 139 optimal weight: 40.0000 chunk 69 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 141 optimal weight: 0.1980 chunk 70 optimal weight: 0.0570 chunk 107 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 HIS 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 = 0.4791 r_free = 0.4791 target = 0.213559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.191641 restraints weight = 18792.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.187799 restraints weight = 28806.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.186548 restraints weight = 30226.665| |-----------------------------------------------------------------------------| r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11708 Z= 0.206 Angle : 0.508 8.345 15960 Z= 0.265 Chirality : 0.044 0.161 1797 Planarity : 0.004 0.070 2051 Dihedral : 3.939 37.906 1631 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.06 % Allowed : 20.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.22), residues: 1482 helix: -1.83 (0.66), residues: 58 sheet: 1.20 (0.23), residues: 538 loop : -0.62 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.011 0.001 HIS C 49 PHE 0.014 0.001 PHE H 80 TYR 0.017 0.001 TYR C 369 ARG 0.003 0.000 ARG H 104 *********************** 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 98 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 46 time to evaluate : 1.125 Fit side-chains REVERT: C 424 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7790 (tptt) REVERT: E 29 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7998 (mt) REVERT: L 8 HIS cc_start: 0.5115 (OUTLIER) cc_final: 0.4912 (t-90) REVERT: L 78 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.7160 (mm) outliers start: 52 outliers final: 42 residues processed: 93 average time/residue: 0.1576 time to fit residues: 25.1729 Evaluate side-chains 86 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 40 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 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 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 84 SER 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 E residue 84 ASP Chi-restraints excluded: chain E residue 106 THR 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 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 2 VAL 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 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 Chi-restraints excluded: chain H residue 202 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 53 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 105 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 ** 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 = 0.4761 r_free = 0.4761 target = 0.202748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.191206 restraints weight = 17984.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.188679 restraints weight = 34627.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.186894 restraints weight = 31786.089| |-----------------------------------------------------------------------------| r_work (final): 0.4595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5996 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11708 Z= 0.352 Angle : 0.570 9.302 15960 Z= 0.299 Chirality : 0.046 0.276 1797 Planarity : 0.004 0.048 2051 Dihedral : 4.248 40.049 1631 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.13 % Allowed : 20.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1482 helix: -1.81 (0.67), residues: 58 sheet: 0.93 (0.22), residues: 560 loop : -0.66 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 436 HIS 0.021 0.001 HIS L 8 PHE 0.018 0.002 PHE H 80 TYR 0.026 0.002 TYR C 369 ARG 0.004 0.001 ARG H 104 *********************** 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 103 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 50 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: C 49 HIS cc_start: 0.3487 (t-170) cc_final: 0.3063 (t-170) REVERT: E 29 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8306 (mt) REVERT: E 106 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8284 (t) REVERT: E 141 ILE cc_start: 0.2619 (tp) cc_final: 0.2115 (mp) REVERT: L 78 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7314 (mm) outliers start: 53 outliers final: 37 residues processed: 100 average time/residue: 0.1723 time to fit residues: 28.5683 Evaluate side-chains 84 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 44 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 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 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 517 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 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 218 VAL 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 E residue 106 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 61 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 147 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 52 CYS Chi-restraints excluded: chain H residue 54 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 19 optimal weight: 20.0000 chunk 21 optimal weight: 50.0000 chunk 2 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 103 optimal weight: 50.0000 chunk 76 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 100 optimal weight: 40.0000 chunk 127 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 overall best weight: 4.8986 ------------------------------------------------------------------------------- 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** C 563 GLN D 39 GLN D 166 ASN L 8 HIS L 35 GLN H 204 ASN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.197970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.185914 restraints weight = 18022.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.182723 restraints weight = 35584.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.181506 restraints weight = 41768.612| |-----------------------------------------------------------------------------| r_work (final): 0.4532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.092 11708 Z= 0.649 Angle : 0.745 14.179 15960 Z= 0.399 Chirality : 0.052 0.266 1797 Planarity : 0.006 0.089 2051 Dihedral : 5.274 51.161 1629 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.45 % Allowed : 19.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.22), residues: 1482 helix: -2.07 (0.65), residues: 58 sheet: 0.55 (0.22), residues: 561 loop : -0.91 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP H 38 HIS 0.008 0.001 HIS C 49 PHE 0.029 0.002 PHE L 2 TYR 0.036 0.003 TYR C 369 ARG 0.007 0.001 ARG H 68 *********************** 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 107 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 50 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: C 465 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: D 48 MET cc_start: 0.8305 (ptt) cc_final: 0.7795 (ptt) REVERT: E 29 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8467 (mt) REVERT: E 83 GLU cc_start: 0.6906 (pp20) cc_final: 0.6623 (pp20) REVERT: E 141 ILE cc_start: 0.2743 (tp) cc_final: 0.2220 (mp) REVERT: L 8 HIS cc_start: 0.5577 (OUTLIER) cc_final: 0.5106 (t-90) REVERT: L 46 THR cc_start: 0.8411 (m) cc_final: 0.7996 (p) REVERT: L 78 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7684 (mm) outliers start: 57 outliers final: 41 residues processed: 102 average time/residue: 0.1923 time to fit residues: 31.3871 Evaluate side-chains 89 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 44 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 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 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 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 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 121 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 218 VAL 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 E residue 106 THR Chi-restraints excluded: chain L residue 8 HIS 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 71 ILE Chi-restraints excluded: chain H residue 92 THR 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 42 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 16 optimal weight: 30.0000 chunk 6 optimal weight: 30.0000 chunk 125 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 58 optimal weight: 30.0000 chunk 74 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** C 544 ASN ** L 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4749 r_free = 0.4749 target = 0.201675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.188266 restraints weight = 17906.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.187050 restraints weight = 37175.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.185842 restraints weight = 39315.927| |-----------------------------------------------------------------------------| r_work (final): 0.4582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11708 Z= 0.242 Angle : 0.579 12.774 15960 Z= 0.298 Chirality : 0.046 0.216 1797 Planarity : 0.004 0.078 2051 Dihedral : 4.614 50.024 1629 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.82 % Allowed : 20.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.22), residues: 1482 helix: -1.79 (0.70), residues: 58 sheet: 0.54 (0.22), residues: 571 loop : -0.80 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 159 HIS 0.021 0.001 HIS L 8 PHE 0.021 0.001 PHE H 173 TYR 0.017 0.001 TYR C 369 ARG 0.003 0.000 ARG C 466 *********************** 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 96 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 47 time to evaluate : 1.220 Fit side-chains REVERT: C 409 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: C 465 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: D 48 MET cc_start: 0.8286 (ptt) cc_final: 0.7740 (ptt) REVERT: D 102 TYR cc_start: 0.8103 (p90) cc_final: 0.7903 (p90) REVERT: E 29 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8260 (mt) REVERT: E 83 GLU cc_start: 0.6638 (pp20) cc_final: 0.6381 (pp20) REVERT: E 141 ILE cc_start: 0.2863 (tp) cc_final: 0.2344 (mp) REVERT: L 78 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7488 (mm) REVERT: L 85 ASP cc_start: 0.6863 (t70) cc_final: 0.6661 (t0) outliers start: 49 outliers final: 38 residues processed: 93 average time/residue: 0.1891 time to fit residues: 28.5880 Evaluate side-chains 86 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 44 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 296 LEU 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 409 GLN 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 610 VAL 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 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 121 THR 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 E residue 138 VAL Chi-restraints excluded: chain L residue 49 ILE 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 L residue 107 LEU 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 71 ILE Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 83 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 114 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 109 optimal weight: 0.4980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.4754 r_free = 0.4754 target = 0.202206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.187420 restraints weight = 17986.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.186275 restraints weight = 40953.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.184690 restraints weight = 39914.427| |-----------------------------------------------------------------------------| r_work (final): 0.4568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11708 Z= 0.221 Angle : 0.561 11.115 15960 Z= 0.287 Chirality : 0.045 0.192 1797 Planarity : 0.004 0.057 2051 Dihedral : 4.411 52.382 1629 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.43 % Allowed : 21.14 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.22), residues: 1482 helix: -1.72 (0.71), residues: 58 sheet: 0.72 (0.23), residues: 555 loop : -0.76 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 110 HIS 0.012 0.001 HIS C 49 PHE 0.015 0.001 PHE H 173 TYR 0.015 0.001 TYR C 369 ARG 0.002 0.000 ARG H 68 *********************** 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 92 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 48 time to evaluate : 1.144 Fit side-chains REVERT: D 48 MET cc_start: 0.8175 (ptt) cc_final: 0.7856 (ptt) REVERT: E 29 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8268 (mt) REVERT: E 83 GLU cc_start: 0.6581 (pp20) cc_final: 0.6337 (pp20) REVERT: E 141 ILE cc_start: 0.3022 (tp) cc_final: 0.2559 (mp) REVERT: L 8 HIS cc_start: 0.5197 (OUTLIER) cc_final: 0.4776 (t-90) REVERT: L 78 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7385 (mm) REVERT: L 85 ASP cc_start: 0.6932 (t70) cc_final: 0.6710 (t0) outliers start: 44 outliers final: 37 residues processed: 88 average time/residue: 0.1750 time to fit residues: 25.9650 Evaluate side-chains 85 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 45 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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 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 402 ILE Chi-restraints excluded: chain C residue 409 GLN 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 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 83 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 121 THR 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 E residue 138 VAL Chi-restraints excluded: chain L residue 8 HIS Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 61 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 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 71 ILE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 128 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 25 optimal weight: 0.0060 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 40.0000 chunk 11 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 141 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.8004 ------------------------------------------------------------------------------- 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 ** 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 = 0.4766 r_free = 0.4766 target = 0.203350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.187827 restraints weight = 17846.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.185899 restraints weight = 34254.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.185219 restraints weight = 38931.373| |-----------------------------------------------------------------------------| r_work (final): 0.4573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11708 Z= 0.182 Angle : 0.549 10.803 15960 Z= 0.279 Chirality : 0.045 0.194 1797 Planarity : 0.004 0.078 2051 Dihedral : 4.322 52.204 1629 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.20 % Allowed : 21.37 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.22), residues: 1482 helix: -1.65 (0.71), residues: 58 sheet: 0.65 (0.22), residues: 568 loop : -0.67 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 110 HIS 0.015 0.001 HIS L 8 PHE 0.013 0.001 PHE H 173 TYR 0.017 0.001 TYR D 187 ARG 0.002 0.000 ARG L 62 ********************** 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 89 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 48 time to evaluate : 1.330 Fit side-chains REVERT: D 48 MET cc_start: 0.8210 (ptt) cc_final: 0.7908 (ptt) REVERT: E 29 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8195 (mt) REVERT: E 141 ILE cc_start: 0.3032 (tp) cc_final: 0.2522 (mp) REVERT: L 78 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7286 (mm) outliers start: 41 outliers final: 36 residues processed: 86 average time/residue: 0.1948 time to fit residues: 27.1835 Evaluate side-chains 82 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 44 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 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 382 VAL Chi-restraints excluded: chain C residue 409 GLN 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 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 83 LEU Chi-restraints excluded: chain D residue 84 SER 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 E residue 138 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 61 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 147 ILE Chi-restraints excluded: chain H residue 52 CYS Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 123 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 6 optimal weight: 30.0000 chunk 146 optimal weight: 9.9990 chunk 11 optimal weight: 40.0000 chunk 117 optimal weight: 0.7980 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 199 HIS L 208 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 = 0.4749 r_free = 0.4749 target = 0.201540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.190114 restraints weight = 17749.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.187642 restraints weight = 33312.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.186060 restraints weight = 27381.712| |-----------------------------------------------------------------------------| r_work (final): 0.4587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6011 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11708 Z= 0.283 Angle : 0.580 10.519 15960 Z= 0.299 Chirality : 0.046 0.192 1797 Planarity : 0.004 0.055 2051 Dihedral : 4.493 54.869 1629 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.96 % Allowed : 21.45 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.22), residues: 1482 helix: -1.61 (0.71), residues: 58 sheet: 0.69 (0.22), residues: 563 loop : -0.73 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 110 HIS 0.012 0.001 HIS C 49 PHE 0.015 0.002 PHE D 29 TYR 0.019 0.002 TYR D 187 ARG 0.003 0.000 ARG H 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3034.14 seconds wall clock time: 56 minutes 29.55 seconds (3389.55 seconds total)