Starting phenix.real_space_refine on Sun Nov 17 14:31:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zho_60110/11_2024/8zho_60110.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zho_60110/11_2024/8zho_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zho_60110/11_2024/8zho_60110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zho_60110/11_2024/8zho_60110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zho_60110/11_2024/8zho_60110.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zho_60110/11_2024/8zho_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 7.04, per 1000 atoms: 0.62 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: 2.70 Conformation dependent library (CDL) restraints added in 1.6 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: 1.76 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: 4.48 Time building geometry restraints manager: 3.11 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: 0.980 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 29.120 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.130 ------------------------------------------------------------------------------- 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 : 1.209 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: 0.2427 time to fit residues: 41.4746 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 : 1.319 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 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 : 1.308 Fit side-chains revert: symmetry clash REVERT: C 285 ILE cc_start: 0.6704 (mt) cc_final: 0.6473 (pt) REVERT: D 43 GLN cc_start: 0.8044 (mp10) cc_final: 0.7549 (mp10) REVERT: D 87 ARG cc_start: 0.7518 (mtm-85) cc_final: 0.7205 (mtt-85) REVERT: D 90 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7446 (t0) REVERT: E 143 ASP cc_start: 0.6723 (t0) cc_final: 0.6476 (t0) REVERT: L 61 ASP cc_start: 0.7649 (t70) cc_final: 0.7331 (t0) REVERT: L 83 THR cc_start: 0.7676 (m) cc_final: 0.7318 (p) REVERT: L 86 GLU cc_start: 0.7381 (tt0) cc_final: 0.6957 (tt0) REVERT: L 109 VAL cc_start: 0.7224 (t) cc_final: 0.6827 (t) REVERT: H 154 PRO cc_start: 0.7427 (Cg_endo) cc_final: 0.7172 (Cg_exo) outliers start: 40 outliers final: 21 residues processed: 101 average time/residue: 0.1805 time to fit residues: 29.4988 Evaluate side-chains 70 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 90 ASP 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 202 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 134 optimal weight: 0.1980 chunk 145 optimal weight: 30.0000 chunk 119 optimal weight: 20.0000 chunk 133 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 HIS C 563 GLN H 171 HIS H 204 ASN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11708 Z= 0.180 Angle : 0.505 9.432 15960 Z= 0.263 Chirality : 0.044 0.196 1797 Planarity : 0.004 0.040 2051 Dihedral : 4.391 58.503 1635 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.12 % Allowed : 20.59 % Favored : 76.29 % 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: 0.07 (0.22), residues: 1482 helix: -2.24 (0.61), residues: 58 sheet: 1.46 (0.23), residues: 518 loop : -0.68 (0.20), residues: 906 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 0.013 0.001 PHE H 80 TYR 0.017 0.001 TYR C 369 ARG 0.004 0.000 ARG E 63 *********************** 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 90 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 50 time to evaluate : 1.273 Fit side-chains REVERT: C 79 PHE cc_start: 0.5101 (p90) cc_final: 0.4883 (p90) REVERT: C 88 ASP cc_start: 0.6902 (m-30) cc_final: 0.6511 (m-30) REVERT: D 43 GLN cc_start: 0.8068 (mp10) cc_final: 0.7604 (mp10) REVERT: D 87 ARG cc_start: 0.7601 (mtm-85) cc_final: 0.7110 (mtt-85) REVERT: D 102 TYR cc_start: 0.7673 (p90) cc_final: 0.7376 (p90) REVERT: D 203 GLN cc_start: 0.2825 (OUTLIER) cc_final: 0.1837 (pt0) REVERT: E 143 ASP cc_start: 0.6715 (t0) cc_final: 0.6469 (t0) REVERT: L 61 ASP cc_start: 0.7606 (t70) cc_final: 0.7270 (t0) REVERT: L 83 THR cc_start: 0.7701 (m) cc_final: 0.7384 (p) REVERT: L 86 GLU cc_start: 0.7360 (tt0) cc_final: 0.7077 (tt0) REVERT: H 154 PRO cc_start: 0.7389 (Cg_endo) cc_final: 0.7134 (Cg_exo) outliers start: 40 outliers final: 23 residues processed: 85 average time/residue: 0.1878 time to fit residues: 25.9813 Evaluate side-chains 69 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 375 SER Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 673 SER 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 181 LEU Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 202 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 40.0000 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 64 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 544 ASN L 8 HIS ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11708 Z= 0.181 Angle : 0.489 8.640 15960 Z= 0.255 Chirality : 0.044 0.249 1797 Planarity : 0.004 0.040 2051 Dihedral : 3.905 54.765 1630 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.90 % Allowed : 19.81 % Favored : 76.29 % 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: 0.12 (0.22), residues: 1482 helix: -2.01 (0.64), residues: 58 sheet: 1.37 (0.23), residues: 521 loop : -0.58 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.010 0.001 HIS L 8 PHE 0.014 0.001 PHE H 80 TYR 0.016 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 104 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 54 time to evaluate : 1.195 Fit side-chains REVERT: C 79 PHE cc_start: 0.5375 (p90) cc_final: 0.5076 (p90) REVERT: C 88 ASP cc_start: 0.6909 (m-30) cc_final: 0.6526 (m-30) REVERT: C 285 ILE cc_start: 0.6596 (mt) cc_final: 0.6394 (pt) REVERT: D 43 GLN cc_start: 0.8038 (mp10) cc_final: 0.7584 (mp10) REVERT: D 87 ARG cc_start: 0.7743 (mtm-85) cc_final: 0.7215 (mtt-85) REVERT: D 102 TYR cc_start: 0.7722 (p90) cc_final: 0.7457 (p90) REVERT: D 203 GLN cc_start: 0.3121 (OUTLIER) cc_final: 0.2176 (tp40) REVERT: E 143 ASP cc_start: 0.6701 (t0) cc_final: 0.6487 (t0) REVERT: E 145 TYR cc_start: 0.3719 (m-10) cc_final: 0.2705 (m-10) REVERT: L 83 THR cc_start: 0.7669 (m) cc_final: 0.7391 (p) REVERT: L 86 GLU cc_start: 0.7090 (tt0) cc_final: 0.6828 (tt0) REVERT: L 155 VAL cc_start: 0.0462 (OUTLIER) cc_final: 0.0249 (m) REVERT: H 154 PRO cc_start: 0.7430 (Cg_endo) cc_final: 0.7184 (Cg_exo) outliers start: 50 outliers final: 32 residues processed: 100 average time/residue: 0.1726 time to fit residues: 28.8951 Evaluate side-chains 81 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 47 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 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 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 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 93 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 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 53 ASN Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 202 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 98 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN L 8 HIS ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 11708 Z= 0.471 Angle : 0.645 11.957 15960 Z= 0.343 Chirality : 0.049 0.268 1797 Planarity : 0.005 0.064 2051 Dihedral : 4.576 18.725 1630 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.21 % Allowed : 20.28 % 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: -0.26 (0.22), residues: 1482 helix: -2.02 (0.64), residues: 58 sheet: 0.81 (0.22), residues: 565 loop : -0.72 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 38 HIS 0.011 0.001 HIS C 49 PHE 0.024 0.002 PHE D 29 TYR 0.037 0.002 TYR C 369 ARG 0.005 0.001 ARG H 68 *********************** 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 111 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 57 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: C 79 PHE cc_start: 0.5457 (p90) cc_final: 0.5107 (p90) REVERT: C 88 ASP cc_start: 0.6904 (m-30) cc_final: 0.6440 (m-30) REVERT: C 285 ILE cc_start: 0.6668 (mt) cc_final: 0.6446 (pt) REVERT: D 43 GLN cc_start: 0.8360 (mp10) cc_final: 0.7841 (mp10) REVERT: D 87 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7205 (mtt-85) REVERT: D 102 TYR cc_start: 0.7755 (p90) cc_final: 0.7416 (p90) REVERT: D 203 GLN cc_start: 0.3246 (OUTLIER) cc_final: 0.2271 (tp40) REVERT: E 47 LYS cc_start: 0.8103 (pttt) cc_final: 0.7760 (ptpp) REVERT: E 106 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7672 (t) REVERT: L 83 THR cc_start: 0.7732 (m) cc_final: 0.7483 (p) REVERT: L 86 GLU cc_start: 0.7402 (tt0) cc_final: 0.7152 (tt0) REVERT: H 154 PRO cc_start: 0.7371 (Cg_endo) cc_final: 0.7056 (Cg_exo) outliers start: 54 outliers final: 40 residues processed: 106 average time/residue: 0.1905 time to fit residues: 32.1988 Evaluate side-chains 92 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 50 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 90 VAL 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 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 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 151 CYS Chi-restraints excluded: chain D residue 203 GLN 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 E residue 138 VAL 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 147 ILE Chi-restraints excluded: chain H residue 52 CYS Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 202 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 8.9990 chunk 128 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 143 optimal weight: 50.0000 chunk 118 optimal weight: 50.0000 chunk 66 optimal weight: 0.6980 chunk 11 optimal weight: 40.0000 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 30.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 204 ASN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.3943 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= 0.266 Angle : 0.554 10.276 15960 Z= 0.288 Chirality : 0.046 0.232 1797 Planarity : 0.004 0.041 2051 Dihedral : 4.221 21.935 1628 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.82 % Allowed : 20.28 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.21 (0.22), residues: 1482 helix: -1.88 (0.66), residues: 58 sheet: 0.81 (0.22), residues: 561 loop : -0.66 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 110 HIS 0.009 0.001 HIS C 49 PHE 0.014 0.001 PHE D 29 TYR 0.019 0.001 TYR C 369 ARG 0.003 0.000 ARG H 68 *********************** 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 104 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 55 time to evaluate : 1.179 Fit side-chains REVERT: C 79 PHE cc_start: 0.5489 (p90) cc_final: 0.5106 (p90) REVERT: C 88 ASP cc_start: 0.6937 (m-30) cc_final: 0.6472 (m-30) REVERT: C 285 ILE cc_start: 0.6623 (mt) cc_final: 0.6401 (pt) REVERT: C 459 SER cc_start: 0.8191 (t) cc_final: 0.7858 (m) REVERT: D 43 GLN cc_start: 0.8318 (mp10) cc_final: 0.7778 (mp10) REVERT: D 87 ARG cc_start: 0.7651 (mtm-85) cc_final: 0.7182 (mtt-85) REVERT: D 102 TYR cc_start: 0.7649 (p90) cc_final: 0.7271 (p90) REVERT: D 203 GLN cc_start: 0.3072 (OUTLIER) cc_final: 0.2210 (tp40) REVERT: E 106 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.7761 (t) REVERT: E 145 TYR cc_start: 0.2876 (m-10) cc_final: 0.2484 (m-10) REVERT: L 83 THR cc_start: 0.7707 (m) cc_final: 0.7496 (p) REVERT: L 86 GLU cc_start: 0.7215 (tt0) cc_final: 0.6968 (tt0) REVERT: H 154 PRO cc_start: 0.7318 (Cg_endo) cc_final: 0.7111 (Cg_exo) outliers start: 49 outliers final: 33 residues processed: 99 average time/residue: 0.1950 time to fit residues: 31.9117 Evaluate side-chains 83 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 48 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 383 SER Chi-restraints excluded: chain C residue 402 ILE 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 71 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 106 THR 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 40.0000 chunk 16 optimal weight: 30.0000 chunk 81 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 120 optimal weight: 50.0000 chunk 79 optimal weight: 0.0010 chunk 142 optimal weight: 0.0670 chunk 89 optimal weight: 4.9990 chunk 86 optimal weight: 0.0980 chunk 65 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 overall best weight: 0.3724 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11708 Z= 0.141 Angle : 0.522 11.927 15960 Z= 0.267 Chirality : 0.044 0.206 1797 Planarity : 0.004 0.045 2051 Dihedral : 3.954 21.238 1628 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.73 % Allowed : 21.37 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.01 (0.22), residues: 1482 helix: -1.55 (0.70), residues: 58 sheet: 1.00 (0.22), residues: 557 loop : -0.55 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 159 HIS 0.010 0.001 HIS C 49 PHE 0.010 0.001 PHE D 29 TYR 0.020 0.001 TYR H 183 ARG 0.003 0.000 ARG C 466 *********************** 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 87 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 52 time to evaluate : 1.150 Fit side-chains REVERT: C 79 PHE cc_start: 0.5454 (p90) cc_final: 0.5036 (p90) REVERT: C 88 ASP cc_start: 0.6913 (m-30) cc_final: 0.6447 (m-30) REVERT: C 285 ILE cc_start: 0.6571 (mt) cc_final: 0.6352 (pt) REVERT: C 424 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7322 (tptt) REVERT: C 459 SER cc_start: 0.8063 (t) cc_final: 0.7795 (m) REVERT: D 43 GLN cc_start: 0.8143 (mp10) cc_final: 0.7527 (mp10) REVERT: D 87 ARG cc_start: 0.7605 (mtm-85) cc_final: 0.7159 (mtt-85) REVERT: D 102 TYR cc_start: 0.7712 (p90) cc_final: 0.7276 (p90) REVERT: D 165 TRP cc_start: 0.2419 (OUTLIER) cc_final: 0.2167 (m100) REVERT: D 203 GLN cc_start: 0.2971 (OUTLIER) cc_final: 0.2135 (tp40) REVERT: L 83 THR cc_start: 0.7673 (m) cc_final: 0.7359 (p) REVERT: L 86 GLU cc_start: 0.7159 (tt0) cc_final: 0.6946 (tt0) outliers start: 35 outliers final: 27 residues processed: 84 average time/residue: 0.1805 time to fit residues: 24.6293 Evaluate side-chains 78 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 48 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 383 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 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 83 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 165 TRP Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 53 ASN 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 H residue 54 TYR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 166 ASN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11708 Z= 0.408 Angle : 0.619 11.341 15960 Z= 0.323 Chirality : 0.047 0.189 1797 Planarity : 0.005 0.091 2051 Dihedral : 4.426 21.388 1628 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.59 % Allowed : 20.59 % 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: -0.22 (0.22), residues: 1482 helix: -1.71 (0.69), residues: 58 sheet: 0.78 (0.22), residues: 562 loop : -0.66 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 110 HIS 0.010 0.001 HIS C 49 PHE 0.023 0.002 PHE H 173 TYR 0.028 0.002 TYR C 369 ARG 0.004 0.001 ARG H 104 *********************** 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 94 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 48 time to evaluate : 1.306 Fit side-chains REVERT: C 65 PHE cc_start: 0.7928 (m-10) cc_final: 0.7697 (m-10) REVERT: C 79 PHE cc_start: 0.5602 (p90) cc_final: 0.5186 (p90) REVERT: C 88 ASP cc_start: 0.6941 (m-30) cc_final: 0.6460 (m-30) REVERT: C 285 ILE cc_start: 0.6533 (mt) cc_final: 0.6322 (pt) REVERT: C 465 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: D 43 GLN cc_start: 0.8402 (mp10) cc_final: 0.7724 (mp10) REVERT: D 87 ARG cc_start: 0.7586 (mtm-85) cc_final: 0.7096 (mtt-85) REVERT: D 102 TYR cc_start: 0.7713 (p90) cc_final: 0.7382 (p90) REVERT: D 203 GLN cc_start: 0.3078 (OUTLIER) cc_final: 0.2243 (tp40) REVERT: L 8 HIS cc_start: 0.6253 (t-90) cc_final: 0.5917 (t-170) REVERT: L 83 THR cc_start: 0.7675 (m) cc_final: 0.7380 (p) REVERT: L 86 GLU cc_start: 0.7411 (tt0) cc_final: 0.7169 (tt0) REVERT: H 155 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.5657 (pt0) outliers start: 46 outliers final: 38 residues processed: 92 average time/residue: 0.2001 time to fit residues: 29.4421 Evaluate side-chains 86 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 45 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 90 VAL Chi-restraints excluded: chain C residue 120 VAL 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 383 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 549 THR 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 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 151 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 73 SER 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 155 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.5980 chunk 124 optimal weight: 50.0000 chunk 132 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 104 optimal weight: 50.0000 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 50.0000 chunk 125 optimal weight: 8.9990 chunk 87 optimal weight: 0.5980 chunk 140 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.4286 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= 0.215 Angle : 0.547 10.491 15960 Z= 0.280 Chirality : 0.045 0.147 1797 Planarity : 0.004 0.083 2051 Dihedral : 4.166 22.210 1628 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.20 % Allowed : 21.14 % Favored : 75.66 % 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: -0.16 (0.22), residues: 1482 helix: -1.57 (0.71), residues: 58 sheet: 0.75 (0.22), residues: 572 loop : -0.59 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 110 HIS 0.012 0.001 HIS C 49 PHE 0.015 0.001 PHE H 173 TYR 0.022 0.001 TYR H 183 ARG 0.002 0.000 ARG H 104 *********************** 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 88 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 47 time to evaluate : 1.341 Fit side-chains REVERT: C 65 PHE cc_start: 0.7941 (m-10) cc_final: 0.7683 (m-10) REVERT: C 79 PHE cc_start: 0.5662 (p90) cc_final: 0.5246 (p90) REVERT: C 88 ASP cc_start: 0.6831 (m-30) cc_final: 0.6369 (m-30) REVERT: C 285 ILE cc_start: 0.6514 (mt) cc_final: 0.6295 (pt) REVERT: C 424 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7419 (tptt) REVERT: C 459 SER cc_start: 0.8125 (t) cc_final: 0.7800 (m) REVERT: C 465 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: D 43 GLN cc_start: 0.8310 (mp10) cc_final: 0.7639 (mp10) REVERT: D 48 MET cc_start: 0.8925 (ptt) cc_final: 0.8594 (ptt) REVERT: D 87 ARG cc_start: 0.7506 (mtm-85) cc_final: 0.7075 (mtt-85) REVERT: D 102 TYR cc_start: 0.7663 (p90) cc_final: 0.7286 (p90) REVERT: D 165 TRP cc_start: 0.2499 (OUTLIER) cc_final: 0.1597 (m100) REVERT: D 203 GLN cc_start: 0.2922 (OUTLIER) cc_final: 0.2146 (tp40) REVERT: L 8 HIS cc_start: 0.6285 (t-90) cc_final: 0.5841 (t-170) REVERT: L 83 THR cc_start: 0.7700 (m) cc_final: 0.7387 (p) outliers start: 41 outliers final: 30 residues processed: 85 average time/residue: 0.1819 time to fit residues: 25.5638 Evaluate side-chains 81 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 47 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 90 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 549 THR 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 71 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 165 TRP Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain E 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 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 87 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 12 optimal weight: 50.0000 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 125 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11708 Z= 0.199 Angle : 0.537 10.042 15960 Z= 0.273 Chirality : 0.044 0.152 1797 Planarity : 0.004 0.082 2051 Dihedral : 4.054 21.585 1628 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.20 % Allowed : 21.06 % 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: -0.07 (0.22), residues: 1482 helix: -1.47 (0.72), residues: 58 sheet: 0.83 (0.22), residues: 563 loop : -0.53 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 110 HIS 0.012 0.001 HIS C 49 PHE 0.013 0.001 PHE H 80 TYR 0.024 0.001 TYR H 183 ARG 0.002 0.000 ARG H 104 ********************** 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 91 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 50 time to evaluate : 1.205 Fit side-chains REVERT: C 79 PHE cc_start: 0.5646 (p90) cc_final: 0.5218 (p90) REVERT: C 88 ASP cc_start: 0.6869 (m-30) cc_final: 0.6427 (m-30) REVERT: C 285 ILE cc_start: 0.6531 (mt) cc_final: 0.6304 (pt) REVERT: C 424 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7401 (tptp) REVERT: C 459 SER cc_start: 0.8154 (t) cc_final: 0.7833 (m) REVERT: D 43 GLN cc_start: 0.8271 (mp10) cc_final: 0.7596 (mp10) REVERT: D 48 MET cc_start: 0.8932 (ptt) cc_final: 0.8566 (ptt) REVERT: D 87 ARG cc_start: 0.7523 (mtm-85) cc_final: 0.7116 (mtt-85) REVERT: D 102 TYR cc_start: 0.7630 (p90) cc_final: 0.7205 (p90) REVERT: D 165 TRP cc_start: 0.2250 (OUTLIER) cc_final: 0.1430 (m100) REVERT: D 203 GLN cc_start: 0.2585 (OUTLIER) cc_final: 0.1859 (tp40) REVERT: L 8 HIS cc_start: 0.6322 (t-90) cc_final: 0.5870 (t-170) REVERT: L 83 THR cc_start: 0.7685 (m) cc_final: 0.7394 (p) outliers start: 41 outliers final: 34 residues processed: 87 average time/residue: 0.1802 time to fit residues: 25.3851 Evaluate side-chains 86 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 49 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 90 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 68 VAL 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 151 CYS Chi-restraints excluded: chain D residue 165 TRP Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 138 VAL 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 H residue 2 VAL Chi-restraints excluded: chain H residue 52 CYS Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 87 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 120 optimal weight: 50.0000 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 103 optimal weight: 40.0000 chunk 6 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.210403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.187394 restraints weight = 18570.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.184478 restraints weight = 30800.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.182493 restraints weight = 31751.194| |-----------------------------------------------------------------------------| r_work (final): 0.4489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11708 Z= 0.214 Angle : 0.542 9.811 15960 Z= 0.277 Chirality : 0.045 0.147 1797 Planarity : 0.004 0.057 2051 Dihedral : 4.046 21.134 1628 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.51 % Allowed : 20.83 % Favored : 75.66 % 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: -0.05 (0.22), residues: 1482 helix: -1.41 (0.72), residues: 58 sheet: 0.87 (0.22), residues: 553 loop : -0.53 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 110 HIS 0.011 0.001 HIS C 49 PHE 0.013 0.001 PHE H 80 TYR 0.025 0.001 TYR H 183 ARG 0.002 0.000 ARG H 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2071.98 seconds wall clock time: 39 minutes 14.65 seconds (2354.65 seconds total)