Starting phenix.real_space_refine on Mon Dec 30 00:56:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u23_26306/12_2024/7u23_26306.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u23_26306/12_2024/7u23_26306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u23_26306/12_2024/7u23_26306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u23_26306/12_2024/7u23_26306.map" model { file = "/net/cci-nas-00/data/ceres_data/7u23_26306/12_2024/7u23_26306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u23_26306/12_2024/7u23_26306.cif" } resolution = 4.6 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= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 7375 2.51 5 N 2039 2.21 5 O 2176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11688 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5380 Classifications: {'peptide': 669} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 633} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5380 Classifications: {'peptide': 669} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 633} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 464 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "D" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 464 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Time building chain proxies: 8.37, per 1000 atoms: 0.72 Number of scatterers: 11688 At special positions: 0 Unit cell: (107.06, 126.14, 149.46, 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 98 16.00 O 2176 8.00 N 2039 7.00 C 7375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS E 3 " - pdb=" SG CYS E 22 " distance=2.03 Simple disulfide: pdb=" SG CYS E 120 " - pdb=" SG CYS E 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 152 " - pdb=" SG CYS E 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 162 " - pdb=" SG CYS E 181 " distance=2.03 Simple disulfide: pdb=" SG CYS E 185 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 205 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 230 " distance=2.04 Simple disulfide: pdb=" SG CYS E 234 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 252 " - pdb=" SG CYS E 273 " distance=2.03 Simple disulfide: pdb=" SG CYS E 277 " - pdb=" SG CYS E 291 " distance=2.03 Simple disulfide: pdb=" SG CYS E 294 " - pdb=" SG CYS E 298 " distance=2.03 Simple disulfide: pdb=" SG CYS E 302 " - pdb=" SG CYS E 323 " distance=2.03 Simple disulfide: pdb=" SG CYS E 425 " - pdb=" SG CYS E 458 " distance=2.03 Simple disulfide: pdb=" SG CYS E 776 " - pdb=" SG CYS E 785 " distance=2.03 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 22 " distance=2.03 Simple disulfide: pdb=" SG CYS F 120 " - pdb=" SG CYS F 148 " distance=2.02 Simple disulfide: pdb=" SG CYS F 152 " - pdb=" SG CYS F 175 " distance=2.03 Simple disulfide: pdb=" SG CYS F 162 " - pdb=" SG CYS F 181 " distance=2.03 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 189 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 209 " distance=2.03 Simple disulfide: pdb=" SG CYS F 205 " - pdb=" SG CYS F 218 " distance=2.03 Simple disulfide: pdb=" SG CYS F 221 " - pdb=" SG CYS F 230 " distance=2.03 Simple disulfide: pdb=" SG CYS F 234 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 252 " - pdb=" SG CYS F 273 " distance=2.03 Simple disulfide: pdb=" SG CYS F 277 " - pdb=" SG CYS F 291 " distance=2.03 Simple disulfide: pdb=" SG CYS F 294 " - pdb=" SG CYS F 298 " distance=2.03 Simple disulfide: pdb=" SG CYS F 302 " - pdb=" SG CYS F 323 " distance=2.03 Simple disulfide: pdb=" SG CYS F 425 " - pdb=" SG CYS F 458 " distance=2.03 Simple disulfide: pdb=" SG CYS F 776 " - pdb=" SG CYS F 785 " distance=2.04 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 47 " distance=2.04 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 52 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 47 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 52 " 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 Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.6 seconds 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2764 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 28 sheets defined 15.6% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'E' and resid 13 through 20 Processing helix chain 'E' and resid 65 through 69 Processing helix chain 'E' and resid 126 through 130 Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 144 through 148 Processing helix chain 'E' and resid 249 through 253 Processing helix chain 'E' and resid 315 through 321 removed outlier: 3.748A pdb=" N MET E 319 " --> pdb=" O SER E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 349 Processing helix chain 'E' and resid 425 through 437 removed outlier: 3.783A pdb=" N ILE E 429 " --> pdb=" O CYS E 425 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU E 434 " --> pdb=" O TYR E 430 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL E 435 " --> pdb=" O ARG E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 685 through 701 removed outlier: 3.760A pdb=" N PHE E 701 " --> pdb=" O HIS E 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 779 through 784 Processing helix chain 'F' and resid 13 through 20 Processing helix chain 'F' and resid 65 through 69 Processing helix chain 'F' and resid 144 through 148 Processing helix chain 'F' and resid 249 through 253 Processing helix chain 'F' and resid 315 through 321 removed outlier: 3.756A pdb=" N MET F 319 " --> pdb=" O SER F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 348 removed outlier: 3.533A pdb=" N GLU F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN F 346 " --> pdb=" O SER F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 351 No H-bonds generated for 'chain 'F' and resid 349 through 351' Processing helix chain 'F' and resid 425 through 437 removed outlier: 3.865A pdb=" N ILE F 429 " --> pdb=" O CYS F 425 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL F 435 " --> pdb=" O ARG F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 701 removed outlier: 3.736A pdb=" N PHE F 701 " --> pdb=" O HIS F 697 " (cutoff:3.500A) Processing helix chain 'F' and resid 779 through 782 Processing helix chain 'C' and resid 7 through 20 removed outlier: 3.572A pdb=" N VAL C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'D' and resid 7 through 20 Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 41 through 48 removed outlier: 3.717A pdb=" N CYS D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 61 Processing sheet with id=AA1, first strand: chain 'E' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'E' and resid 7 through 10 removed outlier: 6.285A pdb=" N LEU E 29 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE E 58 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE E 31 " --> pdb=" O PHE E 58 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL E 60 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU E 33 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR E 85 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ARG E 112 " --> pdb=" O TYR E 85 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU E 87 " --> pdb=" O ARG E 112 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLU E 114 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE E 89 " --> pdb=" O GLU E 114 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE E 111 " --> pdb=" O TYR E 138 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL E 140 " --> pdb=" O ILE E 111 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE E 113 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 164 through 167 removed outlier: 3.724A pdb=" N THR E 165 " --> pdb=" O ASN E 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 205 through 209 removed outlier: 5.783A pdb=" N LEU E 206 " --> pdb=" O CYS E 221 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N CYS E 221 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER E 208 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL E 219 " --> pdb=" O SER E 208 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 224 through 226 Processing sheet with id=AA6, first strand: chain 'E' and resid 245 through 248 removed outlier: 3.840A pdb=" N ARG E 245 " --> pdb=" O PHE E 241 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N CYS E 273 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG E 240 " --> pdb=" O CYS E 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 282 through 283 Processing sheet with id=AA8, first strand: chain 'E' and resid 302 through 311 removed outlier: 10.962A pdb=" N ILE E 325 " --> pdb=" O GLU E 303 " (cutoff:3.500A) removed outlier: 11.563A pdb=" N GLU E 305 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 10.564A pdb=" N LYS E 327 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS E 307 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 302 through 311 removed outlier: 10.962A pdb=" N ILE E 325 " --> pdb=" O GLU E 303 " (cutoff:3.500A) removed outlier: 11.563A pdb=" N GLU E 305 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 10.564A pdb=" N LYS E 327 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS E 307 " --> pdb=" O LYS E 327 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N TYR E 417 " --> pdb=" O SER E 389 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR E 391 " --> pdb=" O TYR E 417 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ALA E 419 " --> pdb=" O TYR E 391 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU E 393 " --> pdb=" O ALA E 419 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 461 through 462 removed outlier: 5.589A pdb=" N ASP E 461 " --> pdb=" O LYS E 568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 465 through 470 removed outlier: 6.653A pdb=" N THR E 478 " --> pdb=" O THR E 466 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR E 468 " --> pdb=" O ILE E 476 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE E 476 " --> pdb=" O THR E 468 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 520 through 525 Processing sheet with id=AB4, first strand: chain 'E' and resid 585 through 590 removed outlier: 4.522A pdb=" N VAL E 587 " --> pdb=" O LYS E 600 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS E 600 " --> pdb=" O VAL E 587 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER E 589 " --> pdb=" O ILE E 598 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE E 598 " --> pdb=" O SER E 589 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 747 through 752 removed outlier: 4.279A pdb=" N TYR E 613 " --> pdb=" O CYS E 776 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 2 through 3 Processing sheet with id=AB7, first strand: chain 'F' and resid 6 through 10 removed outlier: 6.325A pdb=" N LEU F 29 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N PHE F 58 " --> pdb=" O LEU F 29 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE F 31 " --> pdb=" O PHE F 58 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL F 60 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU F 33 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ARG F 112 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL F 88 " --> pdb=" O ARG F 112 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLU F 114 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE F 90 " --> pdb=" O GLU F 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 164 through 167 removed outlier: 3.749A pdb=" N THR F 165 " --> pdb=" O ASN F 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 205 through 209 removed outlier: 3.552A pdb=" N ALA F 220 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N SER F 208 " --> pdb=" O CYS F 218 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N CYS F 218 " --> pdb=" O SER F 208 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 224 through 226 Processing sheet with id=AC2, first strand: chain 'F' and resid 245 through 248 removed outlier: 3.791A pdb=" N ARG F 245 " --> pdb=" O PHE F 241 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N CYS F 273 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG F 240 " --> pdb=" O CYS F 273 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 282 through 283 Processing sheet with id=AC4, first strand: chain 'F' and resid 301 through 311 removed outlier: 11.033A pdb=" N ILE F 325 " --> pdb=" O GLU F 303 " (cutoff:3.500A) removed outlier: 11.594A pdb=" N GLU F 305 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 10.554A pdb=" N LYS F 327 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LYS F 307 " --> pdb=" O LYS F 327 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 301 through 311 removed outlier: 11.033A pdb=" N ILE F 325 " --> pdb=" O GLU F 303 " (cutoff:3.500A) removed outlier: 11.594A pdb=" N GLU F 305 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 10.554A pdb=" N LYS F 327 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LYS F 307 " --> pdb=" O LYS F 327 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS F 415 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F 419 " --> pdb=" O VAL F 392 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 461 through 463 removed outlier: 5.640A pdb=" N ASP F 461 " --> pdb=" O LYS F 568 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 465 through 470 removed outlier: 6.622A pdb=" N THR F 478 " --> pdb=" O THR F 466 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR F 468 " --> pdb=" O ILE F 476 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE F 476 " --> pdb=" O THR F 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 520 through 525 Processing sheet with id=AC9, first strand: chain 'F' and resid 585 through 593 removed outlier: 4.511A pdb=" N VAL F 587 " --> pdb=" O LYS F 600 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS F 600 " --> pdb=" O VAL F 587 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER F 589 " --> pdb=" O ILE F 598 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE F 598 " --> pdb=" O SER F 589 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER F 591 " --> pdb=" O GLN F 596 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLN F 596 " --> pdb=" O SER F 591 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 747 through 752 removed outlier: 4.336A pdb=" N TYR F 613 " --> pdb=" O CYS F 776 " (cutoff:3.500A) 311 hydrogen bonds defined for protein. 759 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: 4.97 Time building geometry restraints manager: 3.30 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: 3846 1.34 - 1.46: 2774 1.46 - 1.58: 5204 1.58 - 1.70: 0 1.70 - 1.83: 120 Bond restraints: 11944 Sorted by residual: bond pdb=" N SER E 579 " pdb=" CA SER E 579 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.15e-02 7.56e+03 7.57e+00 bond pdb=" N VAL E 580 " pdb=" CA VAL E 580 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.23e-02 6.61e+03 6.80e+00 bond pdb=" N THR E 576 " pdb=" CA THR E 576 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.25e-02 6.40e+03 6.45e+00 bond pdb=" N ASN E 577 " pdb=" CA ASN E 577 " ideal model delta sigma weight residual 1.457 1.487 -0.031 1.31e-02 5.83e+03 5.51e+00 bond pdb=" N ALA E 578 " pdb=" CA ALA E 578 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.28e-02 6.10e+03 3.35e+00 ... (remaining 11939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 15499 1.27 - 2.54: 543 2.54 - 3.81: 139 3.81 - 5.08: 12 5.08 - 6.35: 4 Bond angle restraints: 16197 Sorted by residual: angle pdb=" N ARG D 26 " pdb=" CA ARG D 26 " pdb=" C ARG D 26 " ideal model delta sigma weight residual 110.73 117.08 -6.35 1.55e+00 4.16e-01 1.68e+01 angle pdb=" CA ARG D 26 " pdb=" C ARG D 26 " pdb=" N PRO D 27 " ideal model delta sigma weight residual 117.84 121.27 -3.43 9.70e-01 1.06e+00 1.25e+01 angle pdb=" C THR E 107 " pdb=" N ARG E 108 " pdb=" CA ARG E 108 " ideal model delta sigma weight residual 122.17 117.41 4.76 1.54e+00 4.22e-01 9.56e+00 angle pdb=" CA THR E 576 " pdb=" C THR E 576 " pdb=" O THR E 576 " ideal model delta sigma weight residual 121.44 118.21 3.23 1.08e+00 8.57e-01 8.95e+00 angle pdb=" CA SER E 579 " pdb=" C SER E 579 " pdb=" O SER E 579 " ideal model delta sigma weight residual 121.66 118.31 3.35 1.22e+00 6.72e-01 7.53e+00 ... (remaining 16192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.40: 6649 15.40 - 30.79: 479 30.79 - 46.19: 134 46.19 - 61.58: 42 61.58 - 76.98: 9 Dihedral angle restraints: 7313 sinusoidal: 3033 harmonic: 4280 Sorted by residual: dihedral pdb=" CB CYS C 7 " pdb=" SG CYS C 7 " pdb=" SG CYS C 47 " pdb=" CB CYS C 47 " ideal model delta sinusoidal sigma weight residual -86.00 -156.41 70.41 1 1.00e+01 1.00e-02 6.38e+01 dihedral pdb=" CB CYS F 201 " pdb=" SG CYS F 201 " pdb=" SG CYS F 209 " pdb=" CB CYS F 209 " ideal model delta sinusoidal sigma weight residual 93.00 145.08 -52.08 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS E 201 " pdb=" SG CYS E 201 " pdb=" SG CYS E 209 " pdb=" CB CYS E 209 " ideal model delta sinusoidal sigma weight residual 93.00 144.71 -51.71 1 1.00e+01 1.00e-02 3.65e+01 ... (remaining 7310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1180 0.033 - 0.067: 362 0.067 - 0.100: 169 0.100 - 0.133: 76 0.133 - 0.166: 3 Chirality restraints: 1790 Sorted by residual: chirality pdb=" CA VAL E 580 " pdb=" N VAL E 580 " pdb=" C VAL E 580 " pdb=" CB VAL E 580 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CA VAL C 24 " pdb=" N VAL C 24 " pdb=" C VAL C 24 " pdb=" CB VAL C 24 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA PRO E 422 " pdb=" N PRO E 422 " pdb=" C PRO E 422 " pdb=" CB PRO E 422 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 1787 not shown) Planarity restraints: 2091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 4 " -0.047 5.00e-02 4.00e+02 7.14e-02 8.16e+00 pdb=" N PRO F 5 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO F 5 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 5 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 143 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO F 144 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO F 144 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 144 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS F 234 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO F 235 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO F 235 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 235 " -0.022 5.00e-02 4.00e+02 ... (remaining 2088 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 924 2.74 - 3.28: 11587 3.28 - 3.82: 19134 3.82 - 4.36: 23678 4.36 - 4.90: 39111 Nonbonded interactions: 94434 Sorted by model distance: nonbonded pdb=" OD1 ASP E 126 " pdb=" OG SER E 128 " model vdw 2.198 3.040 nonbonded pdb=" O LYS E 503 " pdb=" OH TYR E 573 " model vdw 2.207 3.040 nonbonded pdb=" O LYS F 503 " pdb=" OH TYR F 573 " model vdw 2.209 3.040 nonbonded pdb=" O PHE E 701 " pdb=" OH TYR D 60 " model vdw 2.211 3.040 nonbonded pdb=" OD1 ASN E 698 " pdb=" N GLY D 41 " model vdw 2.234 3.120 ... (remaining 94429 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1 through 256 or resid 265 through 798)) selection = (chain 'F' and (resid 1 through 624 or resid 684 through 798)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.200 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 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 : 0.004 0.045 11944 Z= 0.260 Angle : 0.592 6.353 16197 Z= 0.329 Chirality : 0.043 0.166 1790 Planarity : 0.004 0.071 2091 Dihedral : 11.885 76.976 4435 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.73 % Favored : 92.92 % Rotamer: Outliers : 2.67 % Allowed : 6.79 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -1.99 (0.20), residues: 1426 helix: -1.46 (0.36), residues: 153 sheet: -0.75 (0.30), residues: 289 loop : -1.56 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 79 HIS 0.004 0.001 HIS F 539 PHE 0.021 0.001 PHE F 692 TYR 0.012 0.001 TYR D 25 ARG 0.005 0.000 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2 ILE cc_start: 0.7420 (mt) cc_final: 0.6854 (mt) REVERT: E 100 LEU cc_start: 0.9170 (mt) cc_final: 0.8727 (mt) REVERT: E 169 ASN cc_start: 0.9159 (m-40) cc_final: 0.8858 (p0) REVERT: E 398 LEU cc_start: 0.8993 (tp) cc_final: 0.8741 (tp) REVERT: E 446 ASP cc_start: 0.6518 (m-30) cc_final: 0.6309 (m-30) REVERT: F 76 ILE cc_start: 0.9039 (mt) cc_final: 0.8718 (tt) REVERT: F 353 VAL cc_start: 0.8866 (t) cc_final: 0.8555 (t) REVERT: F 398 LEU cc_start: 0.9277 (tp) cc_final: 0.9043 (tp) REVERT: F 416 MET cc_start: 0.7559 (mtm) cc_final: 0.7232 (ptt) REVERT: F 432 MET cc_start: 0.9004 (ttt) cc_final: 0.8457 (tmm) REVERT: F 436 THR cc_start: 0.7987 (m) cc_final: 0.7439 (m) REVERT: F 448 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8813 (t0) REVERT: F 490 LEU cc_start: 0.9315 (tt) cc_final: 0.9048 (mm) REVERT: D 21 ASN cc_start: 0.7465 (m-40) cc_final: 0.7261 (p0) outliers start: 35 outliers final: 9 residues processed: 281 average time/residue: 0.3363 time to fit residues: 128.3353 Evaluate side-chains 135 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 10.0000 chunk 109 optimal weight: 0.4980 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 58 optimal weight: 30.0000 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN E 136 ASN ** E 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 ASN E 395 ASN E 399 GLN ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 694 ASN ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 ASN F 399 GLN F 421 ASN ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 11944 Z= 0.314 Angle : 0.719 9.459 16197 Z= 0.380 Chirality : 0.049 0.196 1790 Planarity : 0.005 0.061 2091 Dihedral : 5.400 26.421 1610 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.19 % Favored : 94.46 % Rotamer: Outliers : 0.23 % Allowed : 2.98 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -1.82 (0.20), residues: 1426 helix: -1.37 (0.35), residues: 170 sheet: -0.59 (0.30), residues: 292 loop : -1.44 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP F 402 HIS 0.008 0.001 HIS F 539 PHE 0.025 0.002 PHE E 493 TYR 0.031 0.002 TYR E 496 ARG 0.005 0.001 ARG E 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2 ILE cc_start: 0.7220 (mt) cc_final: 0.6718 (mm) REVERT: E 169 ASN cc_start: 0.9202 (m-40) cc_final: 0.8788 (p0) REVERT: E 348 MET cc_start: 0.9036 (mpp) cc_final: 0.8535 (mpp) REVERT: E 395 ASN cc_start: 0.9168 (m110) cc_final: 0.8774 (m-40) REVERT: E 446 ASP cc_start: 0.6451 (m-30) cc_final: 0.6122 (m-30) REVERT: E 521 MET cc_start: 0.0872 (mmt) cc_final: 0.0464 (mmp) REVERT: F 53 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7806 (mt-10) REVERT: F 402 TRP cc_start: 0.8048 (p-90) cc_final: 0.7790 (p-90) REVERT: F 432 MET cc_start: 0.9142 (ttt) cc_final: 0.8733 (tmm) REVERT: F 436 THR cc_start: 0.8440 (m) cc_final: 0.7668 (m) REVERT: F 521 MET cc_start: 0.8087 (mmp) cc_final: 0.7773 (mmm) REVERT: F 529 ASN cc_start: 0.8922 (t0) cc_final: 0.8496 (t0) outliers start: 3 outliers final: 0 residues processed: 160 average time/residue: 0.2898 time to fit residues: 64.7144 Evaluate side-chains 104 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 ASN ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 ASN ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 621 GLN C 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 11944 Z= 0.202 Angle : 0.605 8.407 16197 Z= 0.323 Chirality : 0.047 0.292 1790 Planarity : 0.004 0.055 2091 Dihedral : 5.175 24.196 1610 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.26 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -1.48 (0.21), residues: 1426 helix: -0.94 (0.37), residues: 164 sheet: -0.39 (0.31), residues: 297 loop : -1.22 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 402 HIS 0.004 0.001 HIS F 539 PHE 0.018 0.001 PHE E 692 TYR 0.021 0.002 TYR F 496 ARG 0.007 0.000 ARG E 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 THR cc_start: 0.8946 (m) cc_final: 0.8670 (p) REVERT: E 169 ASN cc_start: 0.9194 (m-40) cc_final: 0.8773 (p0) REVERT: E 348 MET cc_start: 0.9121 (mpp) cc_final: 0.8771 (mpp) REVERT: E 395 ASN cc_start: 0.8963 (m110) cc_final: 0.8458 (m-40) REVERT: E 446 ASP cc_start: 0.6520 (m-30) cc_final: 0.6188 (m-30) REVERT: E 521 MET cc_start: 0.1404 (mmt) cc_final: 0.0713 (mmm) REVERT: F 53 GLU cc_start: 0.8570 (mt-10) cc_final: 0.7923 (tt0) REVERT: F 344 LEU cc_start: 0.9508 (mt) cc_final: 0.9263 (mt) REVERT: F 348 MET cc_start: 0.8447 (mpp) cc_final: 0.8151 (mpp) REVERT: F 398 LEU cc_start: 0.9630 (mm) cc_final: 0.9288 (mm) REVERT: F 400 GLN cc_start: 0.9325 (pm20) cc_final: 0.9063 (pm20) REVERT: F 432 MET cc_start: 0.9010 (ttt) cc_final: 0.8755 (tmm) REVERT: F 436 THR cc_start: 0.8475 (m) cc_final: 0.7529 (m) REVERT: F 521 MET cc_start: 0.8344 (mmp) cc_final: 0.8136 (mmp) REVERT: F 529 ASN cc_start: 0.8978 (t0) cc_final: 0.8493 (t0) REVERT: F 753 ASP cc_start: 0.8093 (t0) cc_final: 0.7877 (t0) REVERT: D 12 VAL cc_start: 0.9511 (m) cc_final: 0.9212 (p) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2741 time to fit residues: 55.8250 Evaluate side-chains 102 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 139 optimal weight: 20.0000 chunk 68 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 ASN ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11944 Z= 0.264 Angle : 0.638 6.992 16197 Z= 0.336 Chirality : 0.047 0.201 1790 Planarity : 0.004 0.046 2091 Dihedral : 5.350 25.491 1610 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.68 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -1.24 (0.22), residues: 1426 helix: -0.30 (0.41), residues: 151 sheet: -0.42 (0.30), residues: 306 loop : -1.07 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 402 HIS 0.007 0.001 HIS E 364 PHE 0.019 0.002 PHE E 692 TYR 0.017 0.002 TYR E 239 ARG 0.004 0.000 ARG C 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 53 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7706 (mt-10) REVERT: E 119 LEU cc_start: 0.9269 (tp) cc_final: 0.8899 (mm) REVERT: E 169 ASN cc_start: 0.9226 (m-40) cc_final: 0.8748 (p0) REVERT: E 345 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8762 (tp30) REVERT: E 348 MET cc_start: 0.8896 (mpp) cc_final: 0.8555 (mpp) REVERT: E 395 ASN cc_start: 0.9058 (m110) cc_final: 0.8778 (m-40) REVERT: E 398 LEU cc_start: 0.9082 (tp) cc_final: 0.8825 (tp) REVERT: E 436 THR cc_start: 0.6402 (m) cc_final: 0.6142 (p) REVERT: E 446 ASP cc_start: 0.6482 (m-30) cc_final: 0.6058 (m-30) REVERT: F 53 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7838 (mm-30) REVERT: F 398 LEU cc_start: 0.9720 (mm) cc_final: 0.9381 (mm) REVERT: F 402 TRP cc_start: 0.7992 (p-90) cc_final: 0.7672 (p-90) REVERT: F 432 MET cc_start: 0.8962 (ttt) cc_final: 0.8575 (tmm) REVERT: F 436 THR cc_start: 0.8523 (m) cc_final: 0.7739 (m) REVERT: F 529 ASN cc_start: 0.9060 (t0) cc_final: 0.8518 (t0) REVERT: F 753 ASP cc_start: 0.8038 (t0) cc_final: 0.7805 (t0) REVERT: D 12 VAL cc_start: 0.9526 (m) cc_final: 0.9193 (p) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2529 time to fit residues: 48.1317 Evaluate side-chains 97 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 0 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11944 Z= 0.291 Angle : 0.674 12.457 16197 Z= 0.351 Chirality : 0.047 0.248 1790 Planarity : 0.005 0.055 2091 Dihedral : 5.505 27.352 1610 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.96 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -1.13 (0.22), residues: 1426 helix: 0.05 (0.42), residues: 148 sheet: -0.46 (0.30), residues: 306 loop : -1.00 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 519 HIS 0.008 0.002 HIS F 697 PHE 0.019 0.002 PHE E 692 TYR 0.017 0.002 TYR F 487 ARG 0.007 0.001 ARG F 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 95 LEU cc_start: 0.9203 (tp) cc_final: 0.8548 (tp) REVERT: E 169 ASN cc_start: 0.9115 (m-40) cc_final: 0.8652 (p0) REVERT: E 345 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8751 (tp30) REVERT: E 348 MET cc_start: 0.8814 (mpp) cc_final: 0.8468 (mpp) REVERT: E 366 LEU cc_start: 0.9142 (mt) cc_final: 0.8921 (mt) REVERT: E 395 ASN cc_start: 0.9047 (m110) cc_final: 0.8801 (m-40) REVERT: E 398 LEU cc_start: 0.9072 (tp) cc_final: 0.8837 (tp) REVERT: E 446 ASP cc_start: 0.6428 (m-30) cc_final: 0.6110 (m-30) REVERT: E 558 MET cc_start: 0.4224 (mpp) cc_final: 0.3980 (tpt) REVERT: F 53 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8049 (mm-30) REVERT: F 348 MET cc_start: 0.8666 (mpp) cc_final: 0.8299 (mpp) REVERT: F 398 LEU cc_start: 0.9677 (mm) cc_final: 0.9429 (mm) REVERT: F 432 MET cc_start: 0.8929 (ttt) cc_final: 0.8579 (tmm) REVERT: F 436 THR cc_start: 0.8500 (m) cc_final: 0.7782 (m) REVERT: F 529 ASN cc_start: 0.9082 (t0) cc_final: 0.8501 (t0) REVERT: D 12 VAL cc_start: 0.9548 (m) cc_final: 0.9186 (p) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2305 time to fit residues: 42.1241 Evaluate side-chains 92 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 5.9990 chunk 125 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.0050 chunk 34 optimal weight: 0.3980 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 64 optimal weight: 40.0000 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11944 Z= 0.173 Angle : 0.588 8.167 16197 Z= 0.309 Chirality : 0.047 0.284 1790 Planarity : 0.004 0.046 2091 Dihedral : 5.231 24.899 1610 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.98 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.97 (0.22), residues: 1426 helix: 0.23 (0.43), residues: 148 sheet: -0.34 (0.30), residues: 308 loop : -0.90 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 404 HIS 0.003 0.001 HIS F 362 PHE 0.016 0.001 PHE F 418 TYR 0.013 0.001 TYR F 391 ARG 0.004 0.000 ARG F 689 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 53 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7885 (mm-30) REVERT: E 74 THR cc_start: 0.8678 (m) cc_final: 0.8343 (p) REVERT: E 95 LEU cc_start: 0.9242 (tp) cc_final: 0.9023 (tp) REVERT: E 169 ASN cc_start: 0.9073 (m-40) cc_final: 0.8612 (p0) REVERT: E 345 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8727 (tp30) REVERT: E 348 MET cc_start: 0.8866 (mpp) cc_final: 0.8486 (mpp) REVERT: E 395 ASN cc_start: 0.8919 (m110) cc_final: 0.8569 (m-40) REVERT: E 398 LEU cc_start: 0.8970 (tp) cc_final: 0.8733 (tp) REVERT: E 436 THR cc_start: 0.6088 (m) cc_final: 0.5749 (p) REVERT: E 446 ASP cc_start: 0.6564 (m-30) cc_final: 0.6179 (m-30) REVERT: F 53 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7915 (mm-30) REVERT: F 348 MET cc_start: 0.8639 (mpp) cc_final: 0.8323 (mpp) REVERT: F 398 LEU cc_start: 0.9623 (mm) cc_final: 0.9321 (mm) REVERT: F 432 MET cc_start: 0.8869 (ttt) cc_final: 0.8562 (tmm) REVERT: F 436 THR cc_start: 0.8491 (m) cc_final: 0.7758 (m) REVERT: F 529 ASN cc_start: 0.9118 (t0) cc_final: 0.8511 (t0) REVERT: D 12 VAL cc_start: 0.9533 (m) cc_final: 0.9204 (p) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2329 time to fit residues: 43.6116 Evaluate side-chains 95 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 40.0000 chunk 85 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN E 21 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 ASN E 395 ASN ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 621 GLN ** F 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 11944 Z= 0.478 Angle : 0.882 18.939 16197 Z= 0.449 Chirality : 0.052 0.310 1790 Planarity : 0.005 0.050 2091 Dihedral : 6.210 32.038 1610 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 27.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.29 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.40 (0.22), residues: 1426 helix: -0.12 (0.42), residues: 143 sheet: -0.80 (0.29), residues: 302 loop : -1.13 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP E 519 HIS 0.009 0.002 HIS F 539 PHE 0.027 0.003 PHE E 90 TYR 0.042 0.003 TYR D 25 ARG 0.013 0.001 ARG E 704 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 26 GLU cc_start: 0.8577 (pt0) cc_final: 0.7851 (pm20) REVERT: E 331 LEU cc_start: 0.7463 (mt) cc_final: 0.7255 (mt) REVERT: E 348 MET cc_start: 0.8607 (mpp) cc_final: 0.8249 (mpp) REVERT: E 366 LEU cc_start: 0.9138 (mt) cc_final: 0.8911 (tp) REVERT: E 398 LEU cc_start: 0.9014 (tp) cc_final: 0.8814 (tp) REVERT: F 53 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8063 (mm-30) REVERT: F 348 MET cc_start: 0.8908 (mpp) cc_final: 0.8491 (mpp) REVERT: F 398 LEU cc_start: 0.9709 (mm) cc_final: 0.9455 (mm) REVERT: D 12 VAL cc_start: 0.9606 (m) cc_final: 0.9246 (p) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2584 time to fit residues: 44.5897 Evaluate side-chains 79 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 88 optimal weight: 0.0470 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 overall best weight: 1.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 395 ASN ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.6162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11944 Z= 0.204 Angle : 0.639 8.900 16197 Z= 0.338 Chirality : 0.048 0.212 1790 Planarity : 0.005 0.048 2091 Dihedral : 5.689 25.472 1610 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.17 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -1.28 (0.22), residues: 1426 helix: -0.00 (0.42), residues: 147 sheet: -0.75 (0.29), residues: 307 loop : -1.04 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 519 HIS 0.005 0.001 HIS E 364 PHE 0.022 0.002 PHE E 58 TYR 0.017 0.002 TYR F 391 ARG 0.011 0.001 ARG C 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 THR cc_start: 0.8975 (m) cc_final: 0.8632 (p) REVERT: E 92 MET cc_start: 0.7826 (ttt) cc_final: 0.7584 (ptm) REVERT: E 95 LEU cc_start: 0.9300 (tp) cc_final: 0.8977 (tp) REVERT: E 348 MET cc_start: 0.8689 (mpp) cc_final: 0.8332 (mpp) REVERT: E 366 LEU cc_start: 0.9180 (mt) cc_final: 0.8918 (mt) REVERT: E 395 ASN cc_start: 0.9045 (m110) cc_final: 0.8830 (m-40) REVERT: E 398 LEU cc_start: 0.8807 (tp) cc_final: 0.8552 (tp) REVERT: F 53 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7979 (mm-30) REVERT: F 330 LEU cc_start: 0.9464 (tt) cc_final: 0.9066 (mm) REVERT: F 348 MET cc_start: 0.8778 (mpp) cc_final: 0.8407 (mpp) REVERT: F 398 LEU cc_start: 0.9611 (mm) cc_final: 0.9324 (mm) REVERT: F 432 MET cc_start: 0.8529 (tmm) cc_final: 0.8015 (tmm) REVERT: D 12 VAL cc_start: 0.9571 (m) cc_final: 0.9267 (p) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2224 time to fit residues: 37.5663 Evaluate side-chains 71 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.0570 chunk 121 optimal weight: 0.0040 chunk 129 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 0.0070 chunk 122 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.6132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 698 ASN C 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11944 Z= 0.185 Angle : 0.617 8.187 16197 Z= 0.325 Chirality : 0.047 0.195 1790 Planarity : 0.005 0.079 2091 Dihedral : 5.434 25.468 1610 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.17 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -1.09 (0.23), residues: 1426 helix: 0.11 (0.42), residues: 146 sheet: -0.58 (0.29), residues: 307 loop : -0.92 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 544 HIS 0.002 0.001 HIS F 362 PHE 0.020 0.002 PHE E 58 TYR 0.015 0.001 TYR E 391 ARG 0.010 0.000 ARG E 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 53 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7624 (mm-30) REVERT: E 74 THR cc_start: 0.8904 (m) cc_final: 0.8603 (p) REVERT: E 95 LEU cc_start: 0.9296 (tp) cc_final: 0.9022 (tp) REVERT: E 345 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8817 (mm-30) REVERT: E 348 MET cc_start: 0.8725 (mpp) cc_final: 0.8363 (mpp) REVERT: E 366 LEU cc_start: 0.9105 (mt) cc_final: 0.8874 (mt) REVERT: E 395 ASN cc_start: 0.9036 (m110) cc_final: 0.8819 (m-40) REVERT: E 398 LEU cc_start: 0.8705 (tp) cc_final: 0.8407 (tp) REVERT: F 29 LEU cc_start: 0.9296 (tp) cc_final: 0.9086 (tp) REVERT: F 53 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7984 (mm-30) REVERT: F 348 MET cc_start: 0.8664 (mpp) cc_final: 0.8380 (mpp) REVERT: F 398 LEU cc_start: 0.9574 (mm) cc_final: 0.9261 (mm) REVERT: D 12 VAL cc_start: 0.9546 (m) cc_final: 0.9245 (p) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.2232 time to fit residues: 37.0890 Evaluate side-chains 79 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 40.0000 chunk 95 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 11 ASN ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.6332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11944 Z= 0.183 Angle : 0.603 8.347 16197 Z= 0.319 Chirality : 0.047 0.200 1790 Planarity : 0.005 0.083 2091 Dihedral : 5.359 24.989 1610 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.17 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.98 (0.23), residues: 1426 helix: 0.23 (0.43), residues: 145 sheet: -0.52 (0.29), residues: 309 loop : -0.84 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 544 HIS 0.003 0.001 HIS E 364 PHE 0.020 0.002 PHE E 70 TYR 0.015 0.001 TYR F 391 ARG 0.005 0.000 ARG F 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 53 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7651 (mm-30) REVERT: E 74 THR cc_start: 0.8911 (m) cc_final: 0.8625 (p) REVERT: E 348 MET cc_start: 0.8691 (mpp) cc_final: 0.8345 (mpp) REVERT: E 366 LEU cc_start: 0.9120 (mt) cc_final: 0.8887 (mt) REVERT: E 395 ASN cc_start: 0.9004 (m110) cc_final: 0.8788 (m-40) REVERT: E 398 LEU cc_start: 0.8872 (tp) cc_final: 0.8589 (tp) REVERT: F 29 LEU cc_start: 0.9314 (tp) cc_final: 0.9111 (tp) REVERT: F 53 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7977 (mm-30) REVERT: F 348 MET cc_start: 0.8657 (mpp) cc_final: 0.8393 (mpp) REVERT: F 398 LEU cc_start: 0.9563 (mm) cc_final: 0.9232 (mm) REVERT: D 12 VAL cc_start: 0.9549 (m) cc_final: 0.9258 (p) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2270 time to fit residues: 38.5928 Evaluate side-chains 79 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.0970 chunk 100 optimal weight: 0.2980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.078012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.056642 restraints weight = 86088.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.058419 restraints weight = 52865.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.059621 restraints weight = 37694.229| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.6401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11944 Z= 0.156 Angle : 0.587 8.490 16197 Z= 0.309 Chirality : 0.046 0.173 1790 Planarity : 0.004 0.075 2091 Dihedral : 5.149 23.924 1610 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.82 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.91 (0.23), residues: 1426 helix: 0.20 (0.42), residues: 148 sheet: -0.35 (0.30), residues: 299 loop : -0.82 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 404 HIS 0.002 0.001 HIS E 364 PHE 0.019 0.001 PHE E 70 TYR 0.018 0.001 TYR F 391 ARG 0.005 0.000 ARG E 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2582.19 seconds wall clock time: 48 minutes 44.16 seconds (2924.16 seconds total)